UCLA ACCESS
Larry Simpson, Ph.D.

Work Address:
MRL
Los Angeles, CA 90095 6-780 MRL
CAMPUS - 166222
CA MRL
Los Angeles, CA 90095

Department / Division Affiliations
Affiliations
Professor, Microbiology, Immunology & Molecular Genetics
Member, JCCC Cancer and Stem Cell Biology Program Area
Research Interests
I am interested in the molecular biology of parasitic protozoa known as trypanosomes or kinetoplastid protozoa. In particular, we are investigating a novel type of RNA modification phenomenon termed ?RNA editing?, that occurs in the single mitochondrion. mRNA transcripts of the mitochondrial maxicircle DNA molecules are modified after transcription by the insertion and deletion of uridine residues at precise sites within coding regions to form a translatable sequence. The information for this editing is contained in small ?guide RNAs?, which hybridize to the pre-edited mRNA and somehow mediate the transfer of uridines to the editing sites. The guide RNAs are encoded mainly in the thousands of minicircular molecules linked by catenation in the single giant network of DNA present in the single mitochondrion of these cells. In some cases multiple overlapping gRNAs mediate the addition of hundreds of uridines at hundreds of sites. We are studying the mechanism of this unusual process by establishing an in vitro editing system. Several classes of ribonucleoprotein complexes appear to be involved, and these are being dissected and analyzed. Proteins involved in the editing process are being isolated and the genes cloned. In addition, we are interested in the evolution of RNA editing in these ancient lower eukaryotic cells. To this end we are analyzing editing in a variety of kinetoplastid protozoa, whose phylogenetic relationships we have determined. By a comparative analysis we can make some deductions about the evolution of this phenomenon. We are also studying the changes in the editing system that occur during prolonged culture of trypanosomes, which appear to involve the loss of minicircle sequence classes encoding specific guide RNA families. I am also interested in other aspects of the mitochondrial genetic system and mitochondrial biogenesis. Since there are no transfer RNAs encoded in the mitochondrial genome of trypanosomes, all the mt tRNAs must be imported, and the mechanism of this process is being actively studied in my laboratory. Mitochondrial transcription and translation are other processes in which I have a great interest.

Molecular biology of parasitic protozoa I am interested in the molecular biology of parasitic protozoa known as trypanosomes or kinetoplastid protozoa. In particular, we are investigating a novel type of RNA modification phenomenon termed ?RNA editing?, that occurs in the single mitochondrion. mRNA transcripts of the mitochondrial maxicircle DNA molecules are modified after transcription by the insertion and deletion of uridine residues at precise sites within coding regions to form a translatable sequence. The information for this editing is contained in small ?guide RNAs?, which hybridize to the pre-edited mRNA and somehow mediate the transfer of uridines to the editing sites. The guide RNAs are encoded mainly in the thousands of minicircular molecules linked by catenation in the single giant network of DNA present in the single mitochondrion of these cells. In some cases multiple overlapping gRNAs mediate the addition of hundreds of uridines at hundreds of sites. We are studying the mechanism of this unusual process by establishing an in vitro editing system. Several classes of ribonucleoprotein complexes appear to be involved, and these are being dissected and analyzed. Proteins involved in the editing process are being isolated and the genes cloned. In addition, we are interested in the evolution of RNA editing in these ancient lower eukaryotic cells. To this end we are analyzing editing in a variety of kinetoplastid protozoa, whose phylogenetic relationships we have determined. By a comparative analysis we can make some deductions about the evolution of this phenomenon. We are also studying the changes in the editing system that occur during prolonged culture of trypanosomes, which appear to involve the loss of minicircle sequence classes encoding specific guide RNA families. I am also interested in other aspects of the mitochondrial genetic system and mitochondrial biogenesis. Since there are no transfer RNAs encoded in the mitochondrial genome of trypanosomes, all the mt tRNAs must be imported, and the mechanism of this process is being actively studied in my laboratory. Mitochondrial transcription and translation are other processes in which I have a great interest.

Publications
URL for all publications. http://dna.kdna.ucla.edu/simpsonlab/mybib.html. ; .
Eckers Elisabeth, Cyrklaff Marek, Simpson Larry, Deponte Marcel Mitochondrial protein import pathways are functionally conserved among eukaryotes despite compositional diversity of the import machineries. Biological chemistry. 2012; 393(6): 513-24.
Simpson Larry A personal scientific odyssey. Protist. 2011; 162(1): 188-206.
