Ruslan Afasizhev

Research description

Our laboratory is broadly interested in molecular mechanisms of RNA processing in Trypanosoma brucei spp. These protozoan hemoflagellates are responsible for a variety of neglected diseases including African sleeping sickness in humans and nagana in cattle. Trypanosomes belong to the order Kinetoplastida and represent some of the earliest mitochondria-containing branches of the eukaryotic lineage. Unsurprisingly, trypanosomes possess many unusual biological processes such as antigenic variation, multi-cistronic RNA Polymease II transcription, trans-splicing and mitochondrial U-insertion/deletion mRNA editing. The main goal of the “mitochondria-centered” program is to understand how genetic information is transferred between minicirlcle and maxicircle genomes via short transcripts called guide RNAs during mRNA editing. Molecular mechanisms of U-insertion/deletion mRNA editing, polyadenylation, translation and decay, and guide RNA biogenesis are investigated by biochemical, genetic, structural and proteomic approaches. We also explore biological roles of nuclear non-canonical poly(A) polymerases (ncPAPs) and cytosolic terminal RNA uridylyl transferases (TUTases) in trypanosomes. Life without transcriptional control practiced by these parasites stimulates us to look at the alternative, RNA decay-based pathways regulating expression of their nuclear genome. Crystallographic studies of substrate recognition by TUTases and ncPAPs are providing a foundation for rational design of trypanocides. Exciting projects are available for motivated graduate and post-doctoral researchers in our state-of-the-art, NIH-funded laboratory.

Currently active projects

1. Mitochondrial transcription
2. Mitochondrial U-insertion/deletion mRNA editing
3. Polyadenylation and translation of mitochondrial mRNAs
4. Guide RNA biogenesis
5. Nuclear non-canonical poly(A) polymerases and mRNA decay
6. Cytosolic mRNA uridylation

Selected Publications

1: Suematsu T, Zhang L, Aphasizheva I, Monti S, Huang L, Wang Q, Costello CE, Aphasizhev R. Antisense Transcripts Delimit Exonucleolytic Activity of the Mitochondrial 3′ Processome to Generate Guide RNAs. Mol Cell. 2016 Feb 4;61(3):364-78.

2: Aphasizheva I, Maslov DA, Qian Y, Huang L, Wang Q, Costello CE, Aphasizhev R. Ribosome-associated pentatricopeptide repeat proteins function as translational activators in mitochondria of trypanosomes. Mol Microbiol. 2016 Mar;99(6):1043-58.

3: Aphasizheva I, Zhang L, Wang X, Kaake RM, Huang L, Monti S, Aphasizhev R. RNA  binding and core complexes constitute the U-insertion/deletion editosome. Mol Cell Biol. 2014 Dec 1;34(23):4329-42.

4: Aphasizheva I, Maslov DA, Aphasizhev R. Kinetoplast DNA-encoded ribosomal protein S12: a possible functional link between mitochondrial RNA editing and translation in Trypanosoma brucei. RNA Biol. 2013 Nov;10(11):1679-88.

5: Aphasizheva I, Maslov D, Wang X, Huang L, Aphasizhev R. Pentatricopeptide repeat proteins stimulate mRNA adenylation/uridylation to activate mitochondrial translation in trypanosomes. Mol Cell. 2011 Apr 8;42(1):106-17.

6: Ringpis GE, Stagno J, Aphasizhev R. Mechanism of U-insertion RNA editing in trypanosome mitochondria: characterization of RET2 functional domains by mutational analysis. J Mol Biol. 2010 Jun 25;399(5):696-706.

7: Stagno J, Aphasizheva I, Bruystens J, Luecke H, Aphasizhev R. Structure of the mitochondrial editosome-like complex associated TUTase 1 reveals divergent mechanisms of UTP selection and domain organization. J Mol Biol. 2010 Jun11;399(3):464-75.

8: Ringpis GE, Aphasizheva I, Wang X, Huang L, Lathrop RH, Hatfield GW, Aphasizhev R. Mechanism of U insertion RNA editing in trypanosome mitochondria:the bimodal TUTase activity of the core complex. J Mol Biol. 2010 Jun 25;399(5):680-95.

9: Aphasizheva I, Aphasizhev R. RET1-catalyzed uridylylation shapes the mitochondrial transcriptome in Trypanosoma brucei. Mol Cell Biol. 2010 Mar;30(6):1555-67.

10: Aphasizheva I, Ringpis GE, Weng J, Gershon PD, Lathrop RH, Aphasizhev R. Novel TUTase associates with an editosome-like complex in mitochondria ofTrypanosoma brucei. RNA. 2009 Jul;15(7):1322-37.

11: Weng J, Aphasizheva I, Etheridge RD, Huang L, Wang X, Falick AM, AphasizhevR. Guide RNA-binding complex from mitochondria of trypanosomatids. Mol Cell. 2008Oct 24;32(2):198-209.

12: Etheridge RD, Aphasizheva I, Gershon PD, Aphasizhev R. 3′ adenylationdetermines mRNA abundance and monitors completion of RNA editing in T. brucei mitochondria. EMBO J. 2008 Jun 4;27(11):1596-608.

Active Grants

Structures and functions of RNA editing TUTases. R01AI091914. PI: R. Afasizhev; NIH/NIAID; 2010-2021.
Guide RNA binding complex. R01AI101057. PI: R. Afasizhev; NIH/NIAID; 2012-2017.
Functional dentition of guide RNAs. R21AI11522. PI: R. Afasizhev; NIH/NIAID; 2015-2016.