Single Subunit RNA Polymerases: An Insight into their Active Sites and Catalytic Mechanism

Aim: To analyze various single subunit DNA dependent RNA polymerases and identify conserved motifs, active site regions among them and propose a plausible mechanism of action for these polymerases using the T7 RNA polymerase as a model system.

Study Design: Bioinformatics, Biochemical, Site-directed mutagenesis and X-ray crystallographic data were analyzed.

Place and Duration of Study: Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai – 625 021, India, from 2010 to 2013.

Methodology: The advanced version of Clustal Omega was used for protein sequence analysis of various SSU DNA dependent RNA polymerases from viruses, mitochondria and chloroplasts. Along with the conserved motifs identified by the bioinformatics analysis and with the data obtained by X-ray crystallographic, biochemical and site-directed mutagenesis were also used to confirm the possible amino acids involved in the active sites and catalysis of these RNA polymerases.

Results: Multiple sequence analyses of various single subunit (SSU) DNA dependent RNA polymerases from different sources showed only a few highly conserved motifs among them, except chloroplast RNA polymerases where a large number of highly conserved motifs were found. Possible catalytic regions in all these polymerases consist of a highly conserved amino acid K and a ‘gate keeper’ YG pair. In addition to, these polymerases also use an invariant R at the -4 position from the YG pair and an invariant S/T, adjacent to the YG pair. Furthermore, two highly conserved Ds are implicated in the metal binding site and thus might participate in the catalytic process. The YG pair appears to be specific for DNA templates as it is not reported in RNA dependent RNA polymerases.

Conclusion: The highly conserved amino acid K, the ‘gate keeper’ YG pair and an invariant R which are reported in all DNA polymerases, are also found in these DNA dependent RNA polymerases. Therefore, these RNA polymerases might be using the same catalytic mechanism like DNA polymerases. The catalytic amino acid K could act as the proton abstractor and generate the necessary nucleophile at the 3’-OH and the YG pair, R and the S/T might involve in the template binding and selection of nucleoside triphosphates (NTPs) for polymerization reactions. The two highly conserved Ds could act as the ‘ NTP charge shielder’ and orient the alpha phosphate of incoming NTPs for reaction at the 3’-OH growing end.