Skip to main content

Transcription Factors That Scavenge Reactive Oxygen Species in Rhizobacteria

  • Chapter
  • First Online:
Sustainable Plant Nutrition under Contaminated Environments

Abstract

Under abiotic stress, the production of reactive oxygen species (ROS) such as hydrogen peroxide or superoxide causes harmful effects on the survival of rhizobacteria, which have an important role in the growth and yield of various crop plants. To cope with ROS stress, rhizobacteria activate certain regulons that are controlled by the OxyR, PerR, or PerR-like homolog and SoxR transcription factors. All these sense peroxides during the oxidation of iron, manganese, zinc, nickel, and other moieties and stimulate overlapping sets of proteins, which defend their weak metalloenzymes. It is also evident that these OxyR, PerR, or PerR-like and SoxR homologs help in detecting electrophilic compounds. In most of the bacteria, various regulatory genes control the redox-cycling compound, whereas in some cases, it protects in contradiction of the same causes. After oxidation of iron-sulfur compounds, the regulons prompt proteins that dispense with, discharge, or adjust them and instigate compounds that defend the cells against oxidative stress. The present book chapter comprehensively describes the role of different transcription factors in scavenging ROS stress faced by so-called rhizobacteria. Moreover, research gaps with prospects for further investigation are also mentioned.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 199.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  • Ahmad S, Lee SY, Kong HG et al (2016) Genetic determinants for pyomelanin production and its protective effect against oxidative stress in Ralstonia solanacearum. PLoS One 11(8):e0160845

    PubMed  PubMed Central  Google Scholar 

  • Ahmad I, Tahir M, Daraz U et al (2020) Responses and tolerance of cereal crops to metals and metalloids toxicity. In: Hassanuzzaman M (ed) Agronomic crops. Springer, Singapore, pp 235–264. https://doi.org/10.1007/978-981-15-0025-1_14

    Chapter  Google Scholar 

  • Anjem A, Imlay JA (2012) Mononuclear iron enzymes are primary targets of hydrogen peroxide stress. J Biol Chem 287:15544–15556

    CAS  PubMed  PubMed Central  Google Scholar 

  • Anjum NA, Gill SS, Gill R et al (2014) Metal/metalloid stress tolerance in plants: role of ascorbate, its redox couple, and associated enzymes. Protoplasma 251(6):1265–1283

    CAS  PubMed  Google Scholar 

  • Antelmann H, Helmann JD (2011) Thiol-based redox switches and gene regulation. Antioxid Redox Signal 14:1049–1063

    CAS  PubMed  PubMed Central  Google Scholar 

  • Aquino P, Honda B, Jaini S et al (2017) Coordinated regulation of acid resistance in Escherichia coli. BMC Syst Biol 11(1):1–5

    PubMed  PubMed Central  Google Scholar 

  • Bang YJ, Lee ZW, Kim D et al (2016) OxyR2 functions as a three-state redox switch to tightly regulate production of Prx2, a peroxiredoxin of Vibrio vulnificus. J Biol Chem 291:16038–16047

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bedard K, Lardy B, Krause KH (2007) NOX family NADPH oxidases: not just in mammals. Biochimie 89:1107–1112

    CAS  PubMed  Google Scholar 

  • Bellini P, Hemmings AM (2006) In vitro characterization of a bacterial manganese uptake regulator of the fur superfamily. Biochemistry 45:2686–2698

    CAS  PubMed  Google Scholar 

  • Bhattacharyya A, Chattopadhyay R, Mitra S et al (2014) Oxidative stress: an essential factor in the pathogenesis of gastrointestinal mucosal diseases. Physiol Rev 94:329–354

    CAS  PubMed  PubMed Central  Google Scholar 

  • Blanchard JL, Wholey WY, Conlon EM et al (2007) Rapid changes in gene expression dynamics in response to superoxide reveal SoxRS-dependent and independent transcriptional networks. PLoS One 2(11):e1186

    PubMed  PubMed Central  Google Scholar 

  • Chatgilialoglu C, Ferreri C, Terzidis MA (2011) Purine 5′,8-cyclonucleoside lesions: chemistry and biology. Chem Soc Rev 40:1368–1382

    CAS  PubMed  Google Scholar 

  • Chiancone E, Ceci P (2010) The multifaceted capacity of Dps proteins to combat bacterial stress conditions: detoxification of iron and hydrogen peroxide and DNA binding. Biochim Biophys Acta 8:798–805

    Google Scholar 

  • Choi HJ, Kim SJ, Mukhopadhyay P et al (2001) Structural basis of the redox switch in the OxyR transcription factor. Cell 105(1):103–113

    CAS  PubMed  Google Scholar 

  • Crack JC, Svistunenko DA, Munnoch J et al (2016) Differentiated, promoter-specific response of [4Fe-4S] NsrR DNA binding to reaction with nitric oxide. J Biol Chem 291:8663–8672

    CAS  PubMed  PubMed Central  Google Scholar 

  • de Paiva SR, Figueiredo MR, Aragao TV et al (2003) Antimicrobial activity in vitro of plumbagin isolated from Plumbago species. Mem Inst Oswaldo Cruz 98:959–961

    PubMed  Google Scholar 

  • Dian C, Vitale S, Leonard GA et al (2011) The structure of the Helicobacter pylori ferric uptake regulator Fur reveals three functional metal binding sites. Mol Microbiol 79:1260–1275

    CAS  PubMed  Google Scholar 

  • Diaz JM, Hansel CM, Apprill A et al (2016) Species-specific control of external superoxide levels by the coral holobiont during a natural bleaching event. Nat Commun 7(1):13801