Li Feng, Herrera Jeremy, Zhou Sharleen, Maslov Dmitri A, Simpson Larry Trypanosome REH1 is an RNA helicase involved with the 3'-5' polarity of multiple gRNA-guided uridine insertion/deletion RNA editing. Proceedings of the National Academy of Sciences of the United States of America. 2011; 108(9): 3542-7.
Simpson Larry, Aphasizhev Ruslan, Lukes Julius, Cruz-Reyes Jorge Guide to the nomenclature of kinetoplastid RNA editing: a proposal. Protist. 2010; 161(1): 2-6.
Gao Guanghan, Rogers Kestrel, Li Feng, Guo Qiang, Osato Daren, Zhou Sharleen X, Falick Arnold M, Simpson Larry Uridine insertion/deletion RNA editing in Trypanosomatids: specific stimulation in vitro of Leishmania tarentolae REL1 RNA ligase activity by the MP63 zinc finger protein. Protist. 2010; 161(3): 489-96.
Simpson Larry Musings on the real problems. Protist. 2009; 160(1): 3.
Nebohácová Martina, Kim Christine E, Simpson Larry, Maslov Dmitri A RNA editing and mitochondrial activity in promastigotes and amastigotes of Leishmania donovani. International journal for parasitology. 2009; 39(6): 635-44.
Simpson Larry Science is a hard mistress. Protist. 2009; 160(4): 481-2.
Sharma Manjuli R, Booth Timothy M, Simpson Larry, Maslov Dmitri A, Agrawal Rajendra K Structure of a mitochondrial ribosome with minimal RNA. Proceedings of the National Academy of Sciences of the United States of America. 2009; 106(24): 9637-42.
Li Feng, Ge Peng, Hui Wong H, Atanasov Ivo, Rogers Kestrel, Guo Qiang, Osato Daren, Falick Arnold M, Zhou Z Hong, Simpson Larry Structure of the core editing complex (L-complex) involved in uridine insertion/deletion RNA editing in trypanosomatid mitochondria. Proceedings of the National Academy of Sciences of the United States of America. 2009; 106(30): 12306-10.
Osato Daren, Rogers Kestrel, Guo Qiang, Li Feng, Richmond Greg, Klug Felix, Simpson Larry Uridine insertion/deletion RNA editing in trypanosomatid mitochondria: In search of the editosome. RNA (New York, N.Y.). 2009; 15(7): 1338-44.
Jensen Robert E, Simpson Larry, Englund Paul T What happens when Trypanosoma brucei leaves Africa. Trends in parasitology. 2008; 24(10): 428-31.
Maslov Dmitri A, Spremulli Linda L, Sharma Manjuli R, Bhargava Kalpana, Grasso Domenick, Falick Arnold M, Agrawal Rajendra K, Parker Carol E, Simpson Larry Proteomics and electron microscopic characterization of the unusual mitochondrial ribosome-related 45S complex in Leishmania tarentolae. Molecular and biochemical parasitology. 2007; 152(2): 203-12.
Maslov Dmitri A, Simpson Larry Strategies of kinetoplastid cryptogene discovery and analysis. Methods in enzymology. 2007; 424(2): 127-39.
Rogers Kestrel, Gao Guanghan, Simpson Larry Uridylate-specific 3' 5'-exoribonucleases involved in uridylate-deletion RNA editing in trypanosomatid mitochondria. The Journal of biological chemistry. 2007; 282(40): 29073-80.
Simpson Larry Death of the "ologies". Protist. 2006; 157(4): 361-2.
Maslov Dmitri A, Sharma Manjuli R, Butler Evelin, Falick Arnold M, Gingery Mari, Agrawal Rajendra K, Spremulli Linda L, Simpson Larry Isolation and characterization of mitochondrial ribosomes and ribosomal subunits from Leishmania tarentolae. Molecular and biochemical parasitology. 2006; 148(1): 69-78.
Kang Xuedong, Gao Guanghan, Rogers Kestrel, Falick Arnold M, Zhou Sharleen, Simpson Larry Reconstitution of full-round uridine-deletion RNA editing with three recombinant proteins. Proceedings of the National Academy of Sciences of the United States of America. 2006; 103(38): 13944-9.
Gao Guanghan, Simpson Agda M, Kang Xuedong, Rogers Kestrel, Nebohacova Martina, Li Feng, Simpson Larry Functional complementation of Trypanosoma brucei RNA in vitro editing with recombinant RNA ligase. Proceedings of the National Academy of Sciences of the United States of America. 2005; 102(13): 4712-7.
Trager Lillian, Spielman Andrew, Simpson Larry Malaria, not down and certainly not out. The American journal of tropical medicine and hygiene. 2005; 73(5): 824-5.
