Ramesh Gupta

Professor and Chair

Ramesh Gupta came to SIUC in 1984 after completing his Ph.D. degree and postdoctoral training with Professor Carl R. Woese at the University of Illinois at Urbana-Champaign. He was appointed Chair in 2007.

phone: (618) 453-6466
email: rgupta@siumed.edu

Molecular Biology of Archaea (laboratory web site)

Our research interests are mainly in the area of gene regulation in archaea (archaebacteria). Archaea are one of the three domains of life; the other two being Bacteria (eubacteria) and Eukarya (eukaryotes). Most of the archaea grow under extreme environments. These include methanogens (producing methane), extreme halophiles (growing in two molar to nearly saturated salt concentrations), thermophiles and hyperthermophiles (growing at 65 to 105 degrees C), acidophiles, alkaliphiles, etc. Archaea, like Bacteria, are prokaryotic in organization, but show similarities to several components of the eukaryotic replication, transcription and translation systems.

Emphasis of our research is on the study of transcription and post-transcriptional processing of transfer RNAs (tRNAs) in the halophilic and thermophilic archaea. I have sequenced nearly a complete set of tRNAs from a halophilic archaeon -- Haloferax volcanii (Halobacterium volcanii). These tRNAs are similar to bacterial tRNAs in some respects, to eukaryotic ones in others, and in yet other ways are quite distinct. Our studies of the transcription of tRNA genes of H. volcanii indicate that transcriptional promoters in halophilic archaea, like other archaea, are somewhat similar to the eukaryotic promoters, especially to their RNA polymerase II promoters. We are also working on the processing of the precursors of tRNAs, which includes splicing of introns, modification of nucleosides, removal and addition of terminal residues, etc. Splicing of introns in archaea is protein-enzyme based, involving at least an endonuclease and a ligase. This is also the case for the splicing of tRNA-introns in the eukaryotes. There are two different mechanisms of the ligation of tRNA exons in the eukaryotes; an animal type and a yeast type. We have determined that the mechanism of ligation of exons in the archaea shows some similarities to the animal type mechanism and is different from that present in the yeast cells.

Selected Publications

Majumder, M., M. S. Bosmeny and R. Gupta. 2016. Structure-function relationships of archaeal Cbf5 during in vivo RNA-guided pseudouridylation. RNA 22:1604-1619.

Joardar, A., S. Jana, E. Fitzek, P. Gurha, M. Majumder, K. Chatterjee, M. Geisler and R. Gupta. 2013. Role of forefinger and thumb loops in production of ψ 54 and ψ 55 in tRNAs by archaeal Pus10. RNA 19:1279-1294.

Chatterjee, K., I. K. Blaby, P. C. Thiaville, M. Majumder, H. Grosjean, Y. A. Yuan, R. Gupta and V. de Crécy-Lagard. 2012. The archaeal COG1901/DUF358 SPOUT-methyltranserase members, together with pdeudouridine synthase Pus10, catalyze the formation of 1-methylpseudouridine at position 54 of tRNA. RNA 18:421-433.

Joardar, A., S. R. Malliahgari, G. Skariah and R. Gupta. 2011. 2'-O-methylation of the wobble residue of elongator pre-tRNAMet in Haloferax volcanii is guided by a box C/D RNA containing unique features. RNA Biol. 8:782-791.

Blaby, I. K., M. Majumdar, K. Chatterjee, S. Jana, H. Grosjean, V. de Crécy-Lagard and R. Gupta. 2011. Pseudouridine formation in archaeal RNAs: the case of Haloferax volcanii. RNA 17: 1367-1380.

Gurha, P., and R. Gupta. 2008. Archaeal Pus10 proteins can produce both pseudouridine 54 and 55 in tRNA. RNA 14:2521-2527.

Joardar, A., P. Gurha, G. Skariah, and R. Gupta. 2008. Box C/D RNA-guided 2'-O methylations and the intron of tRNATrp are not essential for the viability of Haloferax volcanii. J. Bacteriol. 190:7308-7313.

