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18 pages, 2703 KiB

Open AccessArticle

Influence of Redox Imbalances on the Transposition of Insertion Sequences in Deinococcus geothermalis

by Qianying Ye, Chanjae Lee, Eunjung Shin and Sung-Jae Lee

Antioxidants 2021, 10(10), 1623; https://doi.org/10.3390/antiox10101623 - 15 Oct 2021

Cited by 5 | Viewed by 2038

Abstract

The transposition of insertion sequence elements was evaluated among different Deinococcus geothermalis lineages, including the wild-type, a cystine importer-disrupted mutant, a complemented strain, and a cystine importer-overexpressed strain. Cellular growth reached early exponential growth at OD₆₀₀ 2.0 and late exponential growth at [...] Read more.

The transposition of insertion sequence elements was evaluated among different Deinococcus geothermalis lineages, including the wild-type, a cystine importer-disrupted mutant, a complemented strain, and a cystine importer-overexpressed strain. Cellular growth reached early exponential growth at OD₆₀₀ 2.0 and late exponential growth at OD₆₀₀ 4.0. Exposing the cells to hydrogen peroxide (80–100 mM) resulted in the transposition of insertion sequences (ISs) in genes associated with the carotenoid biosynthesis pathway. Particularly, ISDge7 (an IS5 family member) and ISDge5 (an IS701 family member) from the cystine importer-disrupted mutant were transposed into phytoene desaturase (dgeo_0524) via replicative transposition. Further, the cystine importer-overexpressed strain Δdgeo_1985R showed transposition of both ISDge2 and ISDge5 elements. In contrast, IS transposition was not detected in the complementary strain. Interestingly, a cystine importer-overexpressing strain exhibited streptomycin resistance, indicating that point mutation occurred in the rpsL (dgeo_1873) gene encoding ribosomal protein S12. qRT-PCR analyses were then conducted to evaluate the expression of oxidative stress response genes, IS elements, and low-molecular-weight thiol compounds such as mycothiol and bacillithiol. Nevertheless, the mechanisms that trigger IS transposition in redox imbalance conditions remain unclear. Here, we report that the active transposition of different IS elements was affected by intracellular redox imbalances caused by cystine importer deficiencies or overexpression. Full article

(This article belongs to the Special Issue Redox Biology in Microorganisms)

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20 pages, 8738 KiB

Open AccessArticle

Atomic Force Microscopy to Elicit Conformational Transitions of Ferredoxin-Dependent Flavin Thioredoxin Reductases

by Carlos Marcuello, Gifty Animwaa Frempong, Mónica Balsera, Milagros Medina and Anabel Lostao

Antioxidants 2021, 10(9), 1437; https://doi.org/10.3390/antiox10091437 - 9 Sep 2021

Cited by 24 | Viewed by 3279

Abstract

Flavin and redox-active disulfide domains of ferredoxin-dependent flavin thioredoxin reductase (FFTR) homodimers should pivot between flavin-oxidizing (FO) and flavin-reducing (FR) conformations during catalysis, but only FR conformations have been detected by X-ray diffraction and scattering techniques. Atomic force microscopy (AFM) is a single-molecule [...] Read more.

Flavin and redox-active disulfide domains of ferredoxin-dependent flavin thioredoxin reductase (FFTR) homodimers should pivot between flavin-oxidizing (FO) and flavin-reducing (FR) conformations during catalysis, but only FR conformations have been detected by X-ray diffraction and scattering techniques. Atomic force microscopy (AFM) is a single-molecule technique that allows the observation of individual biomolecules with sub-nm resolution in near-native conditions in real-time, providing sampling of molecular properties distributions and identification of existing subpopulations. Here, we show that AFM is suitable to evaluate FR and FO conformations. In agreement with imaging under oxidizing condition, only FR conformations are observed for Gloeobacter violaceus FFTR (GvFFTR) and isoform 2 of Clostridium acetobutylicum FFTR (CaFFTR2). Nonetheless, different relative dispositions of the redox-active disulfide and FAD-binding domains are detected for FR homodimers, indicating a dynamic disposition of disulfide domains regarding the central protein core in solution. This study also shows that AFM can detect morphological changes upon the interaction of FFTRs with their protein partners. In conclusion, this study paves way for using AFM to provide complementary insight into the FFTR catalytic cycle at pseudo-physiological conditions. However, future approaches for imaging of FO conformations will require technical developments with the capability of maintaining the FAD-reduced state within the protein during AFM scanning. Full article

