Model for processive nucleotide and repeat additions by the telomerase

TL;DR

This paper presents a detailed model of telomerase processivity, explaining how nucleotide and repeat additions occur and predicting factors influencing processivity based on thermodynamic energy differences.

Contribution

The model integrates structural and energetic factors to quantitatively explain telomerase processivity and offers testable predictions about its regulation.

Findings

Processivity depends on free energy differences between hybrid disruption and pseudoknot unfolding.

The model aligns well with existing experimental data.

Predicted that manipulating energy barriers affects processivity.

Abstract

A model is presented to describe the nucleotide and repeat addition processivity by the telomerase. In the model, the processive nucleotide addition is implemented on the basis of two requirements: One is that stem IV loop stimulates the chemical reaction of nucleotide incorporation, and the other one is the existence of an ssRNA-binding site adjacent to the polymerase site that has a high affinity for the unpaired base of the template. The unpairing of DNA:RNA hybrid after the incorporation of the nucleotide paired with the last base on the template, which is the prerequisite for repeat addition processivity, is caused by a force acting on the primer. The force is resulted from the unfolding of stem III pseudoknot that is induced by the swinging of stem IV loop towards the nucleotide-bound polymerase site. Based on the model, the dynamics of processive nucleotide and repeat additions by Tetrahymena telomerase are quantitatively studied, which give good explanations to the previous experimental results. Moreover, some predictions are presented. In particular, it is predicted that the repeat addition processivity is mainly determined by the difference between the free energy required to disrupt the DNA:RNA hybrid and that required to unfold the stem III pseudoknot, with the large difference corresponding to a low repeat addition processivity while the small one corresponding to a high repeat addition processivity.