Characterization of two alkyl hydroperoxide reductase C homologs alkyl hydroperoxide reductase C_H1 and alkyl hydroperoxide reductase C_H2 in Bacillus subtilis

Duality of H2O2 detoxification and immune activation of Ralstonia solanacearum alkyl hydroperoxide reductase C (AhpC) in tobacco

Although microbial pathogens utilize various strategies to evade plant immunity, host plants have evolved powerful defense mechanisms that can be activated in preparation for threat by infective organisms. Here, we identified one 24 kDa alkyl hydroperoxide reductase C (AhpC) from the culture supernatant of Ralstonia solanacearum strain FQY-4 (denoted RsAhpC) in the presence of host roots. RsAhpC contributes to H2O2 detoxification and the pathogenicity of R. solanacearum. However, the introduction of RsAhpC into the apoplast could activate immune defense, leading to suppression of pathogen colonization in both Nicotiana benthamiana and the Honghua Dajinyuan (HD) cultivar of N. tabacum. Consequently, overexpression of RsAhpC in the HD cultivar enhanced the resistance of tobacco to bacterial wilt disease caused by FQY-4. Overall, this study provides insight into the arms race between pathogens and their plant hosts. Specifically, it is firstly reported that plants can sense pathogen-derived AhpC to activate defenses, in addition to the role of AhpC in pathogen ROS detoxification. Therefore, the macromolecule AhpC produced by Ralstonia solanacearum has the ability to enhance plant defense as an elicitor, which provides a practical strategy for disease resistance breeding.

Regulation of fadR on the ROS defense mechanism in Shewanalla oneidensis

Protein FadR is known as a fatty acid metabolism global regulator that sustains cell envelope integrity by changing the profile of fatty acid. Here, we present its unique participation in the defense against reactive oxygen species (ROS) in the bacterium. FadR contributes to defending extracellular ROS by maintaining the permeability of the cell membrane. It also facilitates the ROS detoxification process by increasing the expression of ROS neutralizers (KatB, KatG, and AhpCF). FadR also represses the leakage of ROS by alleviating the respiratory action conducted by terminal cytochrome cbb3-type heme-copper oxidases (ccoNOQP). These findings suggest that FadR plays a comprehensive role in modulating the bacterial oxidative stress response, instead of merely strengthening the cellular barrier against the environment. This study sheds light on the complex mechanisms of bacterial ROS defense and offers FadR as a novel target for ROS control research.

Unraveling radiation resistance strategies in two bacterial strains from the high background radiation area of Chavara-Neendakara: A comprehensive whole genome analysis

This paper reports the results of gamma irradiation experiments and whole genome sequencing (WGS) performed on vegetative cells of two radiation resistant bacterial strains, Metabacillus halosaccharovorans (VITHBRA001) and Bacillus paralicheniformis (VITHBRA024) (D10 values 2.32 kGy and 1.42 kGy, respectively), inhabiting the top-ranking high background radiation area (HBRA) of Chavara-Neendakara placer deposit (Kerala, India). The present investigation has been carried out in the context that information on strategies of bacteria having mid-range resistance for gamma radiation is inadequate. WGS, annotation, COG and KEGG analyses and manual curation of genes helped us address the possible pathways involved in the major domains of radiation resistance, involving recombination repair, base excision repair, nucleotide excision repair and mismatch repair, and the antioxidant genes, which the candidate could activate to survive under ionizing radiation. Additionally, with the help of these data, we could compare the candidate strains with that of the extremely radiation resistant model bacterium Deinococccus radiodurans, so as to find the commonalities existing in their strategies of resistance on the one hand, and also the rationale behind the difference in D10, on the other. Genomic analysis of VITHBRA001 and VITHBRA024 has further helped us ascertain the difference in capability of radiation resistance between the two strains. Significantly, the genes such as uvsE (NER), frnE (protein protection), ppk1 and ppx (non-enzymatic metabolite production) and those for carotenoid biosynthesis, are endogenous to VITHBRA001, but absent in VITHBRA024, which could explain the former's better radiation resistance. Further, this is the first-time study performed on any bacterial population inhabiting an HBRA. This study also brings forward the two species whose radiation resistance has not been reported thus far, and add to the knowledge on radiation resistant capabilities of the phylum Firmicutes which are abundantly observed in extreme environment.