    CAS  PubMed  PubMed Central  Google Scholar 

  • Dietrich LE, Price-Whelan A, Petersen A et al (2006) The phenazine pyocyanin is a terminal signaling factor in the quorum sensing network of Pseudomonas aeruginosa. Mol Microbiol 61:1308–1321

    CAS  PubMed  Google Scholar 

  • Dietrich LE, Teal TK, Price-Whelan A et al (2008) Redox-active antibiotics control gene expression and community behavior in divergent bacteria. Science 321:1203–1206

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ditta A (2018) Physiological and phenological responses of crop plants under heat stress. In: Ramakrishna A, Gill SS (eds) Metabolic adaptations in plants during abiotic stress. CRC Press, Taylor & Francis, Boca Raton, pp 55–63

    Google Scholar 

  • Ditta A, Khalid A (2016) Bio-organo-phos: a sustainable approach for managing phosphorus deficiency in agricultural soils. In: Larramendy M, Soloneski S (eds) Organic fertilizers – from basic concepts to applied outcomes. InTech, Croatia, pp 109–136. https://doi.org/10.5772/62473

    Chapter  Google Scholar 

  • Ditta A, Arshad M, Zahir ZA et al (2015) Comparative efficacy of rock phosphate enriched organic fertilizer vs. mineral phosphatic fertilizer for nodulation, growth and yield of lentil. Int J Agric Biol 17:589–595

    CAS  Google Scholar 

  • Ditta A, Imtiaz M, Mehmood S et al (2018a) Rock phosphate enriched organic fertilizer with phosphate solubilizing microorganisms improves nodulation, growth and yield of legumes. Commun Soil Sci Plant Anal 49(21):2715–2725. https://doi.org/10.1080/00103624.2018.1538374

    Article  CAS  Google Scholar 

  • Ditta A, Muhammad J, Imtiaz M et al (2018b) Application of rock phosphate enriched composts increases nodulation, growth and yield of chickpea. Int J Recycl Org Waste Agric 7(1):33–40. https://doi.org/10.1007/s40093-017-0187-1

    Article  Google Scholar 

  • Drazic A, Miura H, Peschek J et al (2013) Methionine oxidation activates a transcription factor in response to oxidative stress. Proc Natl Acad Sci U S A 110:9493–9498

    CAS  PubMed  PubMed Central  Google Scholar 

  • Drazic A, Gebendorfer KM, Mak S et al (2014) Tetramers are the activation-competent species of the HOCl-specific transcription factor HypT. J Biol Chem 289:977–986

    CAS  PubMed  Google Scholar 

  • Drazic A, Kutzner E, Winter J et al (2015) Metabolic response of Escherichia coli upon treatment with hypochlorite at sub-lethal concentrations. PLoS One 10:e0125823

    PubMed  PubMed Central  Google Scholar 

  • Dubbs JM, Mongkolsuk S (2012) Peroxide-sensing transcriptional regulators in bacteria. J Bacteriol 194:5495–5503

    CAS  PubMed  PubMed Central  Google Scholar 

  • Duval V, Lister IM (2013) MarA, SoxS and Rob of Escherichia coli. Global regulators of multidrug resistance, virulence and stress response. Int J Biotechnol Wellness Ind 2:101–124

    PubMed  PubMed Central  Google Scholar 

  • Eser M, Masip L, Kadokura H et al (2009) Disulfide bond formation by exported glutaredoxin indicates glutathione’s presence in the E. coli periplasm. Proc Natl Acad Sci U S A 106:1572–1577

    CAS  PubMed  PubMed Central  Google Scholar 

  • Esteve-Gassent MD, Smith TC II, Small CM et al (2015) Absence of sodA increases the levels of oxidation of key metabolic determinants of Borrelia burgdorferi. PLoS One 10:e0136707

    PubMed  PubMed Central  Google Scholar 

  • Fang FC, Frawley ER, Tapscott T et al (2016) Discrimination and integration of stress signals by pathogenic bacteria. Cell Host Microbe 20:144–153

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ferrandiz MJ, Martin-Galiano AJ, Arnanz C et al (2015) Reactive oxygen species contribute to the bactericidal effects of the fluoroquinolone moxifloxacin in Streptococcus pneumoniae. Antimicrob Agents Chemother 60:409–417

    PubMed  PubMed Central  Google Scholar 

  • Ferrer-Sueta G, Manta B, Botti H et al (2011) Factors affecting protein thiol reactivity and specificity in peroxide reduction. Chem Res Toxicol 24:434–450

    CAS  PubMed  Google Scholar 

  • Fillat MF (2014) The FUR (ferric uptake regulator) superfamily: diversity and versatility of key transcriptional regulators. Arch Biochem Biophys 546:41–52

    CAS  PubMed  Google Scholar 

  • Flohe L, Toppo S, Cozza G et al (2011) A comparison of thiol peroxidase mechanisms. Antioxid Redox Signal 15:763–780

    CAS  PubMed  Google Scholar 

  • Flores-Cruz Z, Allen C (2011) Necessity of OxyR for the hydrogen peroxide stress response and full virulence in Ralstonia solanacearum. Appl Environ Microbiol 77:6426–6432

    CAS  PubMed  PubMed Central  Google Scholar 

  • Fontecave M, Choudens SO, Py B et al (2005) Mechanisms of iron-sulfur cluster assembly: the SUF machinery. J Biol Inorg Chem 10:713–721

