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Venkat Gopalan obtained a B.Sc. (Chemistry) from University of Madras, India, and a Ph.D. (Biochemistry) from the University of New Mexico (Mentor: Prof. Robert H. Glew). He was then a post-doctoral fellow in the group of Prof. Sidney Altman, Yale University. During his post-doctoral tenure, he was also a visiting scholar for brief periods at the MRC Laboratory of Molecular Biology, Cambridge, England. He came to OSU in 1998 and is currently a Professor in the Department of Biochemistry.
Structure and mechanism of action of ribonuclease P, a catalytic ribonucleoprotein (RNP) complex. The endoribonuclease RNase P is a ubiquitous RNP that is involved in the maturation of tRNAs. In Escherichia coli, the RNase P holoenzyme consists of a catalytic RNA subunit (M1 RNA, 377 nts) and a protein cofactor (C5 protein, 119 amino acid residues). The long-term goal of our studies is to elucidate the mechanism of assembly of this unique catalytic RNP complex and thereby understand how an RNA-binding protein influences the structure and function of its RNA ligand. 2. Use of plant RNase P to inhibit gene expression Recently, it has been demonstrated that endogenous, cellular RNase P can be guided to specifically destroy a target mRNA in bacterial and human cells in tissue culture. Our aim is to determine if plant RNase P could be utilized to disrupt gene expression in plants and their pathogens. These studies will help establish plant RNase P as a valuable functional genomics tool. Towards this objective, we have recently made significant progress in partially purifying and characterizing plant RNase P.
Suryanarayanan, T.S., Gopalan, V., Uma Shaanker, R., Sengupta, A. and Ravikanth, G. (2016) Translating endophyte research to applications: prospects and challenges. In “Diversity and benefits of microorganisms from the tropics” (Eds. Acevedo, J. L. and Quecine, M. C.), Springer Verlag (in press)
Biswas, P.K., Behrman, E.J. and Gopalan, V. (2016) Characterization of a Salmonella sugar kinase essential for utilization of fructose-asparagine. Biochem. Cell Biol. (in press)
Mao, G., Chen, T-H., Srivastava, A., Kosek, D., Biswas, P.K., Gopalan, V. & Kirsebom, L.A. (2016) Cleavage of model substrates by Arabidopsis thaliana PRORP1 reveals new insights into its substrate requirements. PLOS One (in press)
Agu, C.V., Ujor, V., Gopalan, V. & Ezeji, T. (2016) Use of Cupriavidus basilensis-aided bioabatement to enhance fermentation of acid-pretreated lignocellulosic biomass to butanol. J. Ind. Microbiol. Biotechnol. (in press)
Sabag-Daigle, A., Blunk, H., Sengupta, A., Wu, J., Bogard, A., Ali, M., Stahl, C., Wysocki, V.H., Gopalan, V., Behrman, E.J. & Ahmer, B.A. (2016) A metabolic intermediate of the fructose-asparagine utilization pathway inhibits growth of a Salmonella fraB mutant. Sci. Rep. 6:28117 | DOI: 10.1038/srep28117
Chen, T-H., Tanimoto, A., Shkriabai, N., Kvaratskhelia, M., Wysocki, V.H. & 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.
Samanta, M., Lai, S.M., Daniels, C.J. & Gopalan, V. (2016) Sequence analysis and comparative study of the protein subunits of archaeal RNase P. Biomolecules 6, 22; doi:10.3390/biom6020022
Wang, Y., Qu, J., Ji, S. Y., Wallace, A.J., Wu, J., Li, Y., Gopalan, V. & 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 Cell 28, 1094-1107.
Suryanarayanan, T.S., Gopalan, V., Sahal, D. and Sanyal, K. (2015) Establishing a national fungal genetic resource to enhance the bioeconomy. Curr. Sci. 109, 1033-1037.
Tirunavakkarasu, N., Jahnes, B., Broadstock, A., Govinda Rajulu, M. B., Murali, T. S., Gopalan, V. and Suryanarayanan, T. S. (2015) Screening marine-derived endophytic fungi for xylan-degrading enzymes. Curr. Sci. 109, 112-121.
Glew, R.H., Challa, A.K. and Gopalan, V. (2015) Who is qualified to instruct scientific manuscript writing? Curr. Sci. 108, 1032.