(This article belongs to the Special Issue Redox Biology in Microorganisms)

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16 pages, 2855 KiB

Open AccessArticle

Atypical Bacilliredoxin AbxC Plays a Role in Responding to Oxidative Stress in Radiation-Resistant Bacterium Deinococcus radiodurans

by Soyoung Jeong, Jong-Hyun Jung, Min-Kyu Kim, Arjan de Groot, Laurence Blanchard, Sangryeol Ryu, Yong-Sun Bahn and Sangyong Lim

Antioxidants 2021, 10(7), 1148; https://doi.org/10.3390/antiox10071148 - 20 Jul 2021

Cited by 6 | Viewed by 3029

Abstract

Deinococcus radiodurans is a robust bacterium with extraordinary resistance to ionizing radiation and reactive oxygen species (ROS). D. radiodurans produces an antioxidant thiol compound called bacillithiol (BSH), but BSH-related enzymes have not been investigated. The D. radiodurans mutant lacking bshA (dr_ [...] Read more.

Deinococcus radiodurans is a robust bacterium with extraordinary resistance to ionizing radiation and reactive oxygen species (ROS). D. radiodurans produces an antioxidant thiol compound called bacillithiol (BSH), but BSH-related enzymes have not been investigated. The D. radiodurans mutant lacking bshA (dr_1555), the first gene of the BSH biosynthetic pathway, was devoid of BSH and sensitive to hydrogen peroxide (H₂O₂) compared to the wild-type D. radiodurans strain. Three bacilliredoxin (Brx) proteins, BrxA, B, and C, have been identified in BSH-producing bacteria, such as Bacillus. D. radiodurans possesses DR_1832, a putative homolog of BrxC. However, because DR_1832 contains a novel signature motif (TCHKT) and a C-terminal region similar to the colicin-like immunity domain, we named it AbxC (atypical BrxC). The deletion of abxC also sensitized cells to H₂O₂. AbxC exhibited peroxidase activity in vitro, which was linked to nicotinamide adenine dinucleotide phosphate (NADPH) oxidation via the BSH disulfide reductase DR_2623 (DrBdr). AbxC proteins were present mainly as dimers after exposure to H₂O₂ in vitro, and the oxidized dimers were resolved to monomers by the reaction coupled with BSH as an electron donor, in which DrBdr transported reducing equivalents from NADPH to AbxC through BSH recycling. We identified 25 D. radiodurans proteins that potentially interact with AbxC using AbxC-affinity chromatography. Most of them are associated with cellular metabolisms, such as glycolysis and amino acid biosynthesis, and stress response. Interestingly, AbxC could bind to the proposed peroxide-sensing transcription regulator, DrOxyR. These results suggest that AbxC may be involved in the H₂O₂ signaling mechanism mediated by DrOxyR. Full article

(This article belongs to the Special Issue Redox Biology in Microorganisms)

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22 pages, 3672 KiB

Open AccessArticle

‘Carbon-Monoxide-Releasing Molecule-2 (CORM-2)’ Is a Misnomer: Ruthenium Toxicity, Not CO Release, Accounts for Its Antimicrobial Effects

by Hannah M. Southam, Michael P. Williamson, Jonathan A. Chapman, Rhiannon L. Lyon, Clare R. Trevitt, Peter J. F. Henderson and Robert K. Poole

Antioxidants 2021, 10(6), 915; https://doi.org/10.3390/antiox10060915 - 5 Jun 2021

Cited by 42 | Viewed by 4870

Abstract

Carbon monoxide (CO)-releasing molecules (CORMs) are used to deliver CO, a biological ‘gasotransmitter’, in biological chemistry and biomedicine. CORMs kill bacteria in culture and in animal models, but are reportedly benign towards mammalian cells. CORM-2 (tricarbonyldichlororuthenium(II) dimer, Ru₂Cl₄(CO)₆ [...] Read more.