    CAS  PubMed  Google Scholar 

  • Fujikawa M, Kobayashi K, Kozawa T (2012) Direct oxidation of the [2Fe-2S] cluster in SoxR protein by superoxide: distinct differential sensitivity to superoxide-mediated signal transduction. J Biol Chem 287:35702–35708

    CAS  PubMed  PubMed Central  Google Scholar 

  • Fujikawa M, Kobayashi K, Kozawa T (2014) Mechanistic studies on formation of the dinitrosyl iron complex of the [2Fe-2S] cluster of SoxR protein. J Biochem 156:163–172

    CAS  PubMed  Google Scholar 

  • Fujikawa M, Kobayashi K, Kozawa T (2015) Redox-dependent DNA distortion in a SoxR protein-promoter complex studied using fluorescent probes. J Biochem 157:389–397

    CAS  PubMed  Google Scholar 

  • Gardner PR, Gardner DP, Gardner AP (2015) Globins scavenge sulfur trioxide anion radical. J Biol Chem 290:27204–27214

    CAS  PubMed  PubMed Central  Google Scholar 

  • Gralnick JA, Downs DM (2003) The YggX protein of Salmonella enterica is involved in Fe(II) trafficking and minimizes the DNA damage caused by hydroxyl radicals: residue CYS-7 is essential for YggX function. J Biol Chem 278:20708–20715

    CAS  PubMed  Google Scholar 

  • Griffith KL, Shah IM, Wolf RE Jr (2004) Proteolytic degradation of Escherichia coli transcription activators SoxS and MarA as the mechanism for reversing the induction of the superoxide (SoxRS) and multiple antibiotic resistance (Mar) regulons. Mol Microbiol 51:1801–1816

    CAS  PubMed  Google Scholar 

  • Gu M, Imlay JA (2011) The SoxRS response of Escherichia coli is directly activated by redox-cycling drugs rather than by superoxide. Mol Microbiol 79:1136–1150

    CAS  PubMed  PubMed Central  Google Scholar 

  • Gu M, Imlay JA (2013) Superoxide poisons mononuclear iron enzymes by causing mismetallation. Mol Microbiol 89:123–134

    CAS  PubMed  PubMed Central  Google Scholar 

  • Guttenberger N, Blankenfeldt W, Breinbauer R (2017) Recent developments in the isolation, biological function, biosynthesis, and synthesis of phenazine natural products. Bioorg Med Chem 5:31180–31184

    Google Scholar 

  • Helmann JD (2014) Specificity of metal sensing: iron and manganese homeostasis in Bacillus subtilis. J Biol Chem 289:28112–28120

    CAS  PubMed  PubMed Central  Google Scholar 

  • Herbig AF, Helmann JD (2001) Roles of metal ions and hydrogen peroxide in modulating the interaction of the Bacillus subtilis PerR peroxide regulon repressor with operator DNA. Mol Microbiol 41:849–859

    CAS  PubMed  Google Scholar 

  • Hillion M, Antelmann H (2015) Thiol-based redox switches in prokaryotes. Biol Chem 396:415–444

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hohle TH, O’Brian MR (2016) Metal-specific control of gene expression mediated by Bradyrhizobium japonicum Mur and Escherichia coli Fur is determined by the cellular context. Mol Microbiol 101:152–166

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hong M, Fuangthong M, Helmann JD et al (2005) Structure of an OhrR-ohrA operator complex reveals the DNA binding mechanism of the MarR family. Mol Cell 20:131–141

    CAS  PubMed  Google Scholar 

  • Huan C, Jiang L, An X et al (2016) Potential role of reactive oxygen species and antioxidant genes in the regulation of peach fruit development and ripening. Plant Physiol Biochem 104:294–303

    CAS  PubMed  Google Scholar 

  • Huang X, Shin JH, Pinochet-Barros A et al (2017) Bacillus subtilis MntR coordinates the transcriptional regulation of manganese uptake and efflux systems. Mol Microbiol 103:253–268

    CAS  PubMed  Google Scholar 

  • Hugo M, Turell L, Manta B et al (2009) Thiol and sulfenic acid oxidation of AhpE, the one-cysteine peroxiredoxin from Mycobacterium tuberculosis: kinetics, acidity constants, and conformational dynamics. Biochemistry 48:9416–9426

    CAS  PubMed  Google Scholar 

  • Hussain A, Zahir ZA, Ditta A et al (2020) Production and implication of bio-activated organic fertilizer enriched with zinc-solubilizing bacteria to boost up maize (Zea mays L.) production and biofortification under two cropping seasons. MDPI-Agronomy 10(39). https://doi.org/10.3390/agronomy10010039

  • Imlay JA (2013) The molecular mechanisms and physiological consequences of oxidative stress: lessons from a model bacterium. Nat Rev Microbiol 11:443–454

    CAS  PubMed  PubMed Central  Google Scholar 

  • Imlay JA (2015) Transcription factors that defend bacteria against reactive oxygen species. Annu Rev Microbiol 69:93–108

    CAS  PubMed  PubMed Central  Google Scholar 

  • Imran QM, Falak N, Hussain A et al (2016) Nitric oxide responsive heavy metal-associated gene AtHMAD1 contributes to development and disease resistance in Arabidopsis thaliana. Front Plant Sci 7:1712

    PubMed  PubMed Central  Google Scholar 

  • Imtiaz M, Ashraf M, Rizwan MS et al (2018) Vanadium toxicity in chickpea (Cicer arietinum L.) grown in red soil: effects on cell death, ROS and antioxidative systems. Ecotox Environ Saf 158:139–144. https://doi.org/10.1016/j.ecoenv.2018.04.022