Ujor, V., Agu, C.V, Gopalan, V. and Ezeji, T. (2015) Allopurinol-mediated lignocellulose-derived microbial inhibitor tolerance by Clostridium beijerinckii during acetone-butanol-ethanol (ABE) fermentation. Appl. Microbiol. Biotechnol. 99, 3729-3740.
Gopalan, V. and McClain, W. H. (2015) RNA: Yesterday, today and tomorrow. RNA 21, 541-543.
Manivannan, S., Lai, L.B., Gopalan, V. and Simcox, A. (2015) Transcriptional control of an essential ribozyme in Drosophila reveals an ancient evolutionary divide in animals. PLoS Genetics 11, e1004893.
Lai, S.M., Lai, L.B., Foster, M.P. and Gopalan, V. (2014) Mapping the binding sites of ribosomal protein L7Ae on the Pyrococcus furiosus RNase P RNA. Nucleic Acids Res. 42, 13328-13338.
Glew, R.H., Challa, A.K. and Gopalan, V. (2014) Training in scientific manuscript writing. Curr. Sci. 107, 1386-1402.
Ma, X., Lai, L.B., Lai, S.M., Tanimoto, A., Foster, M.P., Wysocki, V. 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.
Ujor, V., Agu, C.V, Gopalan, V. and Ezeji, T. (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.
Govindarajulu, M.B., Lai, L.B., Gopalan, V. and Suryanarayanan, T.S. (2014) Several fungi from fire-prone forests of southern India can utilize furaldehydes. Mycol. Prog. 13, 1049-1056.
Suryanarayanan, T.S. and Gopalan, V. (2014) Crowdsourcing to create national repositories of microbial genetic resources: fungi as a model. Curr. Sci., 106, 1196-1200.
Han, B., Ujor, V., Lai, L.B., Gopalan, V., and Ezeji, T.C. (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
Chen, W-Y., Singh, D., Lai, L.B., Stiffler, M.A., Lai, H.D., Foster, M.P., 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.
Xu, Y., Oruganti, S.V., Gopalan, V., and Foster, M.P. (2012) Thermodynamics of coupled folding in the interaction of archaeal RNase P Proteins RPP21 and RPP29. Biochemistry, 51, 926-935.
Susanti, D., Johnson, E.F., Rodriguez, J.R., Anderson, I., Perevalova, A.A., Kyrpides, N., Lucas, S., Han, J., Lapidus, A., Cheng, J-F., Goodwin, L., Pitluck, S., Mavrommatis, K., Peters, L., Land, M.L., Hauser, L., Gopalan, V., Chan, P.P., Lowe, T.M., Atomi, H., Bonch-Osmolovskaya, E.A., 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, T.S., Thirunavukkarasu, N., Govindarajulu, M.B., and Gopalan, V. (2012) Fungal endophytes: an untapped source of biocatalysts. Fungal Divers., 54, 19-30.
Lai, L.B., Bernal-Bayard, P., Mohannath, G., Lai, S.M., Gopalan, V., and Vioque, A. (2011) A functional RNase P protein subunit of bacterial origin in some eukaryotes. Mol. Genet. Genomics, 286, 359-369.
Crowe, B.L., Bohlen, C.J., Wilson, R.C., Gopalan, V., and Foster, M.P. (2011) Assembly of the complex between archaeal RNase P proteins RPP30 and POP5. Archaea, doi: 10.1155/2011/891531.
Chen, W-Y., Xu, Y., Cho, I-M., Oruganti, S., Foster, M. P. and Gopalan, V. (2011) Cooperative RNP assembly: Complementary rescue of structural defects by protein and RNA subunits of archaeal RNase P. J. Mol. Biol. 411:368-83.
Han, B., Gopalan, V. and Ezeji, T. C. (2011) "Acetone production in solventogenic Clostridium species: New insights from non-enzymatic decarboxylation of acetoacetate." Applied Microbiology and Biotechnology 91:565-76.
Cho, I-M., Kazakov, S. A. and Gopalan, V. (2011) "Evidence for recycling of external guide sequences during cleavage of bipartite substrates by in vitro reconstituted archaeal RNase" P. J. Mol. Biol. 405, 1121-1127.
Sinapah, S., Wu, S., Chen, Y., Pettersson, B. M. F., Gopalan, V. and Kirsebom, L. A. (2011) "Cleavage of model substrates by archaeal RNase P: role of protein cofactors in cleavage-site selection." Nucleic Acids Res. 39, 1105-1116.