Carbon monoxide (CO)-releasing molecules (CORMs) are used to deliver CO, a biological ‘gasotransmitter’, in biological chemistry and biomedicine. CORMs kill bacteria in culture and in animal models, but are reportedly benign towards mammalian cells. CORM-2 (tricarbonyldichlororuthenium(II) dimer, Ru₂Cl₄(CO)₆), the first widely used and commercially available CORM, displays numerous pharmacological, biochemical and microbiological activities, generally attributed to CO release. Here, we investigate the basis of its potent antibacterial activity against Escherichia coli and demonstrate, using three globin CO sensors, that CORM-2 releases negligible CO (<0.1 mol CO per mol CORM-2). A strong negative correlation between viability and cellular ruthenium accumulation implies that ruthenium toxicity underlies biocidal activity. Exogenous amino acids and thiols (especially cysteine, glutathione and N-acetyl cysteine) protected bacteria against inhibition of growth by CORM-2. Bacteria treated with 30 μM CORM-2, with added cysteine and histidine, exhibited no significant loss of viability, but were killed in the absence of these amino acids. Their prevention of toxicity correlates with their CORM-2-binding affinities (Cys, K_d 3 μM; His, K_d 130 μM) as determined by ¹H-NMR. Glutathione is proposed to be an important intracellular target of CORM-2, with CORM-2 having a much higher affinity for reduced glutathione (GSH) than oxidised glutathione (GSSG) (GSH, K_d 2 μM; GSSG, K_d 25,000 μM). The toxicity of low, but potent, levels (15 μM) of CORM-2 was accompanied by cell lysis, as judged by the release of cytoplasmic ATP pools. The biological effects of CORM-2 and related CORMs, and the design of biological experiments, must be re-examined in the light of these data. Full article

(This article belongs to the Special Issue Redox Biology in Microorganisms)

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18 pages, 1562 KiB

Open AccessArticle

Methionine Sulfoxide Reductases Contribute to Anaerobic Fermentative Metabolism in Bacillus cereus

by Catherine Duport, Jean-Paul Madeira, Mahsa Farjad, Béatrice Alpha-Bazin and Jean Armengaud

Antioxidants 2021, 10(5), 819; https://doi.org/10.3390/antiox10050819 - 20 May 2021

Cited by 4 | Viewed by 2665

Abstract

Reversible oxidation of methionine to methionine sulfoxide (Met(O)) is a common posttranslational modification occurring on proteins in all organisms under oxic conditions. Protein-bound Met(O) is reduced by methionine sulfoxide reductases, which thus play a significant antioxidant role. The facultative anaerobe Bacillus cereus produces [...] Read more.

Reversible oxidation of methionine to methionine sulfoxide (Met(O)) is a common posttranslational modification occurring on proteins in all organisms under oxic conditions. Protein-bound Met(O) is reduced by methionine sulfoxide reductases, which thus play a significant antioxidant role. The facultative anaerobe Bacillus cereus produces two methionine sulfoxide reductases: MsrA and MsrAB. MsrAB has been shown to play a crucial physiological role under oxic conditions, but little is known about the role of MsrA. Here, we examined the antioxidant role of both MsrAB and MrsA under fermentative anoxic conditions, which are generally reported to elicit little endogenous oxidant stress. We created single- and double-mutant Δmsr strains. Compared to the wild-type and ΔmsrAB mutant, single- (ΔmsrA) and double- (ΔmsrAΔmsrAB) mutants accumulated higher levels of Met(O) proteins, and their cellular and extracellular Met(O) proteomes were altered. The growth capacity and motility of mutant strains was limited, and their energy metabolism was altered. MsrA therefore appears to play a major physiological role compared to MsrAB, placing methionine sulfoxides at the center of the B. cereus antioxidant system under anoxic fermentative conditions. Full article

(This article belongs to the Special Issue Redox Biology in Microorganisms)

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15 pages, 1596 KiB

Open AccessArticle

In Escherichia coli Ammonia Inhibits Cytochrome bo₃ But Activates Cytochrome bd-I

by Elena Forte, Sergey A. Siletsky and Vitaliy B. Borisov

Antioxidants 2021, 10(1), 13; https://doi.org/10.3390/antiox10010013 - 25 Dec 2020

Cited by 13 | Viewed by 3747

Abstract

Interaction of two redox enzymes of Escherichia coli, cytochrome bo₃ and cytochrome bd-I, with ammonium sulfate/ammonia at pH 7.0 and 8.3 was studied using high-resolution respirometry and absorption spectroscopy. At pH 7.0, the oxygen reductase activity of none of the [...] Read more.