Singh, S. K., P. Gurha, and R. Gupta. 2008. Dynamic guide-target interactions contribute to sequential 2'-O-methylation by a unique archaeal dual guide box C/D sRNP. RNA 14:1411-1423.

Grosjean, H., R. Gupta, and E. S. Maxwell. 2008. Modified nucleosides in archaeal RNAs. In: Archaea: New models for prokaryotic biology. P. Blum, Ed., Caister Academic Press, Norfolk, pp. 171-196.

Gurha, P., A. Joardar, P. Chaurasia, and R. Gupta. 2007. Differential roles of archaeal box H/ACA proteins in guide RNA-dependent and independent pseudouridine formation. RNA Biol. 4:101-109.

Singh, S. K., P. Gurha, E. J. Tran, E. S. Maxwell, and R. Gupta. 2004. Sequential 2'-O-methylation of Archaeal pre-tRNATrp nucleotides is guided by the intron-encoded but trans-acting box C/D ribonucleoprotein of pre-tRNA. J. Biol. Chem. 279:47661-47671.

Salgia, S. R., S. K. Singh, P. Gurha, and R. Gupta. 2003. Two reactions of Haloferax volcanii RNA splicing enzymes: Joining of exons and circularization of introns. RNA 9:319-330.

Zofallova, L., Y. Guo, and R. Gupta. 2000. Junction phosphate is derived from the precursor in the tRNA spliced by the archaeon Haloferax volcanii cell extract. RNA 6:1019-1030.

Gomes, I., and R. Gupta. 1997. RNA splicing ligase activity in the archaeon Haloferax volcanii. Biochem. Biophys. Res. Commun. 237:588-594.

McAfee, J. G., S. P. Edmondson, P. K. Datta, J. W. Shriver, and R. Gupta. 1995. Gene cloning, expression, and characterization of the Sac7 proteins from the hyperthermophile Sulfolobus acidocaldarius. Biochemistry 34:10063-10077.

Gupta, R. 1995. Preparation of transfer RNA, aminoacyl-tRNA synthetases and tRNAs specific for an amino acid from extreme halophiles, p. 119-131. In F. T. Robb, A. R. Place, K. R. Sowers, H. J. Schreier, S. DasSarma, and E. M. Fleischmann, (eds.), Archaea: a laboratory manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.

Gregson, J. M., P. F. Crain, C. G. Edmonds, R. Gupta, T. Hashizume, D. W. Phillipson, and J. A. McCloskey. 1993. Structure of the archael transfer RNA nucleoside G*-15 (2-amino-4,7-dihydro-4-oxo-7-b-D-ribofuranosyl-1H-pyrrolo[2,3-d]pyrimidine-5-carboximidamide (archaeosine)). J. Biol. Chem. 268:10076-10086.

Edmonds, C. G., P. F. Crain, R. Gupta, T. Hashizume, C. H. Hocart, J. A. Kowalak, S. C. Pomerantz, K. O. Stetter, and J. A. McCloskey. 1991. Posttranscriptional modification of tRNA in thermophilic archaea (archaebacteria). J. Bacteriol. 173:3138-3148.

Datta, P. K., L. K. Hawkins, and R. Gupta. 1989. Presence of an intron in elongator methionine - tRNA of Halobacterium volcanii. Can. J. Microbiol. 35:189-194.

Gupta, R. 1986. Transfer RNAs of Halobacterium volcanii: Sequences of five leucine and three serine tRNAs. System. Appl. Microbiol. 7:102-105.

Gupta, R. 1984. Halobacterium volcanii tRNAs: Identification of 41 tRNAs covering all amino acids, and the sequences of 33 class I tRNAs. J. Biol. Chem. 259:9461-9471.

Gupta, R., J. M. Lanter, and C. R. Woese. 1983. Sequence of the 16S ribosomal RNA from Halobacterium volcanii, an archaebacterium. Science 221:656-659.

Gupta, R., and C. R. Woese. 1980. Unusual modification patterns in the transfer ribonucleic acids of archaebacteria. Curr. Microbiol. 4:245-249.

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