Research Information
Research Interests
My research focuses on RNA editing, the extraordinary process by which the primary sequence of specific RNAs are altered, leaving the genomic sequence unchanged. Such directed changes in RNA sequence occur in mammalian cells, viruses, plants, and a variety of unicellular organisms, including human pathogens. We have elected to study this process in the slime mold Physarum polycephalum (Pp), which carries out the widest range of RNA editing events yet described. These changes to mitochondrial RNAs involve the site-specific insertion of over 1300 ‘extra’ nucleotides, targeted base conversions, and the removal and replacement of nucleotides at the 5’ end of certain tRNAs. It remains a mystery why these sequence alterations, which are absolutely required for the production of functional transcripts, are not encoded in the mitochondrial genome. The overall goal of our research is to elucidate, at the molecular level, the mechanisms by which these highly precise changes are effected in Pp mitochondria.
We have found that the insertion of non-encoded nucleotides occurs co-transcriptionally. Our data suggest that the inserted nucleotides may be added by the mitochondrial RNA polymerase itself, but one or more other proteins are also required for this process. We have isolated mitochondrial fractions that are highly enriched in transcription/editing complexes via affinity selection and have identified all of their component proteins via mass spectroscopy. To determine which of these factors is involved in editing, we are currently knocking down the expression of individual candidates and assessing effects on the extent of editing. Once editing factors have been identified, we will work to establish an in vitro editing system using purified components in which to study the individual steps in the editing reaction. Ultimately, our work should shed light on the mechanisms of both editing and transcription elongation, leading to insights into the control of gene expression.
Publications
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- Houtz, J., Cremona, N., and Gott, J.M. (2018) Editing of mitochondrial RNAs in Physarum polycephalum In: RNA Metabolism in Mitochondria (Nucleic Acids and Molecular Biology Series)(eds. J. Cruz-Reyes, M. W. Gray), Springer Nature, pp.199-222. Doi:10.1007/978-3-319-78190-8_
8. - Gott, J.M, Naegele, G.M., and Howell, S.J. (2016) Electroporation of DNA into Physarum polycephalum mitochondria: Effects on transcription and RNA editing in isolated organelles. Genes 7(12): 128-141. doi:10.3390/genes7120128
- Schaap P, Barrantes I, Minx P, Sasaki N, Anderson RW, Bénard M, Biggar KK, Buchler NE, Bundschuh R, Chen X, Fronick C, Fulton L, Golderer G, Jahn N, Knoop V, Landweber LF, Maric C, Miller D, Noegel AA, Peace R, Pierron G, Sasaki T, Schallenberg-Rüdinger M, Schleicher M, Singh R, Spaller T, Storey KB, Suzuki T, Tomlinson C, Tyson JJ, Warren WC, Werner ER, Werner-Felmayer G, Wilson RK, Winckler T, Gott JM, Glöckner G, Marwan W. (2015) The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-component and Metazoan-type Tyrosine Kinase Signaling. Genome Biol Evol. 8, 109-125. doi: 10.1093/gbe/evv237.
- Gott JM. (2015) The continuing allure of RNA. RNA Apr;21(4):622-4. doi: 10.1261/rna.050252.115.
- Schallenberg-Rüdinger, M, Lenz, H, Polsakiewicz, M, Gott, J.M., and Knoop, V (2013) A survey of PPR proteins identifies DYW domains like those of land plant RNA editing factors in diverse eukaryotes. RNA Biol. 10(9), 1549-1556.
- Landweber, L. F., Horton, T.L., and Gott, J. M. (2013) Nucleic Acid Biodiversity: Rewriting DNA and RNA in Diverse Organisms. In: Encyclopedia of Biodiversity 5: 568-580, Academic Press.
- Gott, J. M. Mechanisms and Functions of RNA Editing in Physarum polycephalum. (2013) In: RNA Editing: Current Research and Future Trends (ed. S. Maas), Horizon Press: Norwich.