Interaction of two redox enzymes of Escherichia coli, cytochrome bo₃ and cytochrome bd-I, with ammonium sulfate/ammonia at pH 7.0 and 8.3 was studied using high-resolution respirometry and absorption spectroscopy. At pH 7.0, the oxygen reductase activity of none of the enzymes is affected by the ligand. At pH 8.3, cytochrome bo₃ is inhibited by the ligand, with 40% maximum inhibition at 100 mM (NH₄)₂SO₄. In contrast, the activity of cytochrome bd-I at pH 8.3 increases with increasing the ligand concentration, the largest increase (140%) is observed at 100 mM (NH₄)₂SO₄. In both cases, the effector molecule is apparently not NH₄⁺ but NH₃. The ligand induces changes in absorption spectra of both oxidized cytochromes at pH 8.3. The magnitude of these changes increases as ammonia concentration is increased, yielding apparent dissociation constants K_dapp of 24.3 ± 2.7 mM (NH₄)₂SO₄ (4.9 ± 0.5 mM NH₃) for the Soret region in cytochrome bo₃, and 35.9 ± 7.1 and 24.6 ± 12.4 mM (NH₄)₂SO₄ (7.2 ± 1.4 and 4.9 ± 2.5 mM NH₃) for the Soret and visible regions, respectively, in cytochrome bd-I. Consistently, addition of (NH₄)₂SO₄ to cells of the E. coli mutant containing cytochrome bd-I as the only terminal oxidase at pH 8.3 accelerates the O₂ consumption rate, the highest one (140%) being at 27 mM (NH₄)₂SO₄. We discuss possible molecular mechanisms and physiological significance of modulation of the enzymatic activities by ammonia present at high concentration in the intestines, a niche occupied by E. coli. Full article

(This article belongs to the Special Issue Redox Biology in Microorganisms)

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16 pages, 5494 KiB

Open AccessArticle

Suppression of Methane Generation during Methanogenesis by Chemically Modified Humic Compounds

by Elena Efremenko, Olga Senko, Nikolay Stepanov, Nikita Mareev, Alexander Volikov and Irina Perminova

Antioxidants 2020, 9(11), 1140; https://doi.org/10.3390/antiox9111140 - 17 Nov 2020

Cited by 12 | Viewed by 2390

Abstract

The introduction of various concentrations of chemically modified humic compounds (HC) with different redox characteristics into the media with free and immobilized anaerobic consortia accumulating landfill gases was studied as approach to their functioning management. For this purpose, quinone (hydroquinone, naphthoquinone or methylhydroquinone) [...] Read more.

The introduction of various concentrations of chemically modified humic compounds (HC) with different redox characteristics into the media with free and immobilized anaerobic consortia accumulating landfill gases was studied as approach to their functioning management. For this purpose, quinone (hydroquinone, naphthoquinone or methylhydroquinone) derivatives of HC were synthesized, which made it possible to vary the redox and antioxidant properties of HC as terminal electron acceptors in methanogenic systems. The highest acceptor properties were obtained with potassium humate modified by naphthoquinone. To control possible negative effect of HC on the cells of natural methanogenic consortia, different bioluminescent analytical methods were used. The addition of HC derivatives, enriched with quinonones, to nutrient media at concentrations above 1 g/L decreased the energetic status of cells and the efficiency of the methanogenesis. For the first time, the significant decrease in accumulation of biogas was reached as effect of synthetic HC derivatives, whereas both notable change of biogas composition towards increase in the CO₂ content and decrease in CH₄ were revealed. Thus, modification with quinones makes it possible to obtain low-potential HC derivatives with strongly pronounced acceptor properties, promising for inhibition of biogas synthesis by methanogenic communities. Full article

