To avoid molecular damage of biomolecules due to oxidation, all cells have evolved constitutive and responsive systems to mitigate and repair chemical modifications. Archaea have adapted to some of the most extreme environments known to support life, including highly oxidizing conditions. However, in comparison to bacteria and eukaryotes, relatively little is known about the biology and biochemistry of archaea in response to changing conditions and repair of oxidative damage. In this study transcriptome, proteome, and chemical reactivity analyses of hydrogen peroxide (H2O2) induced oxidative stress in Sulfolobus solfataricus (P2) were conducted. Microarray analysis of mRNA expression showed that 102 transcripts were regulated by at least 1.5 fold, 30 minutes after exposure to 30 μM H2O2. Parallel proteomic analyses using two-dimensional differential gel electrophoresis (2D-DIGE), monitored more than 800 proteins 30 and 105 minutes after exposure and found that 18 had significant changes in abundance. A recently characterized ferritin-like antioxidant protein, DPSL, was the most highly regulated species of mRNA and protein, in addition to being post-translationally modified. As expected, a number of antioxidant related mRNAs and proteins were differentially regulated. Three of these, DPSL, superoxide dismutase, and peroxiredoxin were shown to interact and likely form a novel supramolecular complex for mitigating oxidative damage. A scheme for the ability of this complex to perform multi-step reactions is presented. Despite the central role played by DPSL, cells maintained a lower level of protection after disruption of the dpsl gene, indicating a level of redundancy in the oxidative stress pathways of S. solfataricus. This work provides the first “omics” scale assessment of the oxidative stress response for an archeal organism and together with a network analysis using data from previous studies on bacteria and eukaryotes reveals evolutionarily conserved pathways where complex and overlapping defense mechanisms protect against oxygen toxicity.
References
[1]
Imlay JA (2003) Pathways of oxidative damage. Annual Review of Microbiology 57: 395–418.
[2]
Gutteridge JMC, Halliwell B (2000) Free radicals and antioxidants in the year 2000 - A historical look to the future. Reactive Oxygen Species: From Radiation to Molecular Biology 899: 136–147.
[3]
Slupphaug G, Kavli B, Krokan HE (2003) The interacting pathways for prevention and repair of oxidative DNA damage. Mutation Research-Fundamental and Molecular Mechanisms of Mutagenesis 531: 231–251.
[4]
Farr SB, Kogoma T (1991) Oxidative Stress Responses in Escherichia-Coli and Salmonella-Typhimurium. Microbiological Reviews 55: 561–585.
[5]
Power JHT, Asad S, Chataway TK, Chegini F, Manavis J, et al. (2008) Peroxiredoxin 6 in human brain: molecular forms, cellular distribution and association with Alzheimer's disease pathology. Acta Neuropathologica 115: 611–622.
[6]
Iguchi T, Sugita S, Wang CY, Newman NB, Nakatani T, et al. (2009) MnSOD Genotype and Prostate Cancer Risk as a Function of NAT Genotype and Smoking Status. In Vivo 23: 7–12.
[7]
Ritz D, Patel H, Doan B, Zheng M, Aslund F, et al. (2000) Thioredoxin 2 is involved in the oxidative stress response in Escherichia coli. Journal of Biological Chemistry 275: 2505–2512.
[8]
Santos R, Herouart D, Puppo A, Touati D (2000) Critical protective role of bacterial superoxide dismutase in Rhizobium-legume symbiosis. Molecular Microbiology 38: 750–759.
[9]
Wiedenheft B, Mosolf J, Willits D, Yeager M, Dryden KA, et al. (2005) An archaeal antioxidant: Characterization of a Dps-like protein from Sulfolobus solfataricus. Proceedings of the National Academy of Sciences of the United States of America 102: 10551–10556.
[10]
Blokhina O, Virolainen E, Fagerstedt KV (2003) Antioxidants, oxidative damage and oxygen deprivation stress: a review. Annals of Botany 91: 179–194.
[11]
Chen DR, Wilkinson CRM, Watt S, Penkett CJ, Toone WM, et al. (2008) Multiple pathways differentially regulate global oxidative stress responses in fission yeast. Molecular Biology of the Cell 19: 308–317.
[12]
Chen DR, Toone WM, Mata J, Lyne R, Burns G, et al. (2003) Global transcriptional responses of fission yeast to environmental stress. Molecular Biology of the Cell 14: 214–229.
[13]
Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, et al. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Molecular Biology of the Cell 11: 4241–4257.
[14]
Causton HC, Ren B, Koh SS, Harbison CT, Kanin E, et al. (2001) Remodeling of yeast genome expression in response to environmental changes. Molecular Biology of the Cell 12: 323–337.
