All Publications
*Corresponding author(s)
2025 |
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| Seshadri R, Gopalan V(2025) An RNA ligase partner for the prokaryotic protein-only RNase P: insights into the functional diversity of RNase P from genome mining. mBio (accepted for publication) | |
| Law JD, Gao Y, Kovvali S, Thirugnanasambantham P, Wysocki VH, Ahmer BMM, Gopalan V*(2025) Identification of inhibitors of the Salmonella FraB deglycase, a drug target. FEBS Open Bio (accepted for publication) | |
| Law JD*, Gao Y, Wysocki VH, Gopalan V*(2025) Design of a yeast SUMO tag to eliminate internal translation initiation. Prot. Sci., 34(1): e5256 | |
| Sidharthan V, Sibley C, Dunne-Dombrink K, Yang M, Zahurancik W, Balaratnam S, Wilburn D*, Schneekloth J*., Gopalan V*(2025) Use of a small molecule microarray screen to identify inhibitors of the catalytic RNA subunit of Methanobrevibacter smithii RNase P. Nucleic Acids Res., 53(1): gkae1190 | |
2024 |
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| Wadsworth GM, Srinivasan S, Lai LB, Datta M, Gopalan V, Banerjee P (2024) RNA-driven phase transitions in biomolecular condensates. Mol. Cell, 84: 3692-3705 | |
| Gopalan V and Kirsebom LA (2024) A tribute to Sidney Altman, one of the architects of modern RNA biology. J. Biol. Chem. 300: 107364 | |
| Shen Y, Bosch G, Pino L and Gopalan V (2024) Use of the “double diamond” design framework to nurture creativity in life sciences research. Trends Biochem. Sci.49: 654-657 | |
| He S-L, Li B, Zahurancik WJ, Arthur HC, Sidharthan V, Gopalan V*, Wang L*, Jang J-C*(2024) Overexpression of stress granule protein TZF1 enhances salt stress tolerance by targeting ACA11 mRNA for degradation in Arabidopsis. Front. Plant Sci. 15: 1375478 | |
2023 |
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| Gopalan V and Musier-Forsyth K (2023) Transfer RNAs: A treasure trove that keeps on giving. J. Biol. Chem., 299(10):105170. | |
| Wadsworth GM, Zahurancik WJ, Zeng X, Pullara P, Lai LB, Sidharthan V, Pappu RV, Gopalan V*, Banerjee P*. (2023) RNAs undergo phase transitions with lower critical solution temperatures. Nat. Chem., 15(12):1693-1704. | |
| Kovvali S, Gao Y, Cool A, Lindert S, Wysocki VH*, Bell CE*, Gopalan V*. (2023) Insights into the catalytic mechanism of a bacterial deglycase essential for utilization of fructose-lysine. Protein Sci.: e4695. | |
| Elkholi IE, Boulais J, Thibault M-P, Phan H-D, Robert A, Lai LB, Faubert D, Smith MJ, Gopalan V, Côté J-F (2023) Mapping the MOB proteins’ proximity network reveals a unique interaction between human MOB3C and the RNase P complex J. Biol. Chem., 299: 105123 | |
| Roth K, Bannerman T, and Gopalan V. (2023) An outreach activity to enhance pedagogy. Trends Biochem. Sci., 48(5):410-413 | |
| Sabag-Daigle A°, Boulanger EF, Thirugnanasambantham P, Law JD, Bogard AJ, Behrman EJ*, Gopalan V*, and Ahmer BMM*. (2023) Identification of small molecule inhibitors of the Salmonella FraB deglycase using a live-cell assay. Microbiology Spectrum,11: e04606-22. | |
| Thirugnanasambantham P°, Bashian E°, Zaleski R, and Gopalan V*. (2022) GlycoForum-Technical Note Demonstrating the utility of sugar-phosphate phosphatases in coupled enzyme assays: galactose-1-phosphate uridylyltransferase as proof-of-concept. Glycobiology, 33: 95-98. °joint first authors | |
2022 |
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| Lucks JB, and Gopalan V. (2022) Sidney Altman: In his own words. RNA, 28: 1428-1429. | |
| Gopalan V. (2022) Sidney Altman: An exemplary scientist, teacher, and friend (1939-2022).RNA, 28: 1393-1397. | |
| Thirugnanasambantham P, Kovvali S, Cool A, Gao Y, Sabag-Daigle A, Boulanger EF, Mitton-Fry M, Di Capua A, Behrman EJ, Wysocki VH, Lindert S, Ahmer BMM, and Gopalan V*. (2022) Serendipitous Discovery of a Competitive Inhibitor of FraB, a Salmonella Deglycase and Drug Target. Pathogens, 11: 1102. | |
| 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 | |
| Szkoda BE°, Di Capua A°, Shaffer J, Behrman EJ, Wysocki VH*, and Gopalan V*. (2022) Characterization of a Salmonella transcription factor-DNA complex and identification of the inducer metabolite by native mass spectrometry. J. Mol. Biol., 7: 167480. °joint first authors | |
| 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. Proc Natl Acad Sci USA, 119: e2119529119. | |
2021 |
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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. | ||
| 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 | ||
| Boulanger EF, Sabag-Daigle A°, Thirugnanasambantham P°, Gopalan V*, and Ahmer BMM*. (2021) Sugar phosphate toxicities. Microbiol. Mol. Biol. Rev., 85: e0012321. °joint second authors | ||
| Lai SM, Thirugnanasambantham P°, Sidharthan V°, Norris AS, Law JD, Gopalan V*, and Wysocki VH*. (2021) Advancing overexpression and purification of recombinant proteins by pilot optimization through tandem affinity-buffer exchange chromatography online with native mass spectrometry. Methods Enzymol., 659: 37-70. °joint second authors | ||
| 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. | ||
| Ujor VC, Lai LB, Okonkwo CC, Gopalan V*, and Ezeji T*. (2021) Ribozyme-mediated downregulation uncovers DNA integrity scanning protein A (DisA) as a solventogenesis determinant in Clostridium beijerinckii. Front. Bioeng. Biotechnol., 9: 669462. | ||
| Busch F, VanAernum ZL, Lai SM, Gopalan V, and Wysocki VH* (2021) Analysis of Tagged Proteins Using Tandem Affinity-Buffer Exchange Chromatography Online with Native Mass Spectrometry. Biochemistry, 45: 1876-84. | ||
| 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. | ||
| 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 | ||
| Kadowaki J, Jones T, Sengupta A, Gopalan V*, and Subramaniam V* (2021) Copper oxide-based cathode for direct NADPH regeneration. Sci. Rep., 11: 1-12. | ||
| 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. | ||
2020 |
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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. | |
| Zahurancik WJ, Szkoda BE, Lai LB*, and Gopalan V* (2020) Ramping recombinant protein expression in bacteria. Biochemistry, 59: 2122-2124. | |
| Gray MW* and Gopalan V*. (2020) Piece by piece: Building a ribozyme. J. Biol. Chem., 295: 2313-2323. | |
2018 |
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| Lyon SE, Chen T-H, Wallace AJ, Adib KL, and Gopalan V*. (2018) An RNase P-based assay for accurate determination of the 5′-deoxy-5′-azidoguanosine-modified fraction of in vitro transcribed RNAs. ChemBioChem, 19: 2353-2359. | |
| Agu CV, Lai SM, Ujor V, Biswas PK, Jones A, Gopalan V, and Ezeji TC*. (2018) Development of a high-throughput assay for rapid screening of butanologenic strains. Sci. Rep., 8: 3379. [SI] | |
| Wu J°, Sabag-Daigle A°, Borton MA^, Kop LFM^, Szkoda BE^, Deatherage Kaiser BL, Lindemann SR, Renslow RS, Wei S, Nicora CD, Weitz KK, Kim Y-M, Adkins JN, Metz TO, Boyaka P, Gopalan V, Wrighton KC, Wysocki VH*, and Ahmer BMM*. (2018) Salmonella-mediated inflammation eliminates competitors for fructose-asparagine in the gut. Infect. Immun., 86: e00945-17. °joint first authors; ^joint second authors | |
| Wu J, Sabag-Daigle A, Metz TO, Deatherage Kaiser BL, Gopalan V, Behrman EJ, Wysocki VH*, and Ahmer BMM*. (2018) Measurement of fructose–asparagine concentrations in human and animal foods. J. Agric. Food Chem., 66: 212-217. | |
| Sabag-Daigle A, Wu J, Borton MA, Sengupta A, Gopalan V, Wrighton KC, Wysocki VH, and Ahmer BMM*. (2018) Identification of bacterial species that can utilize fructose-asparagine. Appl. Environ. Microbiol., 84: e01957-17. | |
| Lyon S and Gopalan V*. (2018) A T7 RNA polymerase mutant enhances the yield of 5′-thienoguanosine-initiated RNAs. ChemBioChem, 19: 142-146. (Highlighted on the cover) | |
| Gopalan V*, Jarrous N*, and Krasilnikov AS*. (2018) Chance and necessity in the evolution of RNase P. RNA, 24: 1-5. | |
2017 |
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| Sabag-Daigle A, Sengupta A, Blunk HM, Biswas PK, Cron MC, Bogard AJ, Behrman EJ, Gopalan V, and Ahmer BMM*. (2017) Salmonella FraE, an asparaginase homolog, contributes to fructose-asparagine but not asparagine utilization. J. Bacteriol., 199: e00330-17. | |
| Sengupta A, Zabala A^, Tan SY^, Broadstock A^, Suryanarayanan TS, and Gopalan V*. (2017) Characterization of an ionic liquid-tolerant ß-xylosidase from a marine-derived fungal endophyte. Biochem. Cell Biol., 95: 585-591. ^joint second authors | |
| 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 | |
| Suryanarayanan TS, Gopalan V, Uma Shaanker R, Sengupta A, and Ravikanth G. (2017) Translating endophyte research to applications: prospects and challenges. In JL de Azevedo and MC Quecine (Eds.), Diversity and Benefits of Microorganisms from the Tropics (pp. 343-365). Cham, Switzerland: Springer International Publishing AG. | |
| Biswas PK, Behrman EJ*, and Gopalan V*. (2017) Characterization of a Salmonella sugar kinase essential for utilization of fructose-asparagine. Biochem. Cell Biol., 95: 304-309. | |
2007 |
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| Behrman EJ* and Gopalan V. (2007) The anomeric specificity of enzymes which act on sugars. J. Chem. Educ., 84: 1608. | |
| Gopalan V*. (2007) Uniformity amid diversity in RNase P. Proc. Natl. Acad. Sci. USA, 104: 2031-2032. | |
| 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. | |
2006 |
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| Gopichandran V, Lai LB, and Gopalan V*. (2006) Protein-energy malnutrition. In RH Glew and MD Rosenthal (Eds.), Clinical Studies in Medical Biochemistry, (3rd edition; pp. 255-265). New York, NY: Oxford University Press. | |
| Lai LB, Gopichandran V, and Gopalan V*. (2006) Tangier disease: a disorder in the reverse cholesterol transport pathway. In RH Glew and MD Rosenthal (Eds.), Clinical Studies in Medical Biochemistry, (3rd edition; pp. 159-166). New York, NY: Oxford University Press. | |
| 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] | |
2005 |
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| Behrman EJ* and Gopalan V. (2005) Cholesterol and plants. J. Chem. Educ., 82: 1791-1793. | |
2004 |
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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. | |
| 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. | |
2003 |
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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. | |
| 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. | |
| 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. | |
| 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. | |
| 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. | |
2002 |
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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] | |
| Tsai H-Y°, Lai LB°, and Gopalan V*. (2002) A modified pBluescript-based vector for facile cloning and transcription of RNAs. Anal. Biochem., 303: 214-217. °joint first authors | |
| 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. | |
| 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. | |
| Gopalan V, Vioque A, and Altman S*. (2002) RNase P: variations and uses. J. Biol. Chem., 277: 6759-6762. | |
2001 |
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| Wu C-W, Eder PS, Gopalan V*, and Behrman EJ*. (2001) Kinetics of coupling reactions that generate monothiophosphate disulfides: implications for modification of RNAs. Bioconjug. Chem., 12: 842-844. | |
| Biswas R, Kühne H, Brudvig GW, and Gopalan V*. (2001) Use of EPR spectroscopy to study macromolecular structure and function. Sci. Prog., 84: 45-68. | |
| 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. | |
2000 |
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| Altman S*, Gopalan V, and Vioque A. (2000) Varieties of RNase P: a nomenclature problem? RNA, 6: 1689-1694. | |
| 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. | |
1999 |
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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. | |