(This article belongs to the Special Issue Redox Biology in Microorganisms)

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Review

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18 pages, 1042 KiB

Open AccessReview

Redox Regulation in Diazotrophic Bacteria in Interaction with Plants

by Karine Mandon, Fanny Nazaret, Davoud Farajzadeh, Geneviève Alloing and Pierre Frendo

Antioxidants 2021, 10(6), 880; https://doi.org/10.3390/antiox10060880 - 30 May 2021

Cited by 17 | Viewed by 5318

Abstract

Plants interact with a large number of microorganisms that greatly influence their growth and health. Among the beneficial microorganisms, rhizosphere bacteria known as Plant Growth Promoting Bacteria increase plant fitness by producing compounds such as phytohormones or by carrying out symbioses that enhance [...] Read more.

Plants interact with a large number of microorganisms that greatly influence their growth and health. Among the beneficial microorganisms, rhizosphere bacteria known as Plant Growth Promoting Bacteria increase plant fitness by producing compounds such as phytohormones or by carrying out symbioses that enhance nutrient acquisition. Nitrogen-fixing bacteria, either as endophytes or as endosymbionts, specifically improve the growth and development of plants by supplying them with nitrogen, a key macro-element. Survival and proliferation of these bacteria require their adaptation to the rhizosphere and host plant, which are particular ecological environments. This adaptation highly depends on bacteria response to the Reactive Oxygen Species (ROS), associated to abiotic stresses or produced by host plants, which determine the outcome of the plant-bacteria interaction. This paper reviews the different antioxidant defense mechanisms identified in diazotrophic bacteria, focusing on their involvement in coping with the changing conditions encountered during interaction with plant partners. Full article

(This article belongs to the Special Issue Redox Biology in Microorganisms)

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25 pages, 49523 KiB

Open AccessReview

Protein Engineering of Electron Transfer Components from Electroactive Geobacter Bacteria

by Tomás M. Fernandes, Leonor Morgado, David L. Turner and Carlos A. Salgueiro

Antioxidants 2021, 10(6), 844; https://doi.org/10.3390/antiox10060844 - 25 May 2021

Cited by 14 | Viewed by 4742

Abstract

Electrogenic microorganisms possess unique redox biological features, being capable of transferring electrons to the cell exterior and converting highly toxic compounds into nonhazardous forms. These microorganisms have led to the development of Microbial Electrochemical Technologies (METs), which include applications in the fields of [...] Read more.

Electrogenic microorganisms possess unique redox biological features, being capable of transferring electrons to the cell exterior and converting highly toxic compounds into nonhazardous forms. These microorganisms have led to the development of Microbial Electrochemical Technologies (METs), which include applications in the fields of bioremediation and bioenergy production. The optimization of these technologies involves efforts from several different disciplines, ranging from microbiology to materials science. Geobacter bacteria have served as a model for understanding the mechanisms underlying the phenomenon of extracellular electron transfer, which is highly dependent on a multitude of multiheme cytochromes (MCs). MCs are, therefore, logical targets for rational protein engineering to improve the extracellular electron transfer rates of these bacteria. However, the presence of several heme groups complicates the detailed redox characterization of MCs. In this Review, the main characteristics of electroactive Geobacter bacteria, their potential to develop microbial electrochemical technologies and the main features of MCs are initially highlighted. This is followed by a detailed description of the current methodologies that assist the characterization of the functional redox networks in MCs. Finally, it is discussed how this information can be explored to design optimal Geobacter-mutated strains with improved capabilities in METs. Full article

(This article belongs to the Special Issue Redox Biology in Microorganisms)

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17 pages, 1825 KiB

Open AccessFeature PaperReview

ROS Defense Systems and Terminal Oxidases in Bacteria

by Vitaliy B. Borisov, Sergey A. Siletsky, Martina R. Nastasi and Elena Forte

Antioxidants 2021, 10(6), 839; https://doi.org/10.3390/antiox10060839 - 24 May 2021

Cited by 86 | Viewed by 7196

Abstract

Reactive oxygen species (ROS) comprise the superoxide anion (O₂^•−), hydrogen peroxide (H₂O₂), hydroxyl radical (^•OH), and singlet oxygen (¹O₂). ROS can damage a variety of macromolecules, including DNA, RNA, proteins, [...] Read more.