A Physiological Approach to Explore How Thioredoxin-Glutathione Reductase (TGR) and Peroxiredoxin (Prx) Eliminate H2O2 in Cysticerci of Taenia

Peroxiredoxins (Prxs) and glutathione peroxidases (GPxs) are the main enzymes of the thiol-dependent antioxidant systems responsible for reducing the H2O2 produced via aerobic metabolism or parasitic organisms by the host organism. These antioxidant systems maintain a proper redox state in cells. The cysticerci of Taenia crassiceps tolerate millimolar concentrations of this oxidant. To understand the role played by Prxs in this cestode, two genes for Prxs, identified in the genome of Taenia solium (TsPrx1 and TsPrx3), were cloned. The sequence of the proteins suggests that both isoforms belong to the class of typical Prxs 2-Cys. In addition, TsPrx3 harbors a mitochondrial localization signal peptide and two motifs (-GGLG- and -YP-) associated with overoxidation. Our kinetic characterization assigns them as thioredoxin peroxidases (TPxs). While TsPrx1 and TsPrx3 exhibit the same catalytic efficiency, thioredoxin-glutathione reductase from T. crassiceps (TcTGR) was five and eight times higher. Additionally, the latter demonstrated a lower affinity (>30-fold) for H2O2 in comparison with TsPrx1 and TsPrx3. The TcTGR contains a Sec residue in its C-terminal, which confers additional peroxidase activity. The aforementioned aspect implies that TsPrx1 and TsPrx3 are catalytically active at low H2O2 concentrations, and the TcTGR acts at high H2O2 concentrations. These results may explain why the T. crassiceps cysticerci can tolerate high H2O2 concentrations.

8-OxoG-Dependent Regulation of Global Protein Responses Leads to Mutagenesis and Stress Survival in Bacillus subtilis

The guanine oxidized (GO) system of Bacillus subtilis, composed of the YtkD (MutT), MutM and MutY proteins, counteracts the cytotoxic and genotoxic effects of the oxidized nucleobase 8-OxoG. Here, we report that in growing B. subtilis cells, the genetic inactivation of GO system potentiated mutagenesis (HPM), and subsequent hyperresistance, contributes to the damaging effects of hydrogen peroxide (H2O2) (HPHR). The mechanism(s) that connect the accumulation of the mutagenic lesion 8-OxoG with the ability of B. subtilis to evolve and survive the noxious effects of oxidative stress were dissected. Genetic and biochemical evidence indicated that the synthesis of KatA was exacerbated, in a PerR-independent manner, and the transcriptional coupling repair factor, Mfd, contributed to HPHR and HPM of the ΔGO strain. Moreover, these phenotypes are associated with wider pleiotropic effects, as revealed by a global proteome analysis. The inactivation of the GO system results in the upregulated production of KatA, and it reprograms the synthesis of the proteins involved in distinct types of cellular stress; this has a direct impact on (i) cysteine catabolism, (ii) the synthesis of iron-sulfur clusters, (iii) the reorganization of cell wall architecture, (iv) the activation of AhpC/AhpF-independent organic peroxide resistance, and (v) increased resistance to transcription-acting antibiotics. Therefore, to contend with the cytotoxic and genotoxic effects derived from the accumulation of 8-OxoG, B. subtilis activates the synthesis of proteins belonging to transcriptional regulons that respond to a wide, diverse range of cell stressors.

Adenanthin Is an Efficient Inhibitor of Peroxiredoxins from Pathogens, Inhibits Bacterial Growth, and Potentiates Antibiotic Activities

The emergence and re-emergence of bacterial strains resistant to multiple drugs represent a global health threat, and the search for novel biological targets is a worldwide concern. AhpC are enzymes involved in bacterial redox homeostasis by metabolizing diverse kinds of hydroperoxides. In pathogenic bacteria, AhpC are related to several functions, as some isoforms are characterized as virulence factors. However, no inhibitor has been systematically evaluated to date. Here we show that the natural ent-kaurane Adenanthin (Adn) efficiently inhibits AhpC and molecular interactions were explored by computer assisted simulations. Additionally, Adn interferes with growth and potentializes the effect of antibiotics (kanamycin and PMBN), positioning Adn as a promising compound to treat infections caused by multiresistant bacterial strains.