[15]
Fridovich I (1978) Biology of Oxygen Radicals. Science 201: 875–880.
[16]
Munhoz DC, Netto LES (2004) Cytosolic thioredoxin peroxidase I and II are important defenses of yeast against organic hydroperoxide insult - Catalases and peroxiredoxins cooperate in the decomposition of H2O2 by yeast. Journal of Biological Chemistry 279: 35219–35227.
[17]
Kang SW, Chae HZ, Seo MS, Kim KH, Baines IC, et al. (1998) Mammalian peroxiredoxin isoforms can reduce hydrogen peroxide generated in response to growth factors and tumor necrosis factor-alpha. Journal of Biological Chemistry 273: 6297–6302.
[18]
Almiron M, Link AJ, Furlong D, Kolter R (1992) A Novel DNA-Binding Protein with Regulatory and Protective Roles in Starved Escherichia-Coli. Genes & Development 6: 2646–2654.
[19]
Zheng M, Wang X, Templeton LJ, Smulski DR, LaRossa RA, et al. (2001) DNA microarray-mediated transcriptional profiling of the Escherichia coli response to hydrogen peroxide. Journal of Bacteriology 183: 4562–4570.
[20]
Sund CJ, Rocha ER, Tzinabos AO, Wells WG, Gee JM, et al. (2008) The Bacteroides fragilis transcriptome response to oxygen and H2O2: the role of OxyR and its effect on survival and virulence. Molecular Microbiology 67: 129–142.
[21]
Rocha ER, Smith CJ (1995) Biochemical and Genetic Analyses of a Catalase from the Anaerobic Bacterium Bacteroides-Fragilis. Journal of Bacteriology 177: 3111–3119.
[22]
Gregory EM (1985) Characterization of the O-2-Induced Manganese-Containing Superoxide-Dismutase from Bacteroides-Fragilis. Archives of Biochemistry and Biophysics 238: 83–89.
[23]
Mostertz J, Scharf C, Hecker M, Homuth G (2004) Transcriptome and proteome analysis of Bacillus subtilis gene expression in response to superoxide and peroxide stress. Microbiology-Sgm 150: 497–512.
[24]
Kusch H, Engelmann S, Albrecht D, Morschhauser J, Hecker M (2007) Proteomic analysis of the oxidative stress responses in Candida albicans. Proteomics 7: 686–697.
[25]
Vivancos AP, Jara M, Zuin A, Sanso M, Hidalgo E (2006) Oxidative stress in Schizosaccharomyces pombe: different H2O2 levels, different response pathways. Molecular Genetics and Genomics 276: 495–502.
[26]
Kato S, Kosaka T, Watanabe K (2008) Comparative transcriptome analysis of responses of Methanothermobacter thermautotrophicus to different environmental stimuli. Environmental Microbiology 10: 893–905.
[27]
Lumppio HL, Shenvi NV, Summers AO, Voordouw G, Kurtz DM (2001) Rubrerythrin and rubredoxin oxidoreductase in Desulfovibrio vulgaris: a novel oxidative stress protection system. Journal of Bacteriology 183: 101–108.
[28]
Sztukowska M, Bugno M, Potempa J, Travis J, Kurtz DM (2002) Role of rubrerythrin in the oxidative stress response of Porphyromonas gingivalis. Molecular Microbiology 44: 479–488.
[29]
Coulter ED, Shenvi NV, Kurtz DM (1999) NADH peroxidase activity of rubrerythrin. Biochemical and Biophysical Research Communications 255: 317–323.
[30]
deMare F, Kurtz DM, Nordlund P (1996) The structure of Desulfovibrio vulgaris rubrerythrin reveals a unique combination of rubredoxin-like FeS4 and ferritin-like diiron domains. Nature Structural Biology 3: 539–546.
[31]
Gauss GH, Benas P, Wiedenheft B, Young M, Douglas T, et al. (2006) Structure of the DPS-like protein from Sulfolobus solfataricus reveals a bacterioferritin-like dimetal binding site within a DPS-like dodecameric assembly. Biochemistry 45: 10815–10827.
[32]
Ramsay B, Wiedenheft B, Allen M, Gauss GH, Lawrence CM, et al. (2006) Dps-like protein from the hyperthermophilic archaeon Pyrococcus furiosus. Journal of Inorganic Biochemistry 100: 1061–1068.
[33]
Zhao GH, Ceci P, Ilari A, Giangiacomo L, Laue TM, et al. (2002) Iron and hydrogen peroxide detoxification properties of DNA-binding protein from starved cells - A ferritin-like DNA-binding protein of Escherichia coli. Journal of Biological Chemistry 277: 27689–27696.