Kang Xuedong, Rogers Kestrel, Gao Guanghan, Falick Arnold M, Zhou Sharleen, Simpson Larry Reconstitution of uridine-deletion precleaved RNA editing with two recombinant enzymes. Proceedings of the National Academy of Sciences of the United States of America. 2005; 102(4): 1017-22.
Kang Xuedong, Falick Arnold M, Nelson Robert E, Gao Guanghan, Rogers Kestrel, Aphasizhev Ruslan, Simpson Larry Disruption of the zinc finger motifs in the Leishmania tarentolae LC-4 (=TbMP63) L-complex editing protein affects the stability of the L-complex. The Journal of biological chemistry. 2004; 279(6): 3893-9.
Simpson Larry, Aphasizhev Ruslan, Gao Guanghan, Kang Xuedong Mitochondrial proteins and complexes in Leishmania and Trypanosoma involved in U-insertion/deletion RNA editing. RNA (New York, N.Y.). 2004; 10(2): 159-70.
Aphasizhev Ruslan, Aphasizheva Inna, Simpson Larry Multiple terminal uridylyltransferases of trypanosomes. FEBS letters. 2004; 572(1-3): 15-8.
Aphasizheva Inna, Aphasizhev Ruslan, Simpson Larry RNA-editing terminal uridylyl transferase 1: identification of functional domains by mutational analysis. The Journal of biological chemistry. 2004; 279(23): 24123-30.
Nelson Robert E, Aphasizheva Inna, Falick Arnold M, Nebohacova Martina, Simpson Larry The I-complex in Leishmania tarentolae is an uniquely-structured F(1)-ATPase. Molecular and biochemical parasitology. 2004; 135(2): 221-4.
Nebohácová Martina, Maslov Dmitri A, Falick Arnold M, Simpson Larry The effect of RNA interference Down-regulation of RNA editing 3'-terminal uridylyl transferase (TUTase) 1 on mitochondrial de novo protein synthesis and stability of respiratory complexes in Trypanosoma brucei. The Journal of biological chemistry. 2004; 279(9): 7819-25.
Aphasizhev Ruslan, Aphasizheva Inna, Nelson Robert E, Simpson Larry 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 (New York, N.Y.). 2003; 9(1): 62-76.
Aphasizhev Ruslan, Aphasizheva Inna, Simpson Larry A tale of two TUTases. Proceedings of the National Academy of Sciences of the United States of America. 2003; 100(19): 10617-22.
Hong Min, Simpson Larry Genomic organization of Trypanosoma brucei kinetoplast DNA minicircles. Protist. 2003; 154(2): 265-79.
Gao Guanghan, Simpson Larry Is the Trypanosoma brucei REL1 RNA ligase specific for U-deletion RNA editing, and is the REL2 RNA ligase specific for U-insertion editing?. The Journal of biological chemistry. 2003; 278(30): 27570-4.
Aphasizhev Ruslan, Aphasizheva Inna, Nelson Robert E, Gao Guanghan, Simpson Agda M, Kang Xuedong, Falick Arnold M, Sbicego Sandro, Simpson Larry Isolation of a U-insertion/deletion editing complex from Leishmania tarentolae mitochondria. The EMBO journal. 2003; 22(4): 913-24.
Sbicego Sandro, Alfonzo Juan D, Estévez Antonio M, Rubio Mary Anne T, Kang Xuedong, Turck Christoph W, Peris Marian, Simpson Larry RBP38, a novel RNA-binding protein from trypanosomatid mitochondria, modulates RNA stability. Eukaryotic cell. 2003; 2(3): 560-8.
Simpson Larry, Sbicego Sandro, Aphasizhev Ruslan Uridine insertion/deletion RNA editing in trypanosome mitochondria: a complex business. RNA (New York, N.Y.). 2003; 9(3): 265-76.
Kaneko Tomonori, Suzuki Takeo, Kapushoc Stephen T, Rubio Mary Anne, Ghazvini Jafar, Watanabe Kimitsuna, Simpson Larry, Suzuki Tsutomu Wobble modification differences and subcellular localization of tRNAs in Leishmania tarentolae: implication for tRNA sorting mechanism. The EMBO journal. 2003; 22(3): 657-67.
Monzani Paulo S, Alfonzo Juan D, Simpson Larry, Oliva Glaucius, Thiemann Otavio H Cloning, characterization and preliminary crystallographic analysis of Leishmania hypoxanthine-guanine phosphoribosyltransferase. Biochimica et biophysica acta. 2002; 1598(1-2): 3-9.