Reactive oxygen species (ROS) comprise the superoxide anion (O₂^•−), hydrogen peroxide (H₂O₂), hydroxyl radical (^•OH), and singlet oxygen (¹O₂). ROS can damage a variety of macromolecules, including DNA, RNA, proteins, and lipids, and compromise cell viability. To prevent or reduce ROS-induced oxidative stress, bacteria utilize different ROS defense mechanisms, of which ROS scavenging enzymes, such as superoxide dismutases, catalases, and peroxidases, are the best characterized. Recently, evidence has been accumulating that some of the terminal oxidases in bacterial respiratory chains may also play a protective role against ROS. The present review covers this role of terminal oxidases in light of recent findings. Full article

(This article belongs to the Special Issue Redox Biology in Microorganisms)

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16 pages, 1778 KiB

Open AccessReview

Redox Active Antimicrobial Peptides in Controlling Growth of Microorganisms at Body Barriers

by Piotr Brzoza, Urszula Godlewska, Arkadiusz Borek, Agnieszka Morytko, Aneta Zegar, Patrycja Kwiecinska, Brian A. Zabel, Artur Osyczka, Mateusz Kwitniewski and Joanna Cichy

Antioxidants 2021, 10(3), 446; https://doi.org/10.3390/antiox10030446 - 13 Mar 2021

Cited by 10 | Viewed by 3371

Abstract

Epithelia in the skin, gut and other environmentally exposed organs display a variety of mechanisms to control microbial communities and limit potential pathogenic microbial invasion. Naturally occurring antimicrobial proteins/peptides and their synthetic derivatives (here collectively referred to as AMPs) reinforce the antimicrobial barrier [...] Read more.

Epithelia in the skin, gut and other environmentally exposed organs display a variety of mechanisms to control microbial communities and limit potential pathogenic microbial invasion. Naturally occurring antimicrobial proteins/peptides and their synthetic derivatives (here collectively referred to as AMPs) reinforce the antimicrobial barrier function of epithelial cells. Understanding how these AMPs are functionally regulated may be important for new therapeutic approaches to combat microbial infections. Some AMPs are subject to redox-dependent regulation. This review aims to: (i) explore cysteine-based redox active AMPs in skin and intestine; (ii) discuss casual links between various redox environments of these barrier tissues and the ability of AMPs to control cutaneous and intestinal microbes; (iii) highlight how bacteria, through intrinsic mechanisms, can influence the bactericidal potential of redox-sensitive AMPs. Full article

(This article belongs to the Special Issue Redox Biology in Microorganisms)

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16 pages, 1081 KiB

Open AccessReview

Oxidative Stress-Generating Antimicrobials, a Novel Strategy to Overcome Antibacterial Resistance

by Álvaro Mourenza, José A. Gil, Luís M. Mateos and Michal Letek

Antioxidants 2020, 9(5), 361; https://doi.org/10.3390/antiox9050361 - 26 Apr 2020

Cited by 50 | Viewed by 5929

Abstract

Antimicrobial resistance is becoming one of the most important human health issues. Accordingly, the research focused on finding new antibiotherapeutic strategies is again becoming a priority for governments and major funding bodies. The development of treatments based on the generation of oxidative stress [...] Read more.

Antimicrobial resistance is becoming one of the most important human health issues. Accordingly, the research focused on finding new antibiotherapeutic strategies is again becoming a priority for governments and major funding bodies. The development of treatments based on the generation of oxidative stress with the aim to disrupt the redox defenses of bacterial pathogens is an important strategy that has gained interest in recent years. This approach is allowing the identification of antimicrobials with repurposing potential that could be part of combinatorial chemotherapies designed to treat infections caused by recalcitrant bacterial pathogens. In addition, there have been important advances in the identification of novel plant and bacterial secondary metabolites that may generate oxidative stress as part of their antibacterial mechanism of action. Here, we revised the current status of this emerging field, focusing in particular on novel oxidative stress-generating compounds with the potential to treat infections caused by intracellular bacterial pathogens. Full article

(This article belongs to the Special Issue Redox Biology in Microorganisms)

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