Structural Analysis of Redox-sensing Transcriptional Repressor Rex from Thermotoga maritima

Young Woo Park,Jae Young Lee,Hyun Kyu Joo,Young Yoon Jang

doi:10.1038/s41598-018-31676-z

Abstract

The cellular redox state of organisms continues to fluctuate during the metabolism. All organisms have various sensors that help detect and adapt to changes in the redox state. Nicotinamide adenine dinucleotides (NAD+/NADH), which are involved in various cellular metabolic activities as cofactors, have been revealed as the key molecules sensing the intra-cellular redox state. The Rex family members are well conserved transcriptional repressors that regulate the expression of respiratory genes by sensing the redox state according to the intra-cellular NAD+/NADH balance. Herein, we reported crystal structures of apo and NAD+- and NADH-bound forms of Rex from Thermotoga maritima to analyse the structural basis of transcriptional regulation depending on either NAD+ or NADH binding. The different orientation of the reduced nicotinamide group to helix α9 caused the rearrangement of N-terminal DNA binding domain, thus resulting in closed form of Rex to dissociate from cognate DNA. The structural data of Rex from T. maritima also support the previous redox-sensing mechanism models of Rex homologues.

Highlights

Bacteria have adapted and responded to changing environmental oxygen levels for their survival by altering the transcriptional regulation of genes involved in respiratory pathways[1]
The initial structure of the apo TmRex was determined at 2.8 Å resolution using selenomethionine-based single-wavelength anomalous dispersion (SAD) data set collected at the selenium peak (0.9791 Å, Table S1)
The crystal structure of the NAD+-bound form was determined at 2.2 Å resolution, and the NAD+ ligand was clearly observed in the 2Fo-Fc maps (Fig. S2)

Summary

Introduction

Bacteria have adapted and responded to changing environmental oxygen levels for their survival by altering the transcriptional regulation of genes involved in respiratory pathways[1]. The intracellular NAD+/NADH ratio changes when the NADH level is elevated because of low environmental oxygen levels or the inhibition of the electron transport chain[4]. In other words, monitoring the continuous intracellular redox level using the NAD+/NADH ratio enables the sophisticated regulation of gene expressions involved in energy metabolism[5]. The Rex family members are well-conserved transcription factors to control the respiratory pathway, which senses changes in the redox state according to the intracellular NAD+/NADH balance[6,7,8]. To further understand the conformational changes of the Rex protein depending on the intracellular redox level, we determined crystal structures of apo and NAD+- and NADH-bound forms of the Rex proteins from T. maritima (TM0169). A structural comparison revealed that the transcriptional regulation of TmRex was controlled by NAD+/NADH cofactor inducing a conformational change of the dimeric structure

Methods

Results

Conclusion