A Member of the Rieveschl Laboratories for Mass Spectrometry

in the College of Arts & Sciences' Department of Chemistry

Publications 2018-2020

Valérie de Crécy-Lagard, Robert L Ross, Marshall Jaroch, Virginie Marchand, Christina Eisenhart, Damien Brégeon, Yuri Motorin, Patrick A Limbach “Survey and Validation of tRNA Modifications and Their Corresponding Genes in Bacillus subtilis sp Subtilis Strain 168” Biomolecules (2020) 10(7) 977. DOI: 10.3390/biom10070977. PMID: 32629984. PMCID: PMC7408541. [Link]

Yaojuan Liu, Yesenia Rodriguez, Robert L Ross , Ruoxia Zhao, Jason A Watts, Christopher Grunseich, Alan Bruzel, Dongjun Li, Joshua T Burdick, Rajendra Prasad, Robert J Crouch, Patrick A Limbach, Samuel H Wilson, Vivian G Cheung “RNA abasic sites in yeast and human cells”   Proceedings of the Natjional Academy of Sciences of the United States of America (2020) 117(34) 20689-20695. DOI: 10.1073/pnas.2011511117. PMID: 32788345. PMCID: PMC7456069. [Link]

Manasses Jora, Kayla Borland, Scott Abernathy, Ruoxia Zhao, Melissa Kelley, Stefanie Kellner, Balasubrahmanyam Addepalli, and Patrick A. Limbach “Chemical amination/imination of carbonothiolated nucleosides during RNA hydrolysis” Angewandte Chemie International Edition (2020) 60(8) 3961-3966  DOI: 10.1002/anie.202010793. PMID: 33125801. [Link] 

Congliang Sun, Patrick A Limbach and Balasubrahmanyam Addepalli “Characterization of UVA-induced alterations to transfer RNA sequences” Biomolecules (2020) 10(11):1527. DOI: 10.3390/biom10111527. PMID: 33171700. [Link]

Holly M. Funk, Ruoxia Zhao, Maggie Thomas, Sarah M. Spigelmyer, Nichlas J. Sebree, Regan O. Bales, Jamison B. Burchett, Justen B. Mamaril, Patrick A. Limbach, and Michael P. Guy “Identification of the enzymes responsible for m2,2G and acp3U formation on cytosolic tRNA from insects and plants” PLoS One (2020) 15(11) e0242737 DOI: 10.1371/journal.pone.0242737. PMID: 33253256. [Link]

Dirk Iwata-Reuyl, Ben Turner, Brett Burkhart, Katrin Weidenbach, Robert Ross, Patrick Limbach, Ruth Schmitz, Valérie de Crécy-Lagard, Kenneth Stedman, and Thomas Santangelo “Archaeosine modification of archaeal tRNA – a role in structural stabilization" Journal of Bacteriology (2020) 202(8) e00748-19. DOI: 10.1128/JB.00748-19. PMID: 32041795. PMCID: PMC7099136. [Link]

Mellie June Paulines, Collin Wetzel, Patrick A Limbach “Using spectral matching to interpret LC-MS/MS data during RNA modification mapping” Journal of Mass Spectrometry (2019) 54(11) 906-914. DOI: 10.1002/jms.4456. PMID: 31663233. [Link]

Thakur, P.; Estevez, M.; Lobue, P.A.; Limbach, P.A. and Addepalli, B.; “Improved RNA Modification Mapping of Cellular Non-coding RNAs using C- and U-specific RNases” Analyst (2019) 145, 816–827. DOI: 10.1039/c9an02111f. [Link] 

Howell, N.W.; Jora, M.; Jepson, B.F.; Limbach, P.A.; Jackman, J.E.; “Distinct substrate specificities of the human tRNA methyltransferases TRMT10A and TRMT10B” RNA (2019) 25 1366-1376. doi: 10.1261/rna.072090.119. PMID: 31292261. [Link]

Lobue, P.A.; Jora, M.; Addepalli, B; Limbach, P.A.; “Oligonucleotide Analysis by Hydrophilic Interaction Liquid Chromatography-Mass Spectrometry in the Absence of Ion-Pair Reagents” Journal of Chromatography A (2019) DOI: 10.1016/j.chroma.2019.02.016. PMID: 30772056. [Link]

Yu N, Jora M, Solivio B, Thakur P, Acevedo-Rocha CG, Randau L, de Crécy-Lagard V, Addepalli B, Limbach PA. “Transfer RNA Modification Profiles and Codon Decoding Strategies in Methanocaldococcus jannaschii” Journal of Bacteriology (2019) 201 e00690-18. DOI: 10.1128/JB.00690-18 PMID: 30745370. [Link]

Yuliia Sehin, Oksana Koshla, Yuriy Dacyuk, Ruoxia Zhao, Robert Ross, Maksym Myronovskyi, Patrick A. Limbach, Andriy Luzhetskyy, Suzanne Walker, Victor Fedorenko and Bohdan Ostash “Gene ssfg_01967 (miaB) for tRNA modification influences morphogenesis and moenomycin biosynthesis in Streptomyces ghanaensis ATCC14672” Microbiology (2019) 165 233-245. DOI: 10.1099/mic.0.000747 PMID: 30543507. [Link]

Peter Lobue, Ningxi Yu, Manasses Jora, Scott Abernathy, Patrick Limbach “Improved Application of RNAModMapper – an RNA Modification Mapping Software Tool – for Analysis of Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) Data” Methods (2018) 156 128-138. DOI: 10.1016/j.ymeth.2018.10.012 PMID: 30366097. [Link]

Solivio, B.; Yu, N.; Addepalli, B.; Limbach, P.A.; “Improving RNA Modification Mapping Sequence Coverage by LC-MS through a Nonspecific RNase U2-E49A Mutant” Analytica Chimica Acta (2018) 1036 73-79. DOI: 10.1016/j.aca.2018.08.012 PMID: 30253839. [Link]

Sarin, L.P.; Kienast, S.D.; Leufken, J.; Ross, R.L.; Limbach, P.A.; Fufezan, C.; Drexler, H.C.A; Leidel, S.A.; “Nano LC-MS using capillary columns enables accurate quantification of modified ribonucleosides at low femtomol levels” RNA (2018) 1403-1417. DOI: 10.1261/rna.065482 PMID: 30012570 PMCID: PMC6140458. [Link]

van Tran, N.; Muller, L.; Ross, R.L.; Lestini, R.; Létoquart, J.; Ulryck, N.; Limbach, P.A.; de Crécy-Lagard, V.; Cianférani, S.; Graille, M.; “Evolutionary insights into Trm112-methyltransferase holoenzymes involved in translation between archaea and eukaryotes” Nucleic Acids Research (2018) 46 8483-8499. DOI: 10.1093/nar/gky638 PMID: 30010922 PMCID: PMC6144793. [Link]

Jora, M.; Burns, A.P.; Ross, R.L.; Lobue, P.A.; Zhao, R.; Palumbo, C.M.; Beal, P.A.; Addepalli, B; Limbach, P.A.; “Differentiating positional isomers of nucleoside modifications by higher-energy collisional dissociation mass spectrometry (HCD MS)” Journal of the American Society for Mass Spectrometry (2018) 29 1745-1756. DOI: 10.1007/s13361-018-1999-6 PMID: 29949056 PMCID: PMC6062210. [Link]

Baldridge, K.C.; Maranhao, A.C.; Jora, M.; Quick, M.M.; Brodbelt, J.S.; Limbach, P.A.; Ellington, A.D.; Contreras, L.M.; “Directed evolution of heterologous tRNAs leads to independence from post-transcriptional modifications” ACS Synthetic Biology (2018) 7 1315-1327. DOI: 10.1021/acssynbio.7b00421 PMID: 29694026. [Link]

Sharma, I.M.; Rappé, M.C.; Addepalli, B.; Grabow, W.W.; Abeysirigunawardena, S.C.; Limbach, P.A.; Jaeger, L.; Woodson, S.A.; “A metastable rRNA junction essential for bacterial 30S biogenesis” Nucleic Acids Research (2018) 46 5182-5194. DOI: 10.1093/nar/gky120 PMID: 29850893 PMCID: PMC6007441. [Link]

Sun, C.; Jora, M.; Solivio, B; Limbach, P.A.; Addepalli, B.; “The effects of ultraviolet radiation on nucleoside modifications in RNA” ACS Chemical Biology (2018) 13 567-572. DOI: 10.1021/acschembio.7b00898. PMID: 29400945 PMCID: PMC5933051. [Link]

Masuda, I.; Takase, R.; Matsubara, R.; Paulines, M.J.; Gamper, H.; Limbach, P.A.; Hou, Y.-M.; “Selective Terminal Methylation of A tRNA Wobble Base” Nucleic Acids Research (2018) 46 e37. DOI: 10.1093/nar/gky013 PMID: 29361055 PMCID: PMC5909439. [Link]

Boccaletto, P.; Machnicka, M.A.; Purta, E.; Piątkowski, P.; Bagiński, B.; Wirecki, T.; de Crécy-Lagard, V.; Ross, R.; Limbach, P.A.; Kotter, A.; Helm, M.; Bujnicki, J.M.; “MODOMICS: a database of RNA modification pathways. 2017 update” Nucleic Acids Research (2018) 46, Issue D1, D303–D307. DOI: 10.1093/nar/gkx1030.sel PMID: 29106616 PMCID: PMC5753262. [Link]

Kessler AC, Kulkarni SS, Paulines MJ, Rubio MAT, Limbach PA, Paris Z, Alfonzo JD.; “Retrograde nuclear transport from the cytoplasm is required for tRNATyr maturation in T. brucei” RNA Biology (2018) 15 528-536. DOI: 10.1080/15476286.2017.1377878 PMID: 28901827 PMCID: PMC6103694. [Link]