[34]
Su MH, Cavallo S, Stefanini S, Chiancone E, Chasteen ND (2005) The so-called Listeria innocua ferritin is a Dps protein. Iron incorporation, detoxification, and DNA protection properties. Biochemistry 44: 5572–5578.
[35]
Schelert J, Dixit V, Hoang V, Simbahan J, Drozda M, et al. (2004) Occurrence and characterization of mercury resistance in the hyperthermophilic archaeon Sulfolobus solfataricus by use of gene disruption. Journal of Bacteriology 186: 427–437.
[36]
Schelert J, Drozda M, Dixit V, Dillman A, Blum P (2006) Regulation of mercury resistance in the crenarchaeote Sulfolobus solfataricus. Journal of Bacteriology 188: 7141–7150.
[37]
Limauro D, Pedone E, Galdi I, Bartolucci S (2008) Peroxiredoxins as cellular guardians in Sulfolobus solfataricus - characterization of Bcp1, Bcp3 and Bcp4. Febs Journal 275: 2067–2077.
[38]
Noble RW, Gibson QH (1970) Reaction of Ferrous Horseradish Peroxidase with Hydrogen Peroxide. Journal of Biological Chemistry 245: 2409–&.
[39]
Benjamini Y, Hochberg Y (1995) Controlling the False Discovery Rate - a Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society Series B-Methodological 57: 289–300.
[40]
Worthington P, Hoang V, Perez-Pomares F, Blum P (2003) Targeted disruption of the alpha-amylase gene in the hyperthermophilic archaeon Sulfolobus solfataficus. Journal of Bacteriology 185: 482–488.
[41]
Rockabrand D, Livers K, Austin T, Kaiser R, Jensen D, et al. (1998) Roles of DnaK and RpoS in starvation-induced thermotolerance of Escherichia coli. Journal of Bacteriology 180: 846–854.
[42]
Gorg A, Weiss W, Dunn MJ (2004) Current two-dimensional electrophoresis technology for proteomics. Proteomics 4: 3665–3685.
[43]
Maaty WSA, Ortmann AC, Dlakic M, Schulstad K, Hilmer JK, et al. (2006) Characterization of the archaeal thermophile Sulfolobus turreted icosahedral virus validates an evolutionary link among double-stranded DNA viruses from all domains of life. Journal of Virology 80: 7625–7635.
[44]
Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proceedings of the National Academy of Sciences of the United States of America 100: 9440–9445.
[45]
Dabney A, Storey D, Warnes R (2004) qvalue: Q-value estimation for false discovery rate control [R package version 1.1].
[46]
Shevchenko A, Jensen ON, Podtelejnikov AV, Sagliocco F, Wilm M, et al. (1996) Linking genome and proteome by mass spectrometry: large-scale identification of yeast proteins from two dimensional gels. Proc Natl Acad Sci U S A 93: 14440–14445.
[47]
Reimand J, Kull M, Peterson H, Hansen J, Vilo J (2007) g: Profiler - a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic Acids Research 35: W193–W200.
[48]
Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, et al. (2007) Integration of biological networks and gene expression data using Cytoscape. Nature Protocols 2: 2366–2382.
[49]
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research 13: 2498–2504.
[50]
Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, et al. (2008) The Pfam protein families database. Nucleic Acids Research 36: D281–D288.
[51]
Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25: 3389–3402.
[52]
Schaffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, et al. (2001) Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Research 29: 2994–3005.
[53]
Marchler-Bauer A, Anderson JB, Derbyshire MK, DeWeese-Scott C, Gonzales NR, et al. (2007) CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Research 35: D237–D240.
[54]
Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, et al. (2001) The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Research 29: 22–28.
[55]
Tatusov RL, Galperin MY, Natale DA, Koonin EV (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Research 28: 33–36.
[56]
Outten FW, Djaman O, Storz G (2004) A suf operon requirement for Fe-S cluster assembly during iron starvation in Escherichia coli. Molecular Microbiology 52: 861–872.
[57]
Yao F, Strauch MA (2005) Independent and interchangeable multimerization domains of the AbrB, abh, and SpoVT global regulatory proteins. Journal of Bacteriology 187: 6354–6362.
[58]
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, et al. (2007) New developments in the InterPro database. Nucleic Acids Research 35: D224–D228.
[59]
Delany I, Rappuoli R, Scarlato V (2004) Fur functions as an activator and as a repressor of putative virulence genes in Neisseria meningitidis. Molecular Microbiology 52: 1081–1090.
