Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655

Seo, Sang Woo; Kim, Donghyuk; Szubin, Richard; Palsson, Bernhard Ø.

doi:10.1016/j.celrep.2015.07.043

Cited by 148 publications

(133 citation statements)

References 72 publications

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“…E. coli possess redox-sensing transcriptional regulators, such as OxyR, SoxR, and SoxS, that regulate, for example, the expression of the ahpC , ahpF , katG , and sodA genes, as well as genes involved in DNA repair and methionine synthesis [84]. In this, OxyR acts through the formation of an intermolecular Cys-X-X-Cys cysteine bridge to sense oxidation.…”

Section: Damage Repairmentioning

confidence: 99%

Salmonella and Reactive Oxygen Species: A Love-Hate Relationship

Rhen¹

2019

J Innate Immun

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Salmonella enterica represents an enterobacterial species including numerous serovars that cause infections at, or initiated at, the intestinal epithelium. Many serovars also act as facultative intracellular pathogens with a tropism for phagocytic cells. These bacteria not only survive in phagocytes but also undergo de facto replication therein. Phagocytes, through the activities of phagocyte NADPH-dependent oxidase and inducible nitric oxide synthase, are very proficient in converting molecular oxygen to reactive oxygen (ROS) and nitrogen species (RNS). These compounds represent highly efficient effectors of the innate immune defense. Salmonella is by no means resistant to these effectors, which may stand in contrast to the host niches chosen. To cope with this paradox, these bacteria rely on an array of detoxification and repair systems. Combination these systems allows for a high enough tolerance to ROS and RNS to enable establishment of infection. In addition, salmonella possesses protein factors that have the potential to dampen the infection-associated inflammation, which evidently results in a reduced exposure to ROS and RNS. This review attempts to summarize the activities and strategies by which salmonella tries to cope with ROS and RNS and how the bacterium can make use of these innate defense factors.

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Section: Damage Repairmentioning

confidence: 99%

Salmonella and Reactive Oxygen Species: A Love-Hate Relationship

Rhen¹

2019

J Innate Immun

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“…Scavenging the H 2 O 2 using the antioxidants and maintaining metabolic activities to keep growing is beneficial for bacteria. Accordingly, expression of most of the OxyR regulon is governed by the housekeeping factor RpoD ( 70 ) (20). However, when H 2 O 2 exceeds the manageable ranges, maintaining expressions of the antioxidant genes would be worthless because growth and proliferation of bacterial cells under this condition could be reckless.…”

Section: Discussionmentioning

confidence: 99%

“…Bacteria can turn off the antioxidant genes using OxyR, as a three-state redox switch, under conditions in which expression of the antioxidants is useless. It is obviously advantageous that bacteria utilize more cellular resources to express stress tolerance genes encoding many additional protective systems (20,21).…”

Section: Discussionmentioning

confidence: 99%

OxyR2 Functions as a Three-state Redox Switch to Tightly Regulate Production of Prx2, a Peroxiredoxin of Vibrio vulnificus

Bang

Lee

Kim

et al. 2016

Journal of Biological Chemistry

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The bacterial transcriptional regulator OxyR is known to function as a two-state redox switch. OxyR senses cellular levels of H 2 O 2 via a "sensing cysteine" that switches from the reduced to a disulfide state upon H 2 O 2 exposure, inducing the expression of antioxidant genes. The reduced and disulfide states of OxyR, respectively, bind to extended and compact regions of DNA, where the reduced state blocks and the oxidized state allows transcription and further induces target gene expression by interacting with RNA polymerase. Vibrio vulnificus OxyR2 senses H 2 O 2 with high sensitivity and induces the gene encoding the antioxidant Prx2. In this study, we used mass spectrometry to identify a third redox state of OxyR2, in which the sensing cysteine was overoxidized to S-sulfonated cysteine (Cys-SO 3 H) by high H 2 O 2 in vitro and in vivo, where the modification deterred the transcription of prx2. The DNA binding preferences of OxyR2 5CA -C206D, which mimics overoxidized OxyR2, suggested that overoxidized OxyR2 binds to the extended DNA site, masking the ؊35 region of the prx2 promoter. These combined results demonstrate that OxyR2 functions as a three-state redox switch to tightly regulate the expression of prx2, preventing futile production of Prx2 in cells exposed to high levels of H 2 O 2 sufficient to inactivate Prx2. We further provide evidence that another OxyR homolog, OxyR1, displays similar three-state behavior, inviting further exploration of this phenomenon as a potentially general regulatory mechanism.

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“…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).…”

mentioning

confidence: 98%

“…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)(14)(15)(16)(17)(18). Surprisingly, activated SoxR can directly induce several genes (lpxC, aroF, sodA, and mgtA) in E. coli by binding their promoters without soxS (16).…”

mentioning

confidence: 99%

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

Kim

Park

Imlay

et al. 2017

Journal of Biological Chemistry

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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...

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Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655

Cited by 148 publications

References 72 publications

<b><i>Salmonella</i></b> and Reactive Oxygen Species: A Love-Hate Relationship

<b><i>Salmonella</i></b> and Reactive Oxygen Species: A Love-Hate Relationship

OxyR2 Functions as a Three-state Redox Switch to Tightly Regulate Production of Prx2, a Peroxiredoxin of Vibrio vulnificus

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

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