All Publications


*Corresponding author(s)

2020

Gray MW and Gopalan V*. (2020) Piece by piece: Building a ribozyme. J. Biol. Chem., in press.
Lai SM and Gopalan V*. (2020) Using an L7Ae-tethered, hydroxyl radical-mediated footprinting strategy to identify and validate kink-turns in RNAs. Methods Mol. Biol., in press.

 

2019

Sengupta A, Wu J, Seffernick JT, Sabag-Daigle A, Thomsen N, Chen T-H, Di Capua A, Bell CE, Ahmer BMM, Lindert S, Wysocki VH, and Gopalan V*. (2019) Integrated use of biochemical, native mass spectrometry, computational and genome-editing methods to elucidate the mechanism of a Salmonella deglycase. J. Mol. Biol., in press.
Hyde KD, Xu J*, Rapior S, Jeewon R, Lumyong S, Niego AGT, Abeywickrama PD, Aluthmuhandiram JVS, Brahamanage RS, Brooks S, Chaiyasen A, Chethana KWT, Chomnunti P, Chepkirui C, Chuankid B, de Silva NI, Doilom M, Faulds C, Gentekaki E, Gopalan V, Kakumyan P, Harishchandra D, Hemachandran H, Hongsanan S, Karunarathna A, Karunarathna SC, Khan S, Kumla J, Jayawardena RS, Liu J-K, Liu N, Luangharn T, Macabeo APG, Marasinghe DS, Meeks D, Mortimer PE, Mueller P, Nadir S, Nataraja KN, Nontachaiyapoom S, O’Brien M, Penkhrue W, Phukhamsakda C, Ramanan US, Rathnayaka AR, Sadaba RB, Sandargo B, Samarakoon BC, Tennakoon DS, Siva R, Sriprom W, Suryanarayanan TS, Sujarit K, Suwannarach N, Suwunwong T, Thongbai B, Thongklang N, Wei D, Wijesinghe SN, Winiski J, Yan J, Yasanthika E, and Stadler M. (2019) The amazing potential of fungi: 50 ways we can exploit fungi industrially. Fungal Divers., 97: 1-136.
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]
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.