Ruslan Afasizhev

Associate Professor, Microbiology & Molecular Genetics
School of Medicine

Ph.D., Institute of Molecular Biology, Russian Academy of Sciences, 1995, Molecular Biology

Phone: (949) 824-7845
Email: ruslan@uci.edu

University of California, Irvine
C135D Med Sci I
Mail Code: 4025
Irvine, CA 92697

picture of Ruslan  Afasizhev

Research
Interests
molecular parasitology; mitochondria; RNA editing; RNA nucleotidyltransferases
   
Appointments EMBO Fellow, Institut de Biologie Moléculaire et Cellulaire, CNRS, Strasbourg, France

Howard Hughes Medical Institute, University of California, Los Angeles
   
Research
Abstract
Molecular mechanisms of RNA processing in Trypanosomes

Trypanosomatids are protozoan hemoflagellates responsible for a variety of neglected human diseases including Chagas' disease, leishmaniasis and African sleeping sickness. These protists represent one of the earliest mitochondria-containing branches of the eukaryotic lineage and possess many unusual biological processes such as antigenic variation, multi-cistronic Pol II transcription, trans-splicing and mitochondrial RNA editing. Our research efforts concentrate on RNA processing in African trypanosomes.

The main goal of the “mitochondria-centered” program is to understand how genetic information is transferred between RNA molecules during U-insertion/deletion editing. Molecular mechanisms of mRNA editing, polyadenylation, translation and decay, and guide RNA biogenesis are investigated by a variety of biochemical, genetic, structural and proteomic approaches.

We explore biological roles of non-canonical poly(A) polymerases (ncPAPs) and 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 and mitochondrial genomes.

Crystallographic studies of substrate recognition by TUTases and ncPAPs provide a foundation for rational design of trypanocides. Our on-campus collaborations extend into structural biology (Luecke lab), mass spectrometry (Huang lab) and bioinformatics (Amaro and Lathrop labs). Exciting projects are available for highly-motivated graduate and post-doctoral researchers in our state-of-the-art, NIH-funded laboratory.

Currently active projects
1. Cellular functions of RNA uridylylation
2. Polyadenylation of mitochondrial mRNAs
3. Guide RNA biogenesis and function
4. Nuclear non-canonical poly(A) polymerases and mRNA decay
5. NTP Selectivity of template-independent transferases
6. Structure-function of the RNA editing core complex
7. Structure-function of the guide RNA binding complex
   
Available Technologies
  Selected publications:

