| Phan H-D°, Norris A°, Du C, Stachowski K, Khairunisa B, Sidharthan V, Mukhopadhyay B, Foster MP, Wysocki VH*, and Gopalan V*. (2022) Elucidation of structure-function relationships in Methanocaldococcus jannaschii RNase P, a multi-subunit catalytic ribonucleoprotein. Nucleic Acids Res., 50: 8154-8167 °joint first authors |
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| Lai LB, Lai SM, Szymanski ES, Kapur M, Choi EK, Al-Hashimi HM, Ackerman SL*, and Gopalan V*. (2022) Structural basis for impaired 5′ processing of a mutant tRNA associated with defects in neuronal homeostasis. PNAS, 119: e2119529119. |
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| Phan H-D, Lai LB*, Zahurancik WJ, and Gopalan V*. (2021) The many faces of RNA-based RNase P: An RNA-world relic. Trends Biochem. Sci., 46: 976-991. |
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| Marathe IA, Lai SM°, Zahurancik WJ°, Poirier MG, Wysocki VH, and Gopalan V*. (2021) Protein cofactors and substrate dictate Mg2+-dependent structural changes in the catalytic RNA of archaeal RNase P. Nucleic Acids Res., 49: 9444-9458. °joint second authors |
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| Zahurancik WJ, Norris AS, Lai SB, Snyder DT, Wysocki VH*, and Gopalan V*. (2021) Purification, reconstitution, and mass analysis of archaeal RNase P, a multi-subunit ribonucleoprotein enzyme. Methods Enzymol., 659: 71-103. |
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| Lai SM and Gopalan V*. (2021) Using an L7Ae-tethered, hydroxyl radical-mediated footprinting strategy to identify and validate kink-turns in RNAs. Methods Mol. Biol., 2167: 147-69. |
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| Li W, Xiong Y, Lai LB, Zhang K, Li Z, Kang H, Dai L, Gopalan V*, Wang G-L*, and Liu W* (2021) The rice RNase P protein subunit Rpp30 confers broad-spectrum resistance to fungal and bacterial pathogens. Plant Biotechnol. J., 19: 1988-1999 |
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| Yu AM, Gaspar P, Cheng L, Lai LB, Kaur S, Gopalan V, Chen AA*, and Lucks JB* (2021) Computationally reconstructing co-transcriptional RNA folding pathways from experimental data reveals rearrangement of non-native folding intermediates. Mol. Cell, 81: 870-883. |
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| Lai LB, Phan H-D, Zahurancik WJ, and Gopalan V* (2020) Alternative protein topology-mediated evolution of a catalytic ribonucleoprotein. Trends Biochem. Sci., 45: 825-828. |
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| Gray MW* and Gopalan V*. (2020) Piece by piece: Building a ribozyme. J. Biol. Chem., 295: 2313-2323. |
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| Palsule G, Gopalan V, and Simcox A*. (2019) Biogenesis of RNase P RNA from an intron requires co-assembly with cognate protein subunits. Nucleic Acids Res., 47: 8746-8754. [SI] |
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| Daniels CJ*, Lai LB, Chen T-H, and Gopalan V. (2019) Both kinds of RNase P in all domains of life: Surprises galore. RNA, 25: 286-291. |
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| Chen T-H, Sotomayor M, and Gopalan V*. (2019) Biochemical studies provide insights into the necessity for multiple Arabidopsis thaliana protein-only RNase P isoenzymes. J. Mol. Biol., 431: 615-624. |
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| Gopalan V*, Jarrous N*, and Krasilnikov AS*. (2018) Chance and necessity in the evolution of RNase P. RNA, 24: 1-5. |
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| Lai LB*, Tanimoto A^, Lai SM^, Chen W-Y, Marathe IA, Westhof E, Wysocki VH, and Gopalan V*. (2017) A novel double kink-turn module in euryarchaeal RNase P RNAs. Nucleic Acids Res., 45: 7432-7440. [SI] ^joint second authors |