Plant Beneficial Deep-Sea Actinobacterium, Dermacoccus abyssi MT1.1T Promote Growth of Tomato (Solanum lycopersicum) under Salinity Stress

Simple Summary

Salt stress is an important environmental problem that negatively affects agricultural and food production in the world. Currently, the use of plant beneficial bacteria for plant growth promotion is attractive due to the demand for eco-friendly and sustainable agriculture. In this study, salt tolerant deep-sea actinobacterium, Dermacoccus abyssi MT1.1^T was investigated plant growth promotion and salt stress mitigation in tomato seedlings. In addition, D. abyssi MT1.1^T whole genome was analyzed for plant growth promoting traits and genes related to salt stress alleviation in plants. We also evaluated the biosafety of this strain on human health and organisms in the environment. Our results highlight that the inoculation of D. abyssi MT1.1^T could reduce the negative effects of salt stress in tomato seedlings by growth improvement, total soluble sugars accumulation and hydrogen peroxide reduction. Moreover, this strain could survive and colonize tomato roots. Biosafety testing and genome analysis of D. abyssi MT1.1^T showed no pathogenicity risk. In conclusion, we provide supporting evidence on the potential of D. abyssi MT1.1^T as a safe strain for use in plant growth promotion under salt stress.

Abstract

Salt stress is a serious agricultural problem threatens plant growth and development resulted in productivity loss and global food security concerns. Salt tolerant plant growth promoting actinobacteria, especially deep-sea actinobacteria are an alternative strategy to mitigate deleterious effects of salt stress. In this study, we aimed to investigate the potential of deep-sea Dermacoccus abyssi MT1.1^T to mitigate salt stress in tomato seedlings and identified genes related to plant growth promotion and salt stress mitigation. D. abyssi MT1.1^T exhibited plant growth promoting traits namely indole-3-acetic acid (IAA) and siderophore production and phosphate solubilization under 0, 150, 300, and 450 mM NaCl in vitro. Inoculation of D. abyssi MT1.1^T improved tomato seedlings growth in terms of shoot length and dry weight compared with non-inoculated seedlings under 150 mM NaCl. In addition, increased total soluble sugar and total chlorophyll content and decreased hydrogen peroxide content were observed in tomato inoculated with D. abyssi MT1.1^T. These results suggested that this strain mitigated salt stress in tomatoes via osmoregulation by accumulation of soluble sugars and H₂O₂ scavenging activity. Genome analysis data supported plant growth promoting and salt stress mitigation potential of D. abyssi MT1.1^T. Survival and colonization of D. abyssi MT1.1^T were observed in roots of inoculated tomato seedlings. Biosafety testing on D. abyssi MT1.1^T and in silico analysis of its whole genome sequence revealed no evidence of its pathogenicity. Our results demonstrate the potential of deep-sea D. abyssi MT1.1^T to mitigate salt stress in tomato seedlings and as a candidate of eco-friendly bio-inoculants for sustainable agriculture.

Effects of Serine or Threonine in the Active Site of Typical 2-Cys Prx on Hyperoxidation Susceptibility and on Chaperone Activity

Typical 2-Cys peroxiredoxins (2-Cys Prx) are ubiquitous Cys-based peroxidases, which are stable as decamers in the reduced state, and may dissociate into dimers upon disulfide bond formation. A peroxidatic Cys (CP) takes part of a catalytic triad, together with a Thr/Ser and an Arg. Previously, we described that the presence of Ser (instead of Thr) in the active site stabilizes yeast 2-Cys Prx as decamers. Here, we compared the hyperoxidation susceptibilities of yeast 2-Cys Prx. Notably, 2-Cys Prx containing Ser (named here Ser-Prx) were more resistant to hyperoxidation than enzymes containing Thr (Thr-Prx). In silico analysis revealed that Thr-Prx are more frequent in all domains of life, while Ser-Prx are more abundant in bacteria. As yeast 2-Cys Prx, bacterial Ser-Prx are more stable as decamers than Thr-Prx. However, bacterial Ser-Prx were only slightly more resistant to hyperoxidation than Thr-Prx. Furthermore, in all cases, organic hydroperoxide inhibited more the peroxidase activities of 2-Cys Prx than hydrogen peroxide. Moreover, bacterial Ser-Prx displayed increased thermal resistance and chaperone activity, which may be related with its enhanced stability as decamers compared to Thr-Prx. Therefore, the single substitution of Thr by Ser in the catalytic triad results in profound biochemical and structural differences in 2-Cys Prx.

