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Bisubstrate Function of RNA Polymerases Triggered by Molecular Crowding Conditions

Takahashi, Shuntaro, Okura, Hiromichi, Sugimoto, Naoki
Biochemistry 2019 v.58 no.8 pp. 1081-1093
DNA, DNA-directed DNA polymerase, DNA-directed RNA polymerase, cellular microenvironment, dielectric properties, molecular weight, polyethylene glycol, polymerization, ribozymes, solutes
Since the origin of life on Earth, the role of carrying genetic information has been presumably transferred from RNA to DNA. At present, cellular environments are extremely dense, packed with cosolutes and macromolecules. Hence, the preference between RNA-dependent RNA and DNA polymerization may be affected by molecular crowding. In this study, we investigated both RNA-dependent RNA and DNA polymerizations by tC9Y polymerase ribozyme, T7 RNA polymerase (T7 RNAP), and Klenow fragment DNA polymerase (KF) under different molecular crowding conditions. Poly(ethylene glycol) (PEG) of various molecular weights was used as a crowding agent and found to promote both RNA and DNA ribozyme-catalyzed polymerizations. In contrast, PEG with an average molecular weight of 200 (PEG200) reduced the level of RNA polymerization by proteinaceous T7 RNAP but simultaneously promoted DNA polymerization, without affecting the activity of KF. Thus, proteinaceous RNA polymerase might potentially display bisubstrate specificity, which can be switched in response to changes in the dielectric constant and excluded volume in crowded environments. Our findings validate the bisubstrate activity of RNA polymerase from an evolutionary perspective for the development of non-natural materials.