    Article  CAS  Google Scholar 

  • Inbaraj JJ, Chignell CF (2004) Cytotoxic action of juglone and plumbagin: a mechanistic study using HaCaT keratinocytes. Chem Res Toxicol 17:55–62

    CAS  PubMed  Google Scholar 

  • Ishikado A, Sono Y, Matsumoto M et al (2013) Willow bark extract increases antioxidant enzymes and reduces oxidative stress through activation of Nrf2 in vascular endothelial cells and Caenorhabditis elegans. Free Radic Biol Med 65:1506–1515

    CAS  PubMed  Google Scholar 

  • Jacquamet L, Traoré DA, Ferrer JL et al (2009) Structural characterization of the active form of PerR: insights into the metal-induced activation of PerR and Fur proteins for DNA binding. Mol Microbiol 73:20–31

    CAS  PubMed  Google Scholar 

  • Jang S, Imlay JA (2007) Micromolar intracellular hydrogen peroxide disrupts metabolism by damaging iron-sulfur enzymes. J Biol Chem 282:929–937

    CAS  PubMed  Google Scholar 

  • Jaroensuk J, Atichartpongkul S, Chionh YH et al (2016) Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruginosa. Nucleic Acids Res 44:10834–10848

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jo I, Chung IY, Bae HW et al (2015) Structural details of the OxyR peroxide-sensing mechanism. Proc Natl Acad Sci U S A 112:6443–6448

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jo I, Park N, Chung IY et al (2016) Crystal structures of the disulfide reductase DsbM from Pseudomonas aeruginosa. Acta Crystallogr D Struct Biol 72:1100–1109

    CAS  PubMed  Google Scholar 

  • Kehres DG, Janakiraman A, Slauch JM et al (2002) Regulation of Salmonella enterica serovar Typhimurium mntH transcription by H(2)O(2), Fe(2+), and Mn(2+). J Bacteriol 184:3151–3158

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kim J, Park W (2014) Oxidative stress response in Pseudomonas putida. Appl Microbiol Biotechnol 98:6933–6946

    CAS  PubMed  Google Scholar 

  • Kim MS, Dufour YS, Yoo JS et al (2012) Conservation of thiol-oxidative stress responses regulated by SigR orthologues in actinomycetes. Mol Microbiol 85:326–344

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kim S, Bang YJ, Kim D et al (2014) Distinct characteristics of OxyR2, a new OxyR-type regulator, ensuring expression of Peroxiredoxin 2 detoxifying low levels of hydrogen peroxide in Vibrio vulnificus. Mol Microbiol 93:992–1009

    CAS  PubMed  Google Scholar 

  • Kim JH, Ji CJ, Ju SY et al (2016) Bacillus licheniformis contains two more PerR-like proteins in addition to PerR, Fur, and Zur orthologues. PLoS One 11(5):e0155539

    PubMed  PubMed Central  Google Scholar 

  • Kim JH, Won YB, Ji CJ et al (2017a) The difference in in vivo sensitivity between Bacillus licheniformis PerR and Bacillus subtilis PerR is due to the different cellular environments. Biochem Biophys Res Commun 16:30094–30093

    Google Scholar 

  • Kim J, Park C, Imlay JA et al (2017b) Lineage-specific SoxR-mediated regulation of an endoribonuclease protects non-enteric bacteria from redox-active compounds. J Biol Chem 292:121–133

    CAS  PubMed  Google Scholar 

  • Kobayashi K, Fujikawa M, Kozawa T (2015) Binding of promoter DNA to SoxR protein decreases the reduction potential of the [2Fe-2S] cluster. Biochemistry 54:334–339

    CAS  PubMed  Google Scholar 

  • Korshunov SS, Imlay JA (2002) A potential role for periplasmic superoxide dismutase in blocking the penetration of external superoxide into the cytosol of gram-negative bacteria. Mol Microbiol 43:95–106

    CAS  PubMed  Google Scholar 

  • Krapp AR, Rodriguez RE, Poli HO et al (2002) The flavoenzyme ferredoxin (flavodoxin)-NADP(H) reductase modulates NADP(H) homeostasis during the soxRS response of Escherichia coli. J Bacteriol 184:1474–1480

    CAS  PubMed  PubMed Central  Google Scholar 

  • Krapp AR, Humbert MV, Carrillo N (2011) The soxRS response of Escherichia coli can be induced in the absence of oxidative stress and oxygen by modulation of NADPH content. Microbiology 157:957–965

    CAS  PubMed  Google Scholar 

  • Kuehne A, Emmert H, Soehle J et al (2015) Acute activation of oxidative pentose phosphate pathway as first-line response to oxidative stress in human skin cells. Mol Cell 59:359–371

    CAS  PubMed  Google Scholar 

  • Kurtz DM Jr (2004) Microbial detoxification of superoxide: the non-heme iron reductive paradigm for combating oxidative stress. ACC Chem Res 37:902–908

    CAS  PubMed  Google Scholar 

  • Landry AP, Ding H (2014) Redox control of human mitochondrial outer membrane protein MitoNEET [2Fe-2S] clusters by biological thiols and hydrogen peroxide. J Biol Chem 289:4307–4315

    CAS  PubMed  PubMed Central  Google Scholar 

  • Landry AP, Cheng Z, Ding H (2015) Reduction of mitochondrial protein mitoNEET [2Fe-2S] clusters by human glutathione reductase. Free Radic Biol Med 81:119–127

