Ramesh Gupta

Emeritus Professor

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

Laboratory web site

Our current research interests are in the areas of post-transcriptional RNA modification in Archaea and Eukaryotes, and apoptosis and cell cycle progression in human cells. Archaea is one of the three domains of life; the other two being Bacteria and Eukarya. Archaea often have eukaryote-like processes, but at a basic level. Therefore, they can serve as much simpler model systems to gain insights into complex eukaryotic events. Some archaeal proteins involved in RNA processing have acquired additional roles in the biology of eukaryotes.

RNA modification

The tRNAs and rRNAs of all organisms contain many different types of nucleotide modifications. In eukaryotes, most pseudouridines (Ψ) and 2'-O-methylated residues of rRNA are produced by snoRNPs (small nucleolar ribonucleoproteins). The RNA components (box H/ACA and box C/D RNAs) of the snoRNPs function as guides to select the sites of target RNA modification and protein components catalyze the modification. Archaea also contain similar guide RNPs. It is easier to study structure-function relationships of the components of these RNPs in archaeal systems than in eukaryotic systems. We have developed several in vitro and in vivo archaeal systems to study these relationships. We have used these systems to characterize structural requirements of several guide RNA and protein components of the RNPs.

Most tRNAs of Bacteria and eukaryotes have ribothymidine (T) and Ψ at positions 54 and 55, respectively, in their common (TΨC) arm. In Archaea, Ψ is the most common nucleotide at both these positions. We have shown that the Pus10 protein produces both these Ψs in Archaea. This protein is distinct from the TruB/Pus4 family of Ψ synthases that produce Ψ55 in Bacteria and eukaryotes.

Mammalian cells also contain the Pus10 protein. So far it has not been shown to have any Ψ synthase activity. Our current work suggests that human Pus10 does have tRNA pseudouridine synthase activity, but it is restricted to only some specific tRNAs. We are now determining how only certain human tRNAs are selected for Pus10-mediated pseudouridylation.

Apoptosis and cell cycle progression

The human PUS10 gene has been suggested to be involved in TRAIL-induced apoptosis. Apoptosis or programmed cell death is a genetically determined mode of cell death. It is important for natural cell turnover during development and aging, and in the elimination of virus-infected and damaged cells. It is of clinical relevance for cancer treatment by irradiation or drugs. There are two major pathways of apoptosis: extrinsic (death receptor) and intrinsic (mitochondrial).

Recombinant TRAIL can induce apoptosis in several types of cancer cells, but leaves normal cells unaffected. Therefore, it is being developed as a drug for cancer treatment. We analyzed the role of PUS10 in TRAIL-induced apoptosis. PUS10 is mainly present in the nucleus. Early during apoptosis, PUS10 translocates from the nucleus to the mitochondria via CRM1-mediated export with the concurrent release of cytochrome c and SMAC from the mitochondria. Caspase-3 is required for PUS10 translocation, which reciprocally amplifies the activity of caspase-3 through the intrinsic/mitochondrial pathway.

We are also analyzing the role of PUS10 in cell cycle progression. We observed that cell doubling time and levels of several proteins involved in cell cycle progression differs in PUS10 knockdown cells from the parent cells.


Selected Publications

Deogharia, M., S. Mukhopadhyay, A. Joardar and R. Gupta. 2019. The human ortholog of archaeal Pus10 produces pseudouridine 54 in select tRNAs where its recognition sequence contains a modified residue. RNA 25:336-351.

Jana, S., A. C. Hsieh and R. Gupta. 2017. Reciprocal amplification of caspase-3 activity by nuclear export of a putative human RNA modifying protein, PUS10 during TRAIL-induced apoptosis. Cell Death Dis. 8: e3093; doi:10.1038/cddis.2017.476.

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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