Lai, L. B., Chan, P., Cozen, A., Bernick, D. L., Brown, J., Gopalan, V. and Lowe, T. (2010) "Discovery of a minmal form of RNase P in Pyrobaculum." Proc Natl Acad Sci USA 107, 22493-22498.
Chen, W-Y., Pulukkunat, D. K., Cho, I-M., Tsai, H-Y. and Gopalan, V. (2010) "Dissecting functional cooperation among protein subunits in archaeal RNase P." Nucleic Acids Res. 38, 8316-8327.
Jarrous, N. and Gopalan, V. (2010) "Archaeal/eukaryal RNase P: subunits, functions and RNA diversification." Nucleic Acids Res. 38, 7885-7894.
Cho, I-M., Lai, L. B., 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.
McClain, W. H., Lai, L. B. and Gopalan, V. (2010) "Trials, travails and triumphs: an account of RNA catalysis in RNase P." J. Mol. Biol. 397, 627-646.
Lai, L. B., Vioque, A., Kirsebom, L. A. and Gopalan, V. (2010) "Unexpected diversity of RNase P, an ancient tRNA processing enzyme: challenges and prospects." FEBS Lett 584, 287-96.
Xu, Y., Ameros, C., Pulukkunat, D. K., Gopalan, V. and Foster, M. P. (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, 1043-55.
Pulukkunat, D. K. 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.
Kawamoto, S. A., Sudhahar, C. G., Hatfield, C., Sun, J., Behrman, E. J. and Gopalan, V. (2008) "Studies on the mechanism of inhibition of bacterial RNase P by aminoglycoside derivatives." Nucleic Acids Res. 36, 697-704.
Gopalan, V. (2007) "Uniformity amid diversity in RNase P." Proc Natl Acad Sci U S A. 104(7), 2031-2.
Tsai HY, Pulukkunat DK, Woznick WK, Gopalan, V. (2006) "Functional reconstitution and characterization of Pyrococcus furiosus RNase P." Proc Natl Acad Sci U S A. 103(44), 16147-52.
Rangarajan S, Raj ML, Hernandez JM, Grotewold E, Gopalan, V. (2004) "RNase P as a tool for disruption of gene expression in maize cells.", Biochem J. 380(Pt 3), 611-6.
Pulukkunat DK, Raj ML, Pattanayak D, Lai LB, Gopalan, V. (2003) "Exploring the potential of plant RNase P as a functional genomics tool.". Methods Mol Biol. 236, 295-310.
Boomershine, W.P., Stephen Raj, M.L., Gopalan, V., and Foster, M.P. (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, 246-51.
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, 661-75.
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, 5065-73.
Guerrier-Takada, C., Eder, P.S., Gopalan, V. and Altman, S. (2002) "Purification and characterization of Rpp25, an RNA-binding protein subunit of human ribonuclease P." RNA 8, 290-5.
Tsai, H.Y., Lai, L.B., and Gopalan, V. (2002) "A Modified pBluescript-based vector for facile cloning and transcription of RNAs." Anal Biochem.303, 214-7.
Eubank, T.D., Biswas, R., Jovanovic, M., Litovchick, A., Lapidot, A., and Gopalan, V. (2002) "Inhibition of bacterial RNase P by aminoglycoside-arginine conjugates." FEBS Lett. 511, 107-12.
Gopalan, V., Vioque, A., and Altman, S. (2002) "RNase P: variations and uses." J Biol Chem. 277, 6759-62.
Stephen Raj, M. L., Pulukkunat, D. K., Reckard, J. F., Thomas, G. and Gopalan, V. (2001) "Cleavage of bipartite substrates by rice and maize RNase P: Application to targeted degradation of mRNAs in plants." Plant Physiology 125: 1187-1190.
Biswas, R., Kuhne, H., Brudvig, G. and Gopalan, V. (2001) "Use of EPR spectroscopy to study macromolecular function." Science Progress 84: 45-68.
Wu, C-W., Eder, P.S., Gopalan, V. and Behrman, E. J. (2001). "Kinetics of coupling reactions that generate monothiophosphate disulfides Implications for modification of RNAs." Bioconjugate Chemistry 12: 842-844.