RNA polymerase is a molecular motor that converts its transcribing genetic information to free energy for its movement

Abstract

AbstractRNA polymerase (RNAP) is an enzyme that catalyzes RNA synthesis from a DNA template via translocation on the DNA. Several studies on RNAP translocation have shown an unexplainable discrepancy in the experimental value of the average free energy change (ΔG) required for RNAP translocation. To address this inconsistency, we propose a model of the transcription system based on information thermodynamics integrating information theory and thermodynamics. The state function of RNAP was defined from its position on the template DNA, its migration direction, and the deoxyribonucleotide (dNTP) that it transcribes. Based on the state function,ΔGwas defined consisting ofΔGthrequired for determining its positionmand other thermodynamic factors, andΔGdrequired for determining movement orientation orΔGNvalue from the dNTP sequence information of the DNA transcribed by RNAP.ΔGdwas calculated using the fluctuation theorem applying movement orientation andΔGNwas estimated based on information thermodynamics of mutual information given by dNTP appearance ratio. It was found that the involvement of eitherΔG(d)orΔG(N)in free energy caused a discrepancy inΔGvalues. In conclusion, information thermodynamics can be a framework for information processing in the cell, and RNAP serves as a good model of molecular machine moves through the conversion of information.Significance StatementRNA polymerase directly converts deoxyribonucleotide sequence information from template DNA to free energy for its movement along the DNA strand.