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lee JW, Helmann JD (2006) The PerR transcription factor senses H2O2 by metal-catalysed histidine oxidation. Nature 440:363–367

    CAS  PubMed  Google Scholar 

  • Lee C, Lee SM, Mukhopadhyay P et al (2004) Redox regulation of OxyR requires specific disulfide bond formation involving a rapid kinetic reaction path. Nat Struct Mol Biol 11:1179–1185

    CAS  PubMed  Google Scholar 

  • Lee KC, Yeo WS, Roe JH (2008) Oxidant-responsive induction of the suf operon, encoding a Fe-S assembly system, through Fur and IscR in Escherichia coli. J Bacteriol 190:8244–8247

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lee JH, Lee KL, Yeo WS et al (2009) SoxRS-mediated lipopolysaccharide modification enhances resistance against multiple drugs in Escherichia coli. J Bacteriol 191:4441–4450

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lee D, Park S, Bae S et al (2015) Hydrogen peroxide-activatable antioxidant prodrug as a targeted therapeutic agent for ischemia-reperfusion injury. Sci Rep 5:16592

    PubMed  PubMed Central  Google Scholar 

  • Lemke RA, Peterson AC, Ziegelhoffer EC et al (2014) Synthesis and scavenging role of furan fatty acids. Proc Natl Acad Sci U S A 111(33):E3450–E3457

    CAS  PubMed  PubMed Central  Google Scholar 

  • Li Y, Qiu Y, Gao H et al (2009) Characterization of Zur-dependent genes and direct Zur targets in Yersinia pestis. BMC Microbiol 9:1471–2180

    Google Scholar 

  • Lin CN, Syu WJ, Sun WS et al (2010) A role of ygfZ in the Escherichia coli response to plumbagin challenge. J Biomed Sci 17(1):84

    Google Scholar 

  • Lisher JP, Tsui HC, Ramos-Montañez S et al (2017) Biological and chemical adaptation to endogenous hydrogen peroxide production in Streptococcus pneumoniae D39. mSphere 2:00291–00216

    Google Scholar 

  • Liu YZ, Imtiaz M, Ditta A et al (2020) Response of growth, antioxidant enzymes and root exudates production towards As stress in Pteris vittata and Astragalus sinicus colonized by arbuscular mycorrhizal fungi. Environ Sci Pollut Res 27:2340–2352. https://doi.org/10.1007/s11356-019-06785-5

    Article  CAS  Google Scholar 

  • Luo L, Qi MS, Yao SY et al (2005) Role of oxyR from Sinorhizobium meliloti in regulating the expression of catalases. Acta Biochim Biophys Sin 37:421–428

    CAS  PubMed  Google Scholar 

  • Mahavihakanont A, Charoenlap N, Namchaiw P et al (2012) Novel roles of SoxR, a transcriptional regulator from Xanthomonas campestris, in sensing redox-cycling drugs and regulating a protective gene that have overall implications for bacterial stress physiology and virulence on a host plant. J Bacteriol 194:209–217

    CAS  PubMed  PubMed Central  Google Scholar 

  • Marinho HS, Real C, Cyrne L (2014) Hydrogen peroxide sensing, signaling and regulation of transcription factors. Redox Biol 2:535–562

    CAS  PubMed  PubMed Central  Google Scholar 

  • Martin RG, Rosner JL (2011) Promoter discrimination at class I MarA regulon promoters mediated by glutamic acid 89 of the MarA transcriptional activator of Escherichia coli. J Bacteriol 193:506–515

    CAS  PubMed  Google Scholar 

  • Mehmood S, Saeed DA, Rizwan M et al (2018) Impact of different amendments on biochemical responses of sesame (Sesamum indicum L.) plants grown in lead-cadmium contaminated soil. Plant Physiol Biochem 132:345–355. https://doi.org/10.1016/j.plaphy.2018.09.019

    Article  CAS  PubMed  Google Scholar 

  • Mielecki D, Grzesiuk E (2014) Ada response: a strategy for repair of alkylated DNA in bacteria. FEMS Microbiol Lett 355:1–11

    CAS  PubMed  Google Scholar 

  • Milackova I, Rackova L, Majekova M et al (2015) Protection or cytotoxicity mediated by a novel quinonoid-polyphenol compound? Gen Physiol Biophys 34:51–64

    CAS  PubMed  Google Scholar 

  • Mosel M, Li L, Drlica K et al (2013) Superoxide-mediated protection of Escherichia coli from antimicrobials. Antimicrob Agents Chemother 57:5755–5759

    CAS  PubMed  PubMed Central  Google Scholar 

  • Mulrooney SB, Hausinger RP (2003) Nickel uptake and utilization by microorganisms. FEMS Microbiol Rev 27:239–261

    CAS  PubMed  Google Scholar 

  • Munnoch JT, Martinez MT, Svistunenko DA et al (2016) Characterization of a putative NsrR homologue in Streptomyces venezuelae reveals a new member of the Rrf2 superfamily. Sci Rep 6(1):1–4

    Google Scholar 

  • Nakayama T, Yonekura S, Yonei S et al (2013) Escherichia coli pyruvate:flavodoxin oxidoreductase, YdbK: regulation of expression and biological roles in protection against oxidative stress. Genes Genet Syst 88:175–188

    CAS  PubMed  Google Scholar 

  • Naseer N, Shapiro JA, Chander M (2014) RNA-Seq analysis reveals a six-gene SoxR regulon in Streptomyces coelicolor. PLoS One 9:e106181

    PubMed  PubMed Central  Google Scholar 

  • Nelson KJ, Parsonage D, Hall A et al (2008) Cysteine pK(a) values for the bacterial peroxiredoxin AhpC. Biochemistry 47:12860–12868

    CAS  PubMed  Google Scholar 

  • Netto LE, Antunes F (2016) The roles of peroxiredoxin and thioredoxin in hydrogen peroxide sensing and in signal transduction. Mol Cells 39:65–71

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ni K, Steger K, Yang H et al (2016) A comprehensive investigation of sperm DNA damage and oxidative stress injury in infertile patients with subclinical, normozoospermic, and astheno/oligozoospermic clinical varicocoele. Andrology 4:816–824

    CAS  PubMed  Google Scholar 

  • Niamat B, Naveed M, Ahmad Z et al (2019) Calcium-enriched animal manure alleviates the adverse effects of salt stress on growth, physiology and nutrients homeostasis of Zea mays L. MDPI-Plants 8(11):480. https://doi.org/10.3390/plants8110480

    Article  CAS  Google Scholar 

  • Niviere V, Fontecave M (2004) Discovery of superoxide reductase: an historical perspective. J Biol Inorg Chem 9:119–123

    CAS  PubMed  Google Scholar 

  • Outten FW, Djaman O, Storz G (2004) A suf operon requirement for Fe-S cluster assembly during iron starvation in Escherichia coli. Mol Microbiol 52:861–872

    CAS  PubMed  Google Scholar 

  • Ozyigit II, Filiz E, Vatansever R et al (2016) Identification and comparative analysis of H2O2-scavenging enzymes (ascorbate peroxidase and glutathione peroxidase) in selected plants employing bioinformatics approaches. Front Plant Sci 7:301

    PubMed  PubMed Central  Google Scholar 

  • Palma M, Zurita J, Ferreras JA et al (2005) Pseudomonas aeruginosa SoxR does not conform to the archetypal paradigm for SoxR-dependent regulation of the bacterial oxidative stress adaptive response. Infect Immun 73:2958–2966

    CAS  PubMed  PubMed Central  Google Scholar 

  • Pannala VR, Dash RK (2015) Mechanistic characterization of the thioredoxin system in the removal of hydrogen peroxide. Free Radic Biol Med 78:42–55

    CAS  PubMed  Google Scholar 

  • Parent A, Caux-Thang C, Signor L et al (2013) Single glutamate to aspartate mutation makes ferric uptake regulator (Fur) as sensitive to H2O2 as peroxide resistance regulator (PerR). Angew Chem Int Ed Engl 52:10339–10343

    CAS  PubMed  Google Scholar 

  • Passaia G, Margis-Pinheiro M (2015) Glutathione peroxidases as redox sensor proteins in plant cells. Plant Sci 234:22–26

    CAS  PubMed  Google Scholar 

  • Patra KC, Hay N (2014) The pentose phosphate pathway and cancer. Trends Biochem Sci 39:347–354

    CAS  PubMed  PubMed Central  Google Scholar 

  • Peskin AV, Dickerhof N, Poynton RA et al (2013) Hyperoxidation of peroxiredoxins 2 and 3: rate constants for the reactions of the sulfenic acid of the peroxidatic cysteine. J Biol Chem 288:14170–14177

    CAS  PubMed  PubMed Central  Google Scholar 

  • Pisoschi AM, Pop A (2015) The role of antioxidants in the chemistry of oxidative stress: a review. Eur J Med Chem 97:55–74

    CAS  PubMed  Google Scholar 

  • Pomposiello PJ, Koutsolioutsou A, Carrasco D et al (2003) SoxRS-regulated expression and genetic analysis of the yggX gene of Escherichia coli. J Bacteriol 185:6624–6632

    CAS  PubMed  PubMed Central  Google Scholar 

  • Poole LB (2007) The catalytic mechanism of peroxiredoxins. Subcell Biochem 44:61–81

    PubMed  Google Scholar 

  • Pullan ST, Gidley MD, Jones RA et al (2007) Nitric oxide in chemostat-cultured Escherichia coli is sensed by Fnr and other global regulators: unaltered methionine biosynthesis indicates lack of S nitrosation. J Bacteriol 189:1845–1855

    CAS  PubMed  Google Scholar 

  • Rahal A, Kumar A, Singh V et al (2014) Oxidative stress, prooxidants, and antioxidants: the interplay. Biomed Res Int 761264:23

    Google Scholar 

  • Rai P, Cole TD, Wemmer DE et al (2001) Localization of Fe(2+) at an RTGR sequence within a DNA duplex explains preferential cleavage by Fe(2+) and H2O2. J Mol Biol 312:1089–1101

    CAS  PubMed  Google Scholar 

  • Rai P, Parrish M, Tay IJ et al (2015) Streptococcus pneumoniae secretes hydrogen peroxide leading to DNA damage and apoptosis in lung cells. Proc Natl Acad Sci U S A 112(26):E3421–E3430

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rau J, Stolz A (2003) Oxygen-insensitive nitroreductases NfsA and NfsB of Escherichia coli function under anaerobic conditions as lawsone-dependent Azo reductases. Appl Environ Microbiol 69:3448–3455

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rima D, Shiv BK, Bhavna C et al (2016) Oxidative stress induced damage to paternal genome and impact of meditation and yoga: can it reduce incidence of childhood cancer? Asian Pac J Cancer Prev 17:4517–4525