[60]
Li H, Singh AK, McIntyre LM, Sherman LA (2004) Differential gene expression in response to hydrogen peroxide and the putative PerR regulon of Synechocystis sp strain PCC 6803. Journal of Bacteriology 186: 3331–3345.
[61]
Hernandez JA, Pellicer S, Huang L, Peleato ML, Fillat MF (2007) FurA modulates gene expression of alr3808, a DpsA homologue in Nostoc (Anabaena) sp PCC7120. Febs Letters 581: 1351–1356.
[62]
She Q, Singh RK, Confalonieri F, Zivanovic Y, Allard G, et al. (2001) The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc Natl Acad Sci U S A 98: 7835–7840.
[63]
Andrews SC (1998) Iron storage in bacteria. Adv Microb Physiol 40: 281–351.
[64]
Kurtz DM Jr (2006) Avoiding high-valent iron intermediates: superoxide reductase and rubrerythrin. J Inorg Biochem 100: 679–693.
[65]
Weinberg MV, Jenney FE, Cui XY, Adams MWW (2004) Rubrerythrin from the hyperthermophilic archaeon Pyrococcus furiosus is a rubredoxin-dependent, iron-containing peroxidase. Journal of Bacteriology 186: 7888–7895.
[66]
Zhang WW, Culley DE, Hogan M, Vitiritti L, Brockman FJ (2006) Oxidative stress and heat-shock responses in Desulfovibrio vulgaris by genome-wide transcriptomic analysis. Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology 90: 41–55.
[67]
Mydel P, Takahashi Y, Yumoto H, Sztukowska M, Kubica M, et al. (2006) Roles of the host oxidative immune response and bacterial antioxidant rubrerythrin during Porphyromonas gingivalis infection. PLoS Pathog 2: e76.
[68]
Kwast KE, Lai LC, Menda N, James DT, Aref S, et al. (2002) Genomic analyses of anaerobically induced genes in Saccharomyces cerevisiae: Functional roles of Rox1 and other factors in mediating the anoxic response. Journal of Bacteriology 184: 250–265.
[69]
Rhee SG, Chae HZ, Kim K (2005) Peroxiredoxins: A historical overview and speculative preview of novel mechanisms and emerging concepts in cell signaling. Free Radical Biology and Medicine 38: 1543–1552.
[70]
Limauro D, Pedone E, Pirone L, Bartolucci S (2006) Identification and characterization of 1-Cys peroxiredoxin from Sulfolobus solfataricus and its involvement in the response to oxidative stress. Febs Journal 273: 721–731.
[71]
Berndt C, Lillig CH, Holmgren A (2008) Thioredoxins and glutaredoxins as facilitators of protein folding. Biochimica Et Biophysica Acta-Molecular Cell Research 1783: 641–650.
[72]
Pedone E, Limauro D, D'Alterio R, Rossi M, Bartolucci S (2006) Characterization of a multifunctional protein disulfide oxidoreductase from Sulfolobus solfataricus. Febs Journal 273: 5407–5420.
[73]
Rabilloud T, Chevallet M, Luche S, Leize-Wagner E (2005) Oxidative stress response: a proteomic view. Expert Review of Proteomics 2: 949–956.
[74]
Vandenbroucke K, Robbens S, Vandepoele K, Inze D, de Peer YV, et al. (2008) Hydrogen peroxide-induced gene expression across kingdoms: A comparative analysis. Molecular Biology and Evolution 25: 507–516.
[75]
Alscher RG, Erturk N, Heath LS (2002) Role of superoxide dismutases (SODs) in controlling oxidative stress in plants. Journal of Experimental Botany 53: 1331–1341.
[76]
Radak Z, Asano K, Inoue M, Kizaki T, Ohishi S, et al. (1995) Superoxide-Dismutase Derivative Reduces Oxidative Damage in Skeletal-Muscle of Rats during Exhaustive Exercise. Journal of Applied Physiology 79: 129–135.
[77]
Chen E, Proestou G, Bourbeau D, Wang E (2000) Rapid up-regulation of peptide elongation factor EF-1 alpha protein levels is an immediate early event during oxidative stress-induced apoptosis. Experimental Cell Research 259: 140–148.
[78]
Chang RY, Wang E (2007) Mouse translation elongation factor eEF1A-2 interacts with Prdx-I to protect cells against apoptotic death induced by oxidative stress. Journal of Cellular Biochemistry 100: 267–278.
[79]
Rabilloud T, Heller M, Gasnier F, Luche S, Rey C, et al. (2002) Proteomics analysis of cellular response to oxidative stress - Evidence for in vivo overoxidation of peroxiