All Publications


*Corresponding author(s)

2019

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., in press.
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.
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.

 

2018

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

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.

 

2016

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 ONE11: e0160246. [SI] °joint first authors
Agu CV, Ujor V, Gopalan V, and Ezeji TC*. (2016) Use of Cupriavidus basilensis-aided bioabatement to enhance fermentation of acid-pretreated biomass hydrolysates by Clostridium beijerinckii. J. Ind. Microbiol. Biotechnol.43: 1215-1226. [SI]
Sabag-Daigle A, Blunk HM, Sengupta A, Wu J, Bogard AJ, Ali MM, Stahl C, Wysocki VH, Gopalan V, Behrman EJ, and Ahmer BMM*. (2016) A metabolic intermediate of the fructose-asparagine utilization pathway inhibits growth of a Salmonella fraB mutant. Sci. Rep.6: 28117. [SI]
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]
Samanta MP°*, Lai SM°, Daniels CJ, and Gopalan V*. (2016) Sequence analysis and comparative study of the protein subunits of archaeal RNase P. Biomolecules6: 22. [SI] °joint first authors
Wang Y*°, Qu J°, Ji S, Wallace AJ, Wu J, Li Y, Gopalan V, and Ding B. (2016) A land plant-specific transcription factor directly enhances transcription of a pathogenic noncoding RNA template by DNA-dependent RNA polymerase II. Plant Cell28: 1094-1107. [SI] °joint first authors

 

2015

Suryanarayanan TS*, Gopalan V*, Sahal D, and Sanyal K. (2015) Establishing a national fungal genetic resource to enhance the bioeconomy. Curr. Sci.109: 1033-1037.
Thirunavukkarasu N, Jahnes B^, Broadstock A^, Govinda Rajulu MB, Murali TS, Gopalan V*, and Suryanarayanan TS*. (2015) Screening marine-derived endophytic fungi for xylan-degrading enzymes. Curr. Sci.109: 112-120. ^joint second authors
Glew RH*, Challa AK, and Gopalan V*. (2015) Who is qualified to instruct scientific manuscript writing? Curr. Sci.108: 1032.
Gopalan V* and McClain WH*. (2015) RNA: yesterday, today, and tomorrow. RNA21: 541-543. (Invited article for a special issue)
Ujor V, Agu CV, Gopalan V, and Ezeji TC*. (2015) Allopurinol-mediated lignocellulose-derived microbial inhibitor tolerance by Clostridium beijerinckii during acetone–butanol–ethanol (ABE) fermentation. Appl. Microbiol. Biotechnol., 99: 3729-3740.
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]

 

2014

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]
Glew RH*, Challa AK, and Gopalan V*. (2014) Training in scientific manuscript writing. Curr. Sci.107: 1386-1392.
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
Govinda Rajulu MB°, Lai LB°, Murali TS, Gopalan V*, and Suryanarayanan TS*. (2014) Several fungi from fire-prone forests of southern India can utilize furaldehydes. Mycol. Prog.13: 1049-1056. °joint first authors
Ujor V, Agu CV, Gopalan V, and Ezeji TC*. (2014) Glycerol supplementation of the growth medium enhances in situ detoxification of furfural by Clostridium beijerinckii during butanol fermentation. Appl. Microbiol. Biotechnol.98: 6511-6521.
Suryanarayanan TS* and Gopalan V*. (2014) Crowdsourcing to create national repositories of microbial genetic resources: fungi as a model. Curr. Sci.106: 1196-1200.

 

2013

Han B°, Ujor V°, Lai LB, Gopalan V, and Ezeji TC*. (2013) Use of proteomic analysis to elucidate the role of calcium in acetone-butanol-ethanol fermentation by Clostridium beijerinckii NCIMB 8052. Appl. Environ. Microbiol.79: 282-293. [SI] °joint first authors

 

2012

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.
Suryanarayanan TS*, Thirunavukkarasu N, Govindarajulu MB, and Gopalan V. (2012) Fungal endophytes: an untapped source of biocatalysts. Fungal Divers.54: 19-30.
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. Biochemistry51: 926-935. [SI]
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]

 

2011

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.
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. Genomics286: 359-369.
Han B, Gopalan V, and Ezeji TC*. (2011) Acetone production in solventogenic Clostridium species: new insights from non-enzymatic decarboxylation of acetoacetate. Appl. Microbiol. Biotechnol.91: 565-576.
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]
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

 

2010

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)
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. USA107: 22493-22498. [SI] (Highlighted on the cover and in a commentary) °joint first authors
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. USA107: 14573-14578. [SI]
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.
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.
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)

 

2009

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

 

2008

Gopalan V*. (2008) Catalytic RNAs in all guises. [Invited review of the book Ribozymes and RNA catalysis, by D Lilley and F Eckstein (Eds.)]. Chemistry World5: 64.
Behrman EJ* and Gopalan V. (2008) Phosphoenolpyruvate: an end to hand-waving. Biochem. Mol. Biol. Educ.36: 323-324.
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]
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

 

2007

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. USA104: 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

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. USA103: 16147-16152. [SI]

 

2005

Behrman EJ* and Gopalan V. (2005) Cholesterol and plants. J. Chem. Educ.82: 1791-1793.

 

2004

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

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. USA100: 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. Drugs4: 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

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. RNA8: 290-295.
Gopalan V, Vioque A, and Altman S*. (2002) RNase P: variations and uses. J. Biol. Chem.277: 6759-6762.

 

2001

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

Altman S*, Gopalan V, and Vioque A. (2000) Varieties of RNase P: a nomenclature problem? RNA6: 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

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. Biochemistry38: 1705-1714.