    PubMed  Google Scholar 

  • Sabir A, Naveed M, Bashir MA et al (2020) Cadmium mediated phytotoxic impacts in Brassica napus: managing growth, physiological and oxidative disturbances through combined use of biochar and Enterobacter sp. MN17. J Environ Manag 265:110522. https://doi.org/10.1016/j.jenvman.2020.110522

    Article  CAS  Google Scholar 

  • Sainsbury S, Ren J, Nettleship JE et al (2010) The structure of a reduced form of OxyR from Neisseria meningitidis. BMC Struct Biol 10:1472–6807

    Google Scholar 

  • Sakhtah H, Koyama L, Zhang Y et al (2016) The Pseudomonas aeruginosa efflux pump MexGHI-OpmD transports a natural phenazine that controls gene expression and biofilm development. Proc Natl Acad Sci U S A 113(25):E3538–4E3547

    CAS  PubMed  PubMed Central  Google Scholar 

  • Sarfraz R, Hussain A, Sabir A et al (2019) Role of biochar and plant growth-promoting rhizobacteria to enhance soil carbon sequestration: a review. Environ Monit Assess 191:251. https://doi.org/10.1007/s10661-019-7400-9

    Article  PubMed  Google Scholar 

  • Schiaffino S, Reggiani C, Kostrominova TY et al (2015) Mitochondrial specialization revealed by single muscle fiber proteomics: focus on the Krebs cycle. Scand J Med Sci Sports 4:41–48

    Google Scholar 

  • Seaver LC, Imlay JA (2001) Hydrogen peroxide fluxes and compartmentalization inside growing Escherichia coli. J Bacteriol 183:7182–7189

    CAS  PubMed  PubMed Central  Google Scholar 

  • Seth D, Hausladen A, Wang YJ et al (2012) Endogenous protein S-nNitrosylation in E. coli: regulation by OxyR. Science 336:470–473

    CAS  PubMed  Google Scholar 

  • Shah AM, Zhao Y, Wang Y et al (2014) A Mur regulator protein in the extremophilic bacterium Deinococcus radiodurans. PLoS One 9(9):e106341

    Google Scholar 

  • Shahzad H, Ullah S, Iqbal M et al (2019) Effects of salinity sources and levels on growth, physiology and nutrient contents of maize crop. Ital J Agron 14:199–207. https://doi.org/10.4081/ija.2019.1326

    Article  Google Scholar 

  • Sheplock R, Recinos DA, Mackow N et al (2013) Species-specific residues calibrate SoxR sensitivity to redox-active molecules. Mol Microbiol 87:368–381

    CAS  PubMed  Google Scholar 

  • Shi H, Huang G, Xia D et al (2015) Role of in situ resultant H(2)O(2) in the visible-light-driven photocatalytic inactivation of E. coli using natural sphalerite: a genetic study. J Phys Chem B 119:3104–3111

    CAS  PubMed  Google Scholar 

  • Shimberg GD, Michalek JL, Oluyadi AA et al (2016) Cleavage and polyadenylation specificity factor 30: an RNA-binding zinc-finger protein with an unexpected 2Fe-2S cluster. Proc Natl Acad Sci U S A 113:4700–4705

    CAS  PubMed  PubMed Central  Google Scholar 

  • Shin JH, Singh AK, Cheon DJ et al (2011) Activation of the SoxR regulon in Streptomyces coelicolor by the extracellular form of the pigmented antibiotic actinorhodin. J Bacteriol 193:75–81

    CAS  PubMed  Google Scholar 

  • Singh AK, Shin JH, Lee KL et al (2013) Comparative study of SoxR activation by redox-active compounds. Mol Microbiol 90:983–996

    CAS  PubMed  Google Scholar 

  • Sobota JM, Gu M, Imlay JA (2014) Intracellular hydrogen peroxide and superoxide poison 3-deoxy-d-arabinoheptulosonate 7-phosphate synthase, the first committed enzyme in the aromatic biosynthetic pathway of Escherichia coli. J Bacteriol 196:1980–1991

    PubMed  PubMed Central  Google Scholar 

  • Song Y, Huang H, Chen Y et al (2013) Cytotoxic and antibacterial marfuraquinocins from the deep South China Sea-derived Streptomyces niveus SCSIO 3406. J Nat Prod 76:2263–2268

    CAS  PubMed  Google Scholar 

  • Sun H, Li M, Xu G et al (2012) Regulation of MntH by a dual Mn(II)- and Fe(II)-dependent transcriptional repressor (DR2539) in Deinococcus radiodurans. PLoS One 7(4):e35057

    CAS  PubMed  PubMed Central  Google Scholar 

  • Svintradze DV, Peterson DL, Collazo-Santiago EA et al (2013) Structures of the Porphyromonas gingivalis OxyR regulatory domain explain differences in expression of the OxyR regulon in Escherichia coli and P. gingivalis. Acta Crystallogr D Biol Crystallogr 69:2091–2103

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tanner JR, Patel PG, Hellinga JR et al (2017) Legionella pneumophila OxyR is a redundant transcriptional regulator that contributes to expression control of the two-component CpxRA system. J Bacteriol 19:00690–00616

    Google Scholar 

  • Teramoto H, Inui M, Yukawa H (2013) OxyR acts as a transcriptional repressor of hydrogen peroxide-inducible antioxidant genes in Corynebacterium glutamicum R. FEBS J 280:3298–3312

    CAS  PubMed  Google Scholar 

  • Terzidis MA, Chatgilialoglu C (2015) An ameliorative protocol for the quantification of purine 5′,8-cyclo-2′-deoxynucleosides in oxidized DNA. Front Chem 3:47