Kapushoc Stephen T, Alfonzo Juan D, Simpson Larry Differential localization of nuclear-encoded tRNAs between the cytosol and mitochondrion in Leishmania tarentolae. RNA (New York, N.Y.). 2002; 8(1): 57-68.
Simpson Larry Malaria--the biological terminator. Protist. 2002; 153(1): 7-8.
Crain Pamela F, Alfonzo Juan D, Rozenski Jef, Kapushoc Stephen T, McCloskey James A, Simpson Larry Modification of the universally unmodified uridine-33 in a mitochondria-imported edited tRNA and the role of the anticodon arm structure on editing efficiency. RNA (New York, N.Y.). 2002; 8(6): 752-61.
Aphasizhev Ruslan, Sbicego Sandro, Peris Marian, Jang Sei-Heon, Aphasizheva Inna, Simpson Agda M, Rivlin Anatoly, Simpson Larry Trypanosome mitochondrial 3' terminal uridylyl transferase (TUTase): the key enzyme in U-insertion/deletion RNA editing. Cell. 2002; 108(5): 637-48.
Aphasizhev, R Simpson, L Isolation and characterization of a U-specific 3'-5'-exonuclease from mitochondria of Leishmania tarentolae. The Journal of biological chemistry. . 2001; 276(24): 21280-4.
Carillo, R., Thiemann, O.H., Alfonzo, J.D., Simpson, L. Uridine insertion/deletion RNA editing in Leishmania tarentolae mitochondria shows cell cycle dependence. Mol. Biochem. Parasitol 2001; 113 : 175-181 .
Kapushoc, ST Alfonzo, JD Rubio, MA Simpson, L End processing precedes mitochondrial importation and editing of tRNAs in Leishmania tarentolae. The Journal of biological chemistry. . 2000; 275(48): 37907-14.
Simpson, L Thiemann, OH Savill, NJ Alfonzo, JD Maslov, DA Evolution of RNA editing in trypanosome mitochondria. Proceedings of the National Academy of Sciences of the United States of America. . 2000; 97(13): 6986-93.
Rubio, MA Liu, X Yuzawa, H Alfonzo, JD Simpson, L Selective importation of RNA into isolated mitochondria from Leishmania tarentolae. RNA (New York, N.Y.) . 2000; 6(7): 988-1003.
Alfonzo, J.D., Blanc, V., Estevez, A.M., Rubio, M.A.T., Simpson, L. C to U editing of anticodon of imported mitochondrial tRNATrp allows decoding of UGA stop codon in Leishmania. EMBO J 1999; 18: 7056-7062.
Kapushoc, ST Simpson, L In vitro uridine insertion RNA editing mediated by cis-acting guide RNAs. RNA (New York, N.Y.) . 1999; 5(5): 656-69.
Estevez, A.M., Kierzenbaum, F., Wirtz, E., Bringaud, F., Grunstein, J., Simpson, L. Knockoutof the glutamate dehydrogenase gene in bloodstream Trypanosoma brucei in culture has no effect on editing of mitochondrial mRNAs. Mol. Biochem. Parasitol 1999; 100: 5-17.
Estevez,A.E., Thiemann, O.H., Alfonzo, J.D., Simpson, L. T7 RNA polymerase driven transcription in mitochondria of Leishmania tarentolae and Trypanosoma brucei. Mol. Biochem. Parasitol 1999; 103: 251-259.
Blanc, V., Alfonzo, J.D., Aphasizhev, R., Simpson, L. The mitochondrial RNA ligase from Leishmania tarentolae can join RNA molecules bridged by a complementary RNA. J. Biol. Chem. 1999; 274: 24289-24296.
Estevez, A.M., Simpson, L. Uridine insertion/deletion RNA editing in trypanosome mitochondria - a review. Gene 1999; 240: 247-260.
Alfonzo, JD Thiemann, OH Simpson, L Purification and characterization of MAR1. A mitochondrial associated ribonuclease from Leishmania tarentolae. The Journal of biological chemistry. . 1998; 273(45): 30003-11.
Connell, GJ Byrne, EM Simpson, L Guide RNA-independent and guide RNA-dependent uridine insertion into cytochrome b mRNA in a mitochondrial lysate from Leishmania tarentolae. Role of RNA secondary structure. The Journal of biological chemistry. . 1997; 272(7): 4212-8.
Alfonzo, JD Thiemann, O Simpson, L The mechanism of U insertion/deletion RNA editing in kinetoplastid mitochondria. Nucleic acids research. . 1997; 25(19): 3751-9.
Byrne, EM Connell, GJ Simpson, L Guide RNA-directed uridine insertion RNA editing in vitro. The EMBO journal. . 1996; 15(23): 6758-65.