Schultz, S.K., Kothe, U. (2023) Fluorescent labeling of tRNA for rapid kinetic interaction studies with tRNA-binding proteins. Methods in Enzymology, https://doi.org/10.1016/bs.mie.2023.05.007
Schultz, S.K., Meadows, K., Kothe, U. (2023) Molecular mechanism of tRNA binding by the Escherichia coli N7 guanosine methyltransferase TrmB. Journal of Biological Chemistry, 229 (5): 104612
Vos, T.J., Kothe, U. (2022) Synergistic interaction network between the snR30 RNP, Utp23, and ribosomal RNA during ribosome synthesis. RNA Biology, Vol. 19, 764 – 773
Henrickson, A., Gorget, G.E., Savelyev, A., Kim, M., Hargreaves, J., Schultz, S.K., Kothe, U., Demeler, B. (2022) Multi-wavelength analytical ultracentrifugation of biopolymer mixtures and interactions. Analytical Biochemistry, Vol, 652, doi: 10.1016/j.ab.2022.114728
Guegueniat, J.*, Halabelian, L.*, Zeng, H., Dong, A., Li, Y., Wu, H., Arrowsmith, C.H. †, Kothe, U. † (2021) The human pseudouridine synthase PUS7 recognizes RNA with an extended multi-domain binding surface. Nucleic Acids Research, published online ahead of print
* contributed equally; † corresponding author
Schultz, S.K., Kothe, U. (2021) Partially modified tRNAs for the study of tRNA maturation and function. Methods in Enzymology, Vol. 658, 225 – 250
Czekay, D. P., Kothe, U. (2021) H/ACA Small Ribonucleoproteins: Structural and Functional Comparison Between Archaea and Eukaryotes. Frontiers in Microbiology, Vol. 12, Article 654370
Porat, J., Kothe, U., Bayfield, M.A. (2021) Revisiting tRNA chaperones: new players in an ancient game. RNA, Vol. 27 (5), 543 – 559
Vos, T.J., and Kothe, U. (2020) snR30/U17 small nucleolar Ribonucleoprotein: a critical player during ribosome biogenesis. invited featured review, Cells, Vol. 9, Article 2195
Schultz, S. K., and Kothe, U. (2020) tRNA elbow modifications affect the tRNA pseudouridine synthase TruB and the methyltransferase TrmA. RNA 26 (9), pp. 1131-1142, doi: 10.1261/rna.075473.120
Keffer-Wilkes, L.*, Soon, E.*, and Kothe, U. (2020) The methyltransferase TrmA facilitates tRNA folding through interaction with its RNA-binding domain. Nucleic Acids Research, 48 (14), pp. 7981 – 7990,doi: 10.1093/nar/gkaa548,
*equal contribution
Ogailan, A.A., Rintala-Dempsey, A.C., and Kothe, U. Saccharomyces cerevisiae strains display robust phenotypes in the presence of Dyskeratosis Congenita mutations in the Cbf5 gene. PLoS ONE: PONE-D-19-02357, revisions requested; also posted on BioRxiv: https://doi.org/10.1101/535443)
Kelly, E., Czekay, D.E., and Kothe, U. (2019) Base pairing interactions between substrate RNA and H/ACA guide RNA modulate the kinetics of pseudouridylation, but not the affinity of substrate binding by H/ACA small nucleolar Ribonucleoproteins RNA 25 (10), pp. 1393 – 1404, doi: 10.1261/rna.071043.119
Tillault, A.-S., Schultz, S.K., Wieden, H.-J., and Kothe, U. (2018) Molecular determinants for 23S rRNA recognition and modification by the E. coli pseudouridine synthase RluE. Journal of Molecular Biology 430(9), pp. 1284-1294
Caton, E.A., Kelly, E.K., Kamalampeta, R. and Kothe, U. (2018) Efficient RNA pseudouridylation by eukaryotic H/ACA small ribonucleoproteins requires high affinity binding and correct positioning of guide RNA. Nucleic Acids Research 46(2), pp. 905-916, doi: 10.1093/nar/gkx1167
Rintala-Dempsey, A.C., and Kothe, U. (2017) Eukaryotic stand-alone pseudouridine synthases – RNA modifying enzymes and emerging regulators of gene expression? RNA Biology, 14 (9), 1185 – 1196
Keffer-Wilkes, L.C., Veerareddygari, G.R., and Kothe, U. (2016) RNA modification enzyme TruB is a tRNA chaperone. PNAS, 113, 14306 – 14311 (highlighted by a commentary in the same issue)
Tillault, A.S.*, Fourmann, J.-B.*, Loegler, C., Wieden, H.-J., Kothe, U., and Charpentier, B. (2015) Contribution of two conserved histidines to the dual activity of archaeal RNA guide-dependent and –independent pseudouridine synthase Cbf5. RNA, 21, 1233 – 1239; *contributed equally to this work
Friedt, J., Leavens, F.M., Mercier, E., Wieden, H.-J., and Kothe, U. (2014) An arginine-aspartate network in the active site of bacterial TruB is critical for catalysing pseudouridine formation. Nucleic Acids Research, 42, 3857 – 3870
Kamalampeta, R., Keffer-Wilkes, L.C., and Kothe, U. (2013) tRNA binding, positioning and modification by the pseudouridine synthase Pus10. J. Mol. Biol., 425(20), 3863-3874.
Kamalampeta, R., and Kothe, U. (2012) Archaeal proteins Nop10 and Gar1 increase the catalytic activity of Cbf5 in pseudouridylating tRNA. Scientific Reports, 2: 663, DOI: 10.1038/srep00663
Wright, J.R., Keffer-Wilkes, L.C., Dobing, S.R., and Kothe, U. (2011) Pre-steady-state kinetic analysis of the three Escherichia coli pseudouridine synthases TruB, TruA and RluA reveals uniformly slow catalysis. RNA, 17, 2074-2084Kothe, U., and Rodnina, M.V. (2007) Codon reading by tRNAAla with modified uridine in the wobble position. Mol. Cell 25(1), 167-174
Kothe, U., and Rodnina, M.V. (2006) Delayed release of inorganic phosphate from elongation factor Tu following GTP hydrolysis on the ribosome. Biochemistry, 45, 12767-12774
Kothe, U., Paleskava, L., Konevega, A.L., and Rodnina, M.V. (2006) Single-step purification of specific tRNAs by hydrophobic tagging. Analyt. Biochem. 356, 148-150
Savelsbergh, A., Mohr, D., Kothe, U., Wintermeyer, W., and Rodnina, M.V. (2005) Control of Phosphate Release from Elongation Factor G by Ribosomal Protein L7/12. EMBO J. 24(24), 4316-4323
Diaconu, M.*, Kothe, U.*, Schluenzen, F., Fischer, N., Harms, J., Tonevitski, A.G., Stark, H., Rodnina, M.V., and Wahl, M.C. (2005) Structural basis for the Function of the Ribosomal L7/12 Stalk in Factor Binding and Activation of GTP Hydrolysis. Cell 121(7), 991-1004*contributed equally to this work
Rodnina, M.V., Gromadski, K.B., Kothe, U., and Wieden, H.-J. (2005) Recognition and selection of tRNA in translation. FEBS Lett. 579, 938-942
Kothe, U., Wieden, H.-J., Mohr, D., and Rodnina, M. V. (2004) Interaction of Helix D of Elongation Factor Tu with Helices 4 and 5 of Protein L7/12 on the Ribosome. J. Mol. Biol. 336, 1011-1021