    PubMed  PubMed Central  Google Scholar 

  • Terzidis MA, Prisecaru A, Molphy Z et al (2016) Radical-induced purine lesion formation is dependent on DNA helical topology. Free Radic Res 50:S91–S101

    CAS  PubMed  Google Scholar 

  • Uhl L, Dukan S (2016) Hydrogen peroxide induced cell death: the major defences relative roles and consequences in E. coli. PLoS One 11:e0159706

    PubMed  PubMed Central  Google Scholar 

  • Ullah N, Ditta A, Khalid A et al (2020) Integrated effect of algal biochar and plant growth promoting rhizobacteria on physiology and growth of maize under deficit irrigations. J Soil Sci Plant Nutr 20:346–356. https://doi.org/10.1007/s42729-019-00112-0

    Article  Google Scholar 

  • Varghese S, Tang Y, Imlay JA (2003) Contrasting sensitivities of Escherichia coli aconitases A and B to oxidation and iron depletion. J Bacteriol 185:221–230

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wang Y, Newman DK (2008) Redox reactions of phenazine antibiotics with ferric (hydr)oxides and molecular oxygen. Environ Sci Technol 42:2380–2386

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wang Y, Kern SE, Newman DK (2010) Endogenous phenazine antibiotics promote anaerobic survival of Pseudomonas aeruginosa via extracellular electron transfer. J Bacteriol 192:365–369

    CAS  PubMed  Google Scholar 

  • Wang Y, Wilks JC, Danhorn T et al (2011) Phenazine-1-carboxylic acid promotes bacterial biofilm development via ferrous iron acquisition. J Bacteriol 193:3606–3617

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wang H, Naseer N, Chen Y et al (2017) OxyR2 modulates OxyR1 activity and Vibrio cholerae oxidative stress response. Infect Immun 30:00929–00916

    Google Scholar 

  • Watanabe S, Kita A, Kobayashi K et al (2008) Crystal structure of the [2Fe-2S] oxidative-stress sensor SoxR bound to DNA. Proc Natl Acad Sci U S A 105:4121–4126

    CAS  PubMed  PubMed Central  Google Scholar 

  • Yamamoto K, Ishihama A, Busby SJ et al (2011) The Escherichia coli K-12 MntR miniregulon includes dps, which encodes the major stationary-phase DNA-binding protein. J Bacteriol 193:1477–1480

    CAS  PubMed  PubMed Central  Google Scholar 

  • Yang L, Yurkovich JT, Lloyd CJ et al (2016) Principles of proteome allocation are revealed using proteomic data and genome-scale models. Sci Rep 6:36734

    CAS  PubMed  PubMed Central  Google Scholar 

  • Yeo WS, Lee JH, Lee KC et al (2006) IscR acts as an activator in response to oxidative stress for the suf operon encoding Fe-S assembly proteins. Mol Microbiol 61:206–218

    CAS  PubMed  Google Scholar 

  • Yesilkaya H, Andisi VF, Andrew PW et al (2013) Streptococcus pneumoniae and reactive oxygen species: an unusual approach to living with radicals. Trends Microbiol 21:187–195

    CAS  PubMed  Google Scholar 

  • Yu C, Wang N, Wu M et al (2016) OxyR-regulated catalase CatB promotes the virulence in rice via detoxifying hydrogen peroxide in Xanthomonas oryzae pv. oryzae. BMC Microbiol 16(1):269

    PubMed  PubMed Central  Google Scholar 

  • Zeb H, Hussain A, Naveed M et al (2018) Compost enriched with ZnO and Zn-solubilizing bacteria improves yield and Zn-fortification in flooded rice. Ital J Agron 13(4):310–316. https://doi.org/10.4081/ija.2018.1295

    Article  Google Scholar 

  • Zhao Y, Pluth MD (2016) Hydrogen sulfide donors activated by reactive oxygen species. Angew Chem Int Ed Engl 55:14638–14642

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zhao Y, Nickels LM, Wang H et al (2016) OxyR-regulated catalase activity is critical for oxidative stress resistance, nodulation and nitrogen fixation in Azorhizobium caulinodans. FEMS Microbiol Lett 363:13

    Google Scholar 

  • Zheng M, Wang X, Templeton LJ et al (2001) DNA microarray-mediated transcriptional profiling of the Escherichia coli response to hydrogen peroxide. J Bacteriol 183:4562–4570

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zheng JY, Tan HL, Matsudaira PT et al (2017) Excess reactive oxygen species production mediates monoclonal antibody-induced human embryonic stem cell death via oncosis. Cell Death Differ 20:164

    Google Scholar 

  • Zou Y, Wang J, Peng J et al (2016) Oregano essential oil Induces SOD1 and GSH expression through Nrf2 activation and alleviates hydrogen peroxide-induced oxidative damage in IPEC-J2 cells. Oxidative Med Cell Longev 5987183:26

    Google Scholar 

  • Zuber P (2009) Management of oxidative stress in Bacillus. Annu Rev Microbiol 63:575–597

    CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Allah Ditta .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2022 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Shah, A.M.U.H., Ditta, A., Parveen, A., Thind, S., Ebadi, A.G. (2022). Transcription Factors That Scavenge Reactive Oxygen Species in Rhizobacteria. In: Mahmood, Q. (eds) Sustainable Plant Nutrition under Contaminated Environments. Sustainable Plant Nutrition in a Changing World. Springer, Cham. https://doi.org/10.1007/978-3-030-91499-8_12

Download citation

Publish with us

Policies and ethics