- Jackman, J. E., Gott, J. M., and Gray, M. W. (2012) Doing it in reverse: 3’ to 5’ polymerization by the Thg1 superfamily. RNA 18, 886-899. doi/10.1261/rna.032300.112
- Bundschuh, R., Altmüller, J., Becker, C., Nürnberg, P., and Gott, J.M. (2011) Complete characterization of the edited transcriptome of the mitochondrion of Physarum polycephalum using deep sequencing of RNA. Nucl. Acids Res. Nucl. Acids Res. 39(4), 6044-6055. doi:10.1093/nar/gkr180 [featured article]
- Abad, M.G., Long, Y., Willcox, A., Gott, J.M., Gray, M.W., and Jackman, J.E. (2011) A role for tRNAHis guanylyltransferase (Thg1)-like proteins from Dictyostelium discoideum in mitochondrial 5'-tRNA editing. RNA 17, 613-623.
- Gott, J. M. (June 2011) RNA Editing and Human Disorders. In: Encyclopedia of Life Sciences (ELS). John Wiley & Sons, Ltd: Chichester. DOI: 10.1002/9780470015902.a0005494.pub2
- Bullerwell, C.E., Burger, G., Gott, J.M., Kourennaia, O., Schnare, M.N., and Gray, M.W. (2010) Abundant 5S rRNA-like transcripts by the mitochondrial genome in amoebozoa. Eukaryot Cell 9, 762-73
- Gott, J.M., Somerlot,B.H., and Gray, M.W. (2010) Two forms of RNA editing are required for tRNA maturation in Physarum mitochondria. RNA 16, 482-488.
- deHaseth, P.L. and Gott, J.M. (2010) Conformational flexibility of 70 in anti-terminator loading. Molecular Microbiology 75, 543-546.
- Rhee, A.C., Somerlot, B.H., Parimi, N., and Gott, J.M. (2009) Distinct roles for sequences upstream of and downstream from Physarum editing sites. RNA 15, 1753-1765.
- Beargie, C., Liu, T, Corriveau, M., Lee, H.Y., Gott, J.M., and Bundschuh, R. (2008) Genome annotation in the presence of insertional RNA editing. Bioinformatics. 24(22), 2571-2578.
- Gott, J.M., editor (2007) Methods in Enzymology: RNA Editing, volume 424. Elsevier Press.
- Gott, J.M., editor (2007) Methods in Enzymology: RNA Modification, volume 425. Elsevier Press.
- Byrne, EB, Visomirski-Robic, LM, Cheng, YW, Rhee, AC, and Gott, JM (2007) RNA editing in Physarum mitochondria: assays and biochemical approaches. In Methods in Enzymology: RNA Editing and Modification. Elsevier Press, pp. 143-172.
- Gott, JM and Rhee, AC (2007) Insertion/deletion editing in Physarum polycephalum. In RNA Editing (Nucleic Acids and Molecular Biology Series), Springer, pp. 85-104.
- Gott, J.M., Parimi, N. and Bundschuh, R. (2005) Discovery of new genes and deletion editing in Physarum mitochondria enabled by a novel algorithm for finding edited mRNAs. Nuc. Acids Res. 33, 5063-5072.
- Byrne, E.M. and Gott, J.M. (2004) Unexpectly complex editing site patterns at dinucleotide insertion sites in Physarum mitochondria. Mol.Cell Biol. 24, 7821-7828.
- Byrne, E.M., Stout, A. and Gott, J.M. (2002) Editing site recognition and nucleotide insertion are separable processes in Physarum mitochondria. EMBO J 21, 6154-6161.
- Byrne, E.M. and Gott, J.M. (2002) Co-transcriptional editing of Physarum mitochondrial RNA requires local features of the native template. RNA 8, 1174-1185.
- Cheng, Y.-W., Visomirski-Robic, L.M. and Gott, J.M. (2001) Non-templated addition of nucleotides to the 3' end of nascent RNA during RNA editing in Physarum. EMBO J 20, 1405-1414.