Signal Recognition Particle RNA Contributes to Oxidative Stress Response in Deinococcus radiodurans by Modulating Catalase Localization

Runhua Han,Elena K Gaidamakova,Rok Tkavc,Jessie Jiang,Lydia M Contreras,Michael J Daly,Jaden Fang

doi:10.3389/fmicb.2020.613571

Abstract

The proper functioning of many proteins requires their transport to the correct cellular compartment or their secretion. Signal recognition particle (SRP) is a major protein transport pathway responsible for the co-translational movement of integral membrane proteins as well as periplasmic proteins. Deinococcus radiodurans is a ubiquitous bacterium that expresses a complex phenotype of extreme oxidative stress resistance, which depends on proteins involved in DNA repair, metabolism, gene regulation, and antioxidant defense. These proteins are located extracellularly or subcellularly, but the molecular mechanism of protein localization in D. radiodurans to manage oxidative stress response remains unexplored. In this study, we characterized the SRP complex in D. radiodurans R1 and showed that the knockdown (KD) of the SRP RNA (Qpr6) reduced bacterial survival under hydrogen peroxide and growth under chronic ionizing radiation. Through LC-mass spectrometry (MS/MS) analysis, we detected 162 proteins in the periplasm of wild-type D. radiodurans, of which the transport of 65 of these proteins to the periplasm was significantly reduced in the Qpr6 KD strain. Through Western blotting, we further demonstrated the localization of the catalases in D. radiodurans, DR_1998 (KatE1) and DR_A0259 (KatE2), in both the cytoplasm and periplasm, respectively, and showed that the accumulation of KatE1 and KatE2 in the periplasm was reduced in the SRP-defective strains. Collectively, this study establishes the importance of the SRP pathway in the survival and the transport of antioxidant proteins in D. radiodurans under oxidative stress.

Highlights

Spatial and temporal coordination between biochemical processes allows bacteria to rapidly adapt to the constantly changing environment
These results indicate that Qpr6 might act as a part of the Signal recognition particle (SRP) complex in D. radiodurans
Considering catalase as the most well-studied protein that protects D. radiodurans from oxidative stresses, we further investigated whether the periplasmic localization of KatE1 and KatE2 could be affected by D. radiodurans SRP (DrSRP)

Summary

Introduction

Spatial and temporal coordination between biochemical processes allows bacteria to rapidly adapt to the constantly changing environment. Proper localization of proteins to their correct cellular destinations is a crucial part of this adaptation, enabling bacteria to sense and respond to the changes in different subcellular compartments (Holland, 2004). While most bacterial proteins are initially synthesized in the cytoplasm, more than one-third of them execute their function outside of the cytosol and have to be transported into the extracytoplasmic compartments (e.g., the periplasm; Weiner and Li, 2008). The SRP pathway mainly targets ribosome-bound nascent integral membrane proteins or periplasmic proteins in a co-translational fashion (Schibich et al, 2016). These two pathways converge at the SecYEG translocon, a protein-conducting pore in the membrane (Supplementary Figure S1A; Kuhn et al, 2011)

Methods

Results

Conclusion