Analysis of disulphide bond linkage between CoA and protein cysteine thiols during sporulation and in spores of Bacillus species

Spores of Bacillus species have novel properties, which allow them to lie dormant for years and then germinate under favourable conditions. In the current work, the role of a key metabolic integrator, coenzyme A (CoA), in redox regulation of growing cells and during spore formation in Bacillus megaterium and Bacillus subtilis is studied. Exposing these growing cells to oxidising agents or carbon deprivation resulted in extensive covalent protein modification by CoA (termed protein CoAlation), through disulphide bond formation between the CoA thiol group and a protein cysteine. Significant protein CoAlation was observed during sporulation of B. megaterium, and increased largely in parallel with loss of metabolism in spores. Mass spectrometric analysis identified four CoAlated proteins in B. subtilis spores as well as one CoAlated protein in growing B. megaterium cells. All five of these proteins have been identified as moderately abundant in spores. Based on these findings and published studies, protein CoAlation might be involved in facilitating establishment of spores' metabolic dormancy, and/or protecting sensitive sulfhydryl groups of spore enzymes.

AhpA is a peroxidase expressed during biofilm formation in Bacillus subtilis

Organisms growing aerobically generate reactive oxygen species such as hydrogen peroxide. These reactive oxygen molecules damage enzymes and DNA, potentially causing cell death. In response, Bacillus subtilis produces at least nine potential peroxide-scavenging enzymes; two belong to the alkylhydroperoxide reductase (Ahp) class of peroxidases. Here, we explore the role of one of these Ahp homologs, AhpA. While previous studies demonstrated that AhpA can scavenge peroxides and thus defend cells against peroxides, they did not clarify when during growth the cell produces AhpA. The results presented here show that the expression of ahpA is regulated in a manner distinct from that of the other peroxide-scavenging enzymes in B. subtilis. While the primary Ahp, AhpC, is expressed during exponential growth and stationary phase, these studies demonstrate that the expression of ahpA is dependent on the transition-state regulator AbrB and the sporulation and biofilm formation transcription factor Spo0A. Furthermore, these results show that ahpA is specifically expressed during biofilm formation, and not during sporulation or stationary phase, suggesting that derepression of ahpA by AbrB requires a signal other than those present upon entry into stationary phase. Despite this expression pattern, ahpA mutant strains still form and maintain robust biofilms, even in the presence of peroxides. Thus, the role of AhpA with regard to protecting cells within biofilms from environmental stresses is still uncertain. These studies highlight the need to further study the Ahp homologs to better understand how they differ from one another and the unique roles they may play in oxidative stress resistance.

Insights into the Function of a Second, Nonclassical Ahp Peroxidase, AhpA, in Oxidative Stress Resistance in Bacillus subtilis

Organisms growing aerobically generate reactive oxygen-containing molecules, such as hydrogen peroxide (H2O2). These reactive oxygen molecules damage enzymes and DNA and may even cause cell death. In response, Bacillus subtilis produces at least nine potential peroxide-scavenging enzymes, two of which appear to be the primary enzymes responsible for detoxifying peroxides during vegetative growth: a catalase (encoded by katA) and an alkylhydroperoxide reductase (Ahp, encoded by ahpC). AhpC uses two redox-active cysteine residues to reduce peroxides to nontoxic molecules. A specialized thioredoxin-like protein, AhpF, is then required to restore oxidized AhpC back to its reduced state. Curiously, B. subtilis has two genes encoding Ahp: ahpC and ahpA. Although AhpC is well characterized, very little is known about AhpA. In fact, numerous bacterial species have multiple ahp genes; however, these additional Ahp proteins are generally uncharacterized. We seek to understand the role of AhpA in the bacterium's defense against toxic peroxide molecules in relation to the roles previously assigned to AhpC and catalase. Our results demonstrate that AhpA has catalytic activity similar to that of the primary enzyme, AhpC. Furthermore, our results suggest that a unique thioredoxin redox protein, AhpT, may reduce AhpA upon its oxidation by peroxides. However, unlike AhpC, which is expressed well during vegetative growth, our results suggest that AhpA is expressed primarily during postexponential growth.

IMPORTANCE

B. subtilis appears to produce nine enzymes designed to protect cells against peroxides; two belong to the Ahp class of peroxidases. These studies provide an initial characterization of one of these Ahp homologs and demonstrate that the two Ahp enzymes are not simply replicates of each other, suggesting that they instead are expressed at different times during growth of the cells. These results highlight the need to further study the Ahp homologs to better understand how they differ from one another and to identify their function, if any, in protection against oxidative stress. Through these studies, we may better understand why bacteria have multiple enzymes designed to scavenge peroxides and thus have a more accurate understanding of oxidative stress resistance.