1. Aphasizhev, R., Sbicego, S., Peris, M., Jang, S. H., Aphasizheva, I., Simpson, A. M., Rivlin, A. & Simpson, L. (2002). Trypanosome Mitochondrial 3' Terminal Uridylyl Transferase (TUTase): The Key Enzyme in U-insertion/deletion RNA Editing. Cell 108: 637-648.
2. Aphasizhev, R., Aphasizheva, I., Nelson, R. E., Gao, G., Simpson, A. M., Kang, X., Falick, A. M., Sbicego, S. & Simpson, L. (2003). Isolation of a U-insertion/deletion editing complex from Leishmania tarentolae mitochondria. EMBO J. 22: 913-924.
3. Aphasizhev, R., Aphasizheva, I., Nelson, R. E. & Simpson, L. (2003). A 100-kD complex of two RNA-binding proteins from mitochondria of Leishmania tarentolae catalyzes RNA annealing and interacts with several RNA editing components. RNA 9: 62-76.
4. Simpson, L., Sbicego, S. & Aphasizhev, R. (2003). Uridine insertion/deletion RNA editing in trypanosome mitochondria: A complex business. RNA. 9: 265-276.
5. Aphasizhev, R., Aphasizheva, I. & Simpson, L. (2003). A tale of two TUTases. Proc. Natl. Acad. Sci. U. S. A 100: 10617-10622.
6. Simpson, L., Aphasizhev, R., Gao, G. & Kang, X. (2004). Mitochondrial proteins and complexes in Leishmania and Trypanosoma involved in U-insertion/deletion RNA editing. RNA. 10: 159-170.
7. Aphasizheva, I., Aphasizhev, R. & Simpson, L. (2004). RNA-editing terminal uridylyl transferase 1: identification of functional domains by mutational analysis. J. Biol. Chem. 279: 24123-24130.
8. Aphasizhev, R., Aphasizheva, I. & Simpson, L. (2004). Multiple terminal uridylyltransferases of trypanosomes. FEBS Lett. 572, 15-18.
9. Kang, X., Falick, A. M., Nelson, R. E., Gao, G., Rogers, K., Aphasizhev, R. & Simpson, L. (2004). Disruption of the zinc finger motifs in the Leishmania tarentolae LC-4 (=TbMP63) L-complex editing protein affects the stability of the L-complex
6. J. Biol. Chem. 279: 3893-3899.
10. Aphasizhev, R. (2005). RNA uridylyltransferases. Cell Mol. Life Sci. 62: 2194-2203.
11. Stagno, J., Aphasizheva, I., Rosengarth, A., Luecke, H. & Aphasizhev, R. (2007). UTP-bound and Apo structures of a minimal RNA uridylyltransferase. J. Mol. Biol. 366: 882-899.
12. Aphasizhev, R. & Aphasizheva, I. (2007). RNA Editing Uridylyltransferases of Trypanosomatids. Methods Enzymol. 424, 51-67.
13. Pelletier, M., Read, L. K. & Aphasizhev, R. (2007). Isolation of RNA Binding Proteins Involved in Insertion/deletion Editing. Methods Enzymol. 424: 69-96.
14. Stagno, J., Aphasizheva, I., Aphasizhev, R. & Luecke, H. (2007). Dual Role of the RNA Substrate in Selectivity and Catalysis by Terminal Uridylyl Transferases. Proc Natl Acad Sci U S A. 104: 14634-14639.
15. Aphasizhev, R. (2007). RNA editing. Molecular Biology 41: 227-239.
16. Aphasizhev, R. & Aphasizheva, I. (2008). Terminal RNA uridylyltransferases of trypanosomes. Biochim. Biophys. Acta 1779: 270-280.
17. Etheridge, R. D., Aphasizheva, I., Gershon, P. D. & Aphasizhev, R. (2008). 3' adenylation determines mRNA abundance and monitors completion of RNA editing in T. brucei mitochondria. EMBO J. 27: 1596-1608.
18. Weng, J., Aphasizheva, I., Etheridge, R. D., Huang, L., Wang, X., Falick, A. M. & Aphasizhev, R. (2008). Guide RNA-Binding Complex from Mitochondria of Trypanosomatids. Molecular Cell 32: 198-209.
19. Etheridge, R. D., Clemens, D. M. & Aphasizhev, R. (2009). Identification and characterization of nuclear non-canonical poly(A) polymerases from Trypanosoma brucei. Mol Biochem Parasitol 164: 66-73.
20. Aphasizheva, I., Ringpis, G. E., Weng, J., Gershon, P. D., Lathrop, R. H. & Aphasizhev, R. (2009). Novel TUTase associates with an editosome-like complex in mitochondria of Trypanosoma brucei. RNA 15: 1322-1337.
21. Aphasizheva I. and Aphasizhev R. (2010). RET1-catalyzed uridylylation shapes the mitochondrial transcriptome in Trypanosoma brucei. Mol. Cell. Biol., 30: 1555-1567.
22. Ringpis, G. E., Aphasizheva, I., Wang, X., Huang, L., Hatfield, G. W. & Aphasizhev, R. (2010). Mechanism of RNA editing in Trypanosome mitochondria: the bimodal U-insertion activity of the core complex. J. Mol. Biol., 399: 680-695.
23. Ringpis, G. E., Stagno, J. & Aphasizhev, R. (2010). Mechanism of U-insertion RNA editing in Trypanosome mitochondria: characterization of RET2 functional domains by mutational analysis. J. Mol Biol., 399: 696-706.
24. Stagno, J., Aphasizheva, I., Bruystens, J., Luecke, H. & Aphasizhev, R. (2010). Structure of the mitochondrial editosome-like complex associated TUTase 1 reveals divergent mechanisms of UTP selection and domain organization. J. Mol. Biol., 399: 464–475.
25. Ringpis, G.E., Lathrop, R. and Aphasizhev, R. iCODA: RNAi-based inducible knock-in system in Trypanosoma brucei. Methods in Molecular Biology, 2011, 718: 23-37.
26. Aphasizheva, I., Maslov, D., Wang, X., Huang, L. and Aphasizhev, R. (2011). Pentatricopeptide repeat proteins stimulate mRNA adenylation/uridylation to activate mitochondrial translation in trypanosomes. Molecular Cell, 42: 16-117.
27. Aphasizhev, R. and Aphasizheva, I. Uridine Insertion / Deletion mRNA Editing In Trypanosomes: A Playground for RNA-guided Information Transfer. WIREs RNA reviews, 2011, 2: 669-685.
28. Aphasizhev, R. and Aphasizheva, I. Mitochondrial RNA processing in Trypanosomes. Research in Microbiology, 2011, 162: 655-663.
   
Grant NIAID/NIH
   
Graduate Programs Cellular and Molecular Biosciences

   
Research Center Institute for Genomics and Bioinformatics
   
   
Link to this profile http://www.faculty.uci.edu/profile.cfm?faculty_id=5240
   
Last updated 11/15/2011