Lineage-specific SoxR-mediated Regulation of an Endoribonuclease Protects Non-enteric Bacteria from Redox-active Compounds

Abstract

Edited by F. Peter GuengerichBacteria use redox-sensitive transcription factors to coordinate responses to redox stress. The [2Fe-2S] cluster-containing transcription factor SoxR is particularly tuned to protect cells against redox-active compounds (RACs). In enteric bacteria, SoxR is paired with a second transcription factor, SoxS, that activates downstream effectors. However, SoxS is absent in nonenteric bacteria, raising questions as to how SoxR functions. Here, we first show that SoxR of Acinetobacter oleivorans displayed similar activation profiles in response to RACs as did its homolog from Escherichia coli but controlled a different set of target genes, including sinE, which encodes an endoribonuclease. Expression, gel mobility shift, and mutational analyses indicated that sinE is a direct target of SoxR. Redox potentials and permeability of RACs determined optimal sinE induction. Bioinformatics suggested that only a few ␥-and ␤-proteobacteria might have SoxR-regulated sinE. Purified SinE, in the presence of Mg 2؉ ions, degrades rRNAs, thus inhibiting protein synthesis. Similarly, pretreatment of cells with RACs demonstrated a role for SinE in promoting persistence in the presence of antibiotics that inhibit protein synthesis. Our data improve our understanding of the physiology of soil microorganisms by suggesting that both non-enteric SoxR and its target SinE play protective roles in the presence of RACs and antibiotics.Oxidative stress is an unavoidable consequence of aerobic and anaerobic metabolism when cells are exposed to O 2 . Bacteria have evolved to harbor defense mechanisms against various reactive oxygen species (ROS).4 Bacteria protect themselves by activating ROS-sensing transcription factors, including OxyR and PerR, that detect hydrogen peroxide (H 2 O 2 ) using cysteine residues and iron, respectively, and SoxR, which responds to superoxide or redox-active compounds (RACs) using a [2Fe-2S] cluster (1-3). Bacteria can produce many natural RACs, such as pyocyanin (PYO), actinorhodin, and plumbagin (PL), that act as antibiotics, toxic compounds, and quorum signals (4). RACs can generate toxic doses of ROS inside cells by mediating electron transfer from redox enzymes to O 2 . When Escherichia coli is exposed to RACs, SoxR is activated by the oxidation of its [2Fe-2S] cluster, and it subsequently induces the transcription of soxS (5-8). SoxS then induces the transcription of numerous genes involved in the repair of oxidatively damaged enzymes and DNA and the elimination of ROS (9 -12). However, the E. coli-SoxRS paradigm does not apply to nonenteric bacteria because of the absence of SoxS and no induction of many known E. coli SoxRS regulon (13-18). Surprisingly, activated SoxR can directly induce several genes (lpxC, aroF, sodA, and mgtA) in E. coli by binding their promoters without soxS (16). SoxR can be activated directly by RACs rather than by superoxide, as evidenced by the fact that RACs can oxidize the [2Fe-2S] 1ϩ cluster of SoxR even under anaerobic conditions (1, 2, 12). Activated S...

Alternative fate of glyoxylate during acetate and hexadecane metabolism in Acinetobacter oleivorans DR1

“…Previously, our lab has shown that GS-participating genes in a soil-borne bacterium, A . oleivorans DR1, are upregulated upon exposure to ampicillin, paraquat (PQ), phenazine methosulfate (PMS), hexadecane (Hex), and triacontane (TRI)-treated condition 14–18 . Examination of an aceA -deficient strain in triaconatane (C30 alkane)-containing minimal salt basal (MSB) media showed retarded growth with a long lag phase in contrast to that observed for the parent strain, and the susceptibility of the ICL-lacking mutant to H 2 O 2 was considerably increased 17 .…”

Genomic and Physiological Traits of the Marine Bacterium Alcaligenes aquatilis QD168 Isolated From Quintero Bay, Central Chile, Reveal a Robust Adaptive Response to Environmental Stressors

“…In non-enteric bacteria, a different response mechanism occurs, in which SoxS is not present. SoxR directly activates, not only the expression of genes involved in antioxidant defense, but also up-regulates mono- and dioxygenases-encoding genes (Dietrich and Kiley, 2011; Kim et al, 2017). Accordingly, SoxR2 of A. aquatilis QD168 clustered with proteins from non-enteric bacteria and the soxS gene is not present in its genome.…”

Catalase Expression in Azospirillum brasilense Sp7 Is Regulated by a Network Consisting of OxyR and Two RpoH Paralogs and Including an RpoE1→RpoH5 Regulatory Cascade

“…For the leakproof and tightly regulated expression of each regulon, promoters of the target genes of each regulon need to differentiate distinctly. At the same time, the amino acid residues of regions 2.4, 3.0, and 4.2 of the RpoH, which are involved in the recognition of the Ϫ10, extended Ϫ10, and Ϫ35 promoter elements of the heat shock genes (14), also need to change accordingly so as to recognize their target promoters and to insulate each regulon from the other (57,58).…”

“…The levels of ROS in the cell are monitored by two types of transcription regulators. In response to the elevated levels of ROS, DNA binding transcription regulators such as OxyR, SoxR, or OhrR activate oxidative stress-responsive genes by binding to their promoter upstream regions (14). OxyR is a global transcriptional regulator of the LysR family which helps in coping with H 2 O 2 -induced oxidative damage by inducing expression of several genes (15,16).…”