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| Mao G°, Chen T-H°, Srivastava AS, Kosek D, Biswas PK, Gopalan V, and Kirsebom LA*. (2016) Cleavage of model substrates by Arabidopsis thaliana PRORP1 reveals new insights into its substrate requirements. PLoS ONE, 11: e0160246. [SI] °joint first authors |
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| Chen T-H, Tanimoto A, Shkriabai N, Kvaratskhelia M, Wysocki V*, and Gopalan V*. (2016) Use of chemical modification and mass spectrometry to identify substrate-contacting sites in proteinaceous RNase P, a tRNA processing enzyme. Nucleic Acids Res., 44: 5344-5355. [SI] |
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| Samanta MP°*, Lai SM°, Daniels CJ, and Gopalan V*. (2016) Sequence analysis and comparative study of the protein subunits of archaeal RNase P. Biomolecules, 6: 22. [SI] °joint first authors |
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| Manivannan SN, Lai LB, Gopalan V*, and Simcox A*. (2015) Transcriptional control of an essential ribozyme in Drosophila reveals an ancient evolutionary divide in animals. PLoS Genet., 11: e1004893. [SI 1, 2] |
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| Lai SM, Lai LB, Foster MP*, and Gopalan V*. (2014) The L7Ae protein binds to two kink-turns in the Pyrococcus furiosus RNase P RNA. Nucleic Acids Res., 42: 13328-13338. [SI] |
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| Ma X°, Lai LB°, Lai SM°, Tanimoto A, Foster MP, Wysocki VH*, and Gopalan V*. (2014) Uncovering the stoichiometry of Pyrococcus furiosus RNase P, a multi-subunit catalytic ribonucleoprotein complex, by surface-induced dissociation and ion mobility mass spectrometry. Angew. Chem. Int. Ed. Engl., 53: 11483-11487. [SI] °joint first authors |
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| Susanti D, Johnson EF, Rodriguez JR, Anderson I, Perevalova AA, Kyrpides N, Lucas S, Han J, Lapidus A, Cheng J-F, Goodwin L, Pitluck S, Mavrommatis K, Peters L, Land ML, Hauser L, Gopalan V, Chan PP, Lowe TM, Atomi H, Bonch-Osmolovskaya EA, Woyke T, and Mukhopadhyay B*. (2012) Complete genome sequence of Desulfurococcus fermentans, a hyperthermophilic cellulolytic crenarchaeon isolated from a freshwater hot spring in Kamchatka, Russia. J. Bacteriol., 194: 5703-5704. |
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| Xu Y, Oruganti SV, Gopalan V, and Foster MP*. (2012) Thermodynamics of coupled folding in the interaction of archaeal RNase P proteins RPP21 and RPP29. Biochemistry, 51: 926-935. [SI] |
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| Chen W-Y, Singh D, Lai LB, Stiffler MA, Lai HD, Foster MP, and Gopalan V*. (2012) Fidelity of tRNA 5′-maturation: a possible basis for the functional dependence of archaeal and eukaryal RNase P on multiple protein cofactors. Nucleic Acids Res., 40: 4666-4680. [SI] |
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| Crowe BL, Bohlen CJ, Wilson RC, Gopalan V, and Foster MP*. (2011) Assembly of the complex between archaeal RNase P proteins RPP30 and Pop5. Archaea, doi:10.1155/2011/891531. |
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| Lai LB, Bernal-Bayard P, Mohannath G, Lai SM, Gopalan V*, and Vioque A*. (2011) A functional RNase P protein subunit of bacterial origin in some eukaryotes. Mol. Genet. Genomics, 286: 359-369. |
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| Sinapah S°, Wu S°, Chen Y°, Pettersson BMF, Gopalan V, and Kirsebom LA*. (2011) Cleavage of model substrates by archaeal RNase P: role of protein cofactors in cleavage-site selection. Nucleic Acids Res., 39: 1105-1116. [SI] °joint first authors |
|
| Cho I-M, Kazakov SA, and Gopalan V*. (2011) Evidence for recycling of external guide sequences during cleavage of bipartite substrates in vitro by reconstituted archaeal RNase P. J. Mol. Biol., 405: 1121-1127. [SI] |
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| Chen W-Y°, Xu Y°, Cho I-M, Oruganti SV, Foster MP*, and Gopalan V*. (2011) Cooperative RNP assembly: complementary rescue of structural defects by protein and RNA subunits of archaeal RNase P. J. Mol. Biol., 411: 368-383. °joint first authors |
|
| Chen W-Y°, Pulukkunat DK°, Cho I-M, Tsai H-Y, and Gopalan V*. (2010) Dissecting functional cooperation among protein subunits in archaeal RNase P, a catalytic ribonucleoprotein complex. Nucleic Acids Res., 38: 8316-8327. [SI] °joint first authors |
|
| Jarrous N* and Gopalan V. (2010) Archaeal/Eukaryal RNase P: subunits, functions, and RNA diversification. Nucleic Acids Res., 38: 7885-7894. [SI] (Highlighted as a featured article) |
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| Lai LB°, Chan PP°, Cozen AE, Bernick DL, Brown JW, Gopalan V*, and Lowe TM*. (2010) Discovery of a minimal form of RNase P in Pyrobaculum. Proc. Natl. Acad. Sci. USA, 107: 22493-22498. [SI] (Highlighted on the cover and in a commentary) °joint first authors |
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| Cho I-M, Lai LB, Susanti D, Mukhopadhyay B, and Gopalan V*. (2010) Ribosomal protein L7Ae is a subunit of archaeal RNase P. Proc. Natl. Acad. Sci. USA, 107: 14573-14578. [SI] |
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| Lai LB, Cho I-M, Chen W-Y, and Gopalan V*. (2010) Archaeal RNase P: a mosaic of its bacterial and eukaryal relatives. In F Liu and S Altman (Eds.), Ribonuclease P (Protein Reviews, vol. 10; pp. 153-172). New York, NY: Springer Science + Business Media, LLC. |
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| McClain WH*, Lai LB, and Gopalan V. (2010) Trials, travails, and triumphs: an account of RNA catalysis in RNase P. J. Mol. Biol., 397: 627-646. |
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| Lai LB, Vioque A, Kirsebom LA*, and Gopalan V*. (2010) Unexpected diversity of RNase P, an ancient tRNA processing enzyme: challenges and prospects. FEBS Lett., 584: 287-296. (Invited article for a special issue) |
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| Xu Y, Amero CD^, Pulukkunat DK^, Gopalan V*, and Foster MP*. (2009) Solution structure of an archaeal RNase P binary protein complex: Formation of the 30-kDa complex between Pyrococcus furiosus RPP21 and RPP29 is accompanied by coupled protein folding and highlights critical features for protein–protein and protein–RNA interactions. J. Mol. Biol., 393: 1043-1055. [SI] (Highlighted on the cover) ^joint second authors |
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| Pulukkunat DK and Gopalan V*. (2008) Studies on Methanocaldococcus jannaschii RNase P reveal insights into the roles of RNA and protein cofactors in RNase P catalysis. Nucleic Acids Res., 36: 4172-4180. [SI] |
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| Kawamoto SA°, Sudhahar CG°, Hatfield CL°, Sun J, Behrman EJ, and Gopalan V*. (2008) Studies on the mechanism of inhibition of bacterial ribonuclease P by aminoglycoside derivatives. Nucleic Acids Res., 36: 697-704. [SI] °joint first authors |
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| Gopalan V*. (2007) Uniformity amid diversity in RNase P. Proc. Natl. Acad. Sci. USA, 104: 2031-2032. |
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| Gopalan V and Altman S*. (2007) Ribonuclease P: structure and catalysis. In RF Gesteland, TR Cech, and JF Atkins (Eds.), The RNA World (3rd edition; online version only). New York, NY: Cold Spring Harbor Laboratory Press. |
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| Tsai H-Y, Pulukkunat DK, Woznick WK, and Gopalan V*. (2006) Functional reconstitution and characterization of Pyrococcus furiosus RNase P. Proc. Natl. Acad. Sci. USA, 103: 16147-16152. [SI] |
