The major interest of our lab is to study how the protein synthesis machinery maintains translational accuracy. One of the aspects of this involves studying the effect of small ribosomal subunit proteins, rpS4, rpS5 and rpS12 in E. coli, on translational accuracy. Mutations in rpS12 confer streptomycin resistance or dependence and show hyperaccurate phenotype. Mutations in rpS4 and rpS5 reverse the streptomycin dependence phenotype, but these mutations make translation more error prone, thus called ribosomal ambiguity mutations (ram). The rpS12 restrictive mutations in Salmonella typhimurium were found to result in loss of virulence while that of rpS4 restored virulence in mice. The main aim of my project is to study the interactions at the interface between rpS4 and rpS5 proteins in E.coli (identical to S. typhimurium rpS4 and rpS5) which might eventually give us clues about their role in maintenance of translational accuracy.

 Another major research area in our lab is studying the accuracy of reading frame maintenance by the ribosome with a focus on +1 programmed translational frameshifting. It is a process in which specific heptameric sequences on mRNA evolved to increase translational errors locally, stimulating the ribosome to change the reading frame in either +1 or -1 direction. Studying how these programmed sites could bypass the proof reading translational machinery would help us better understand the mechanism of accuracy.

Our lab has been studying the mechanism of programmed +1 frameshifting in the Ty1 and Ty3 retrotransposons of yeast from many years. Programmed frameshifting is utilized by many retroviruses and retrotransposons for the expression of two different products (retroviral gag and pol proteins) from the same transcript. Many eukaryotic viruses like the HIV-1, SARS corona virus and Rous sarcoma virus utilize programmed -1 frameshifting for expression of fusion proteins necessary for virus replication. Recently we became interested in studying the frameshifting mechanism in the ciliate protozoan Euplotes. The frequency of frameshifting in Euplotes is found to be high with approximately 8.5% of less than 100 sequenced genes likely requiring frameshifting for their expression. Another unusual feature in Euplotes is that the translation termination codon UGA is reassigned to cysteine. The frameshift sequence motif in Euplotes is AAA-UAA/G, involving a stop codon at the A site. We hypothesized that changes in the release factor protein that facilitated stop codon reassignment might have resulted in less efficient termination at other stop codons, enhancing frameshifting at this motif. My main aim is to study the mechanism of frameshifting in Euplotes and also to test if there is any correlation between stop codon reassignment and frequent frameshifting in Euplotes.