STRIKING SIMILARITIES IN DIVERSE TELOMERASE PROTEINS REVEALED BY COMBINING STRUCTURE PREDICTION AND MACHINE LEARNING APPROACHES

Jae-Hyung Lee,Cornelia Caragea,Colin Gleeson,Drena Dobbs,Michael Hamilton,Xue Li,Peter Zaback,Michael Terribilini,Feihong Wu,Vasant Honavar,Jeffry D Sander

doi:10.1142/9789812776136_0048

Abstract

Telomerase is a ribonucleoprotein enzyme that adds telomeric DNA repeat sequences to the ends of linear chromosomes. The enzyme plays pivotal roles in cellular senescence and aging, and because it provides a telomere maintenance mechanism for approximately 90% of human cancers, it is a promising target for cancer therapy. Despite its importance, a high-resolution structure of the telomerase enzyme has been elusive, although a crystal structure of an N-terminal domain (TEN) of the telomerase reverse transcriptase subunit (TERT) from Tetrahymena has been reported. In this study, we used a comparative strategy, in which sequence-based machine learning approaches were integrated with computational structural modeling, to explore the potential conservation of structural and functional features of TERT in phylogenetically diverse species. We generated structural models of the N-terminal domains from human and yeast TERT using a combination of threading and homology modeling with the Tetrahymena TEN structure as a template. Comparative analysis of predicted and experimentally verified DNA and RNA binding residues, in the context of these structures, revealed significant similarities in nucleic acid binding surfaces of Tetrahymena and human TEN domains. In addition, the combined evidence from machine learning and structural modeling identified several specific amino acids that are likely to play a role in binding DNA or RNA, but for which no experimental evidence is currently available.

Highlights

In most eukaryotes, a remarkable ribonucleoprotein enzyme, telomerase, is responsible for the synthesis and maintenance of telomeres, the ends of linear chromosomes [1, 2, 3]
An alignment of the N-terminal sequences of telomerase reverse transcriptase subunit (TERT) from organisms ranging from human to T. thermophila to S. cerevisiae, revealed several highly conserved residues distributed throughout the N-terminal domain, suggesting that TEN domains from diverse organisms may share similar architectures [12]
The chosen templates were portions of the following Protein Data Bank (PDB) structures: 1imhC, Tonicity-responsive enhancer binding protein (TONEBP)-DNA complex; 1jfiB, Negative Cofactor 2-TATA box binding protein-DNA complex (NC2-TBP-DNA); 2dyrM, bovine heart cytochrome C oxidase; 1b1uA, bifunctional inhibitor of Trypsin and Alpha-amylase from Ragi seeds; 2b2aA, N-terminal domain of tTERT

Summary

Introduction

A remarkable ribonucleoprotein enzyme, telomerase, is responsible for the synthesis and maintenance of telomeres, the ends of linear chromosomes [1, 2, 3]. An alignment of the N-terminal sequences of TERTs from organisms ranging from human to T. thermophila to S. cerevisiae, revealed several highly conserved residues distributed throughout the N-terminal domain, suggesting that TEN domains from diverse organisms may share similar architectures [12]. Based on this suggestion, we set out to test the hypothesis that the N-terminal domains of TERTs in diverse organisms share a similar overall three-dimensional fold, but may have phylogenetically conserved DNA and RNA binding surfaces. We used a strategy in which comparative protein structural modeling approaches were integrated with sequence-based machine learning approaches for predicting DNA or RNA binding residues

Datasets

Structural modeling of telomerase TEN domains in human and yeast

Experimental identification of RNA and DNA binding residues

Results

Structural modeling of N-terminal domain of TERT from human and yeast

Analysis of RNA and DNA binding surfaces in human and Tetrahymena TEN domains