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| Rangarajan S, Stephen Raj ML, Hernandez JM, Grotewold E, and Gopalan V*. (2004) RNase P as a tool for disruption of gene expression in maize cells. Biochem. J., 380: 611-616. |
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| Gopalan V, Vioque A, and Altman S*. (2004) RNase P: variations and uses. In E Keinan, I Schechter, and M Sela (Eds.), Life Sciences for the 21st Century, (pp. 49-59). Weinheim, Germany: Wiley-VCH. |
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| Boomershine WP, McElroy CA, Tsai H-Y, Wilson RC, Gopalan V, and Foster MP*. (2003) Structure of Mth11/Mth Rpp29, an essential protein subunit of archaeal and eukaryotic RNase P. Proc. Natl. Acad. Sci. USA, 100: 15398-15403. |
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| Eder PS, Hatfield C, Vioque A, and Gopalan V*. (2003) Bacterial RNase P as a potential target for novel anti-infectives. Curr. Opin. Investig. Drugs, 4: 937-943. |
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| Boomershine WP, Stephen Raj ML, Gopalan V, and Foster MP*. (2003) Preparation of uniformly labeled NMR samples in Escherichia coli under the tight control of the araBAD promoter: expression of an archaeal homolog of the RNase P Rpp29 protein. Protein Expr. Purif., 28: 246-251. |
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| Pulukkunat DK, Stephen Raj ML, Pattanayak D, Lai LB, and Gopalan V*. (2003) Exploring the potential of plant RNase P as a functional genomics tool. In E. Grotewold (Ed.), Plant Functional Genomics (Methods in Molecular Biology, vol. 236; pp. 295-309). Totowa, NJ: Humana Press, Inc. |
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| Tsai H-Y, Masquida B, Biswas R, Westhof E, and Gopalan V*. (2003) Molecular modeling of the three-dimensional structure of the bacterial RNase P holoenzyme. J. Mol. Biol., 325: 661-675. |
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| Jovanovic M, Sanchez R, Altman S, and Gopalan V*. (2002) Elucidation of structure–function relationships in the protein subunit of bacterial RNase P using a genetic complementation approach. Nucleic Acids Res., 30: 5065-5073. [SI] |
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| Eubank TD, Biswas R, Jovanovic M, Litovchick A, Lapidot A, and Gopalan V*. (2002) Inhibition of bacterial RNase P by aminoglycoside–arginine conjugates. FEBS Lett., 511: 107-112. |
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| Guerrier-Takada C, Eder PS, Gopalan V, and Altman S*. (2002) Purification and characterization of Rpp25, an RNA-binding protein subunit of human ribonuclease P. RNA, 8: 290-295. |
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| Gopalan V, Vioque A, and Altman S*. (2002) RNase P: variations and uses. J. Biol. Chem., 277: 6759-6762. |
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| Stephen Raj ML, Pulukkunat DK, Reckard JF III, Thomas G, and Gopalan V*. (2001) Cleavage of bipartite substrates by rice and maize ribonuclease P. Application to degradation of target mRNAs in plants. Plant Physiol., 125: 1187-1190. |
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| Altman S*, Gopalan V, and Vioque A. (2000) Varieties of RNase P: a nomenclature problem? RNA, 6: 1689-1694. |
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| Biswas R, Ledman DW, Fox RO, Altman S, and Gopalan V*. (2000) Mapping RNA-protein interactions in ribonuclease P from Escherichia coli using disulfide-linked EDTA-Fe. J. Mol. Biol., 296: 19-31. |
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| Gopalan V*, Kühne H, Biswas R, Li H, Brudvig GW, and Altman S. (1999) Mapping RNA–protein interactions in ribonuclease P from Escherichia coli using electron paramagnetic resonance spectroscopy. Biochemistry, 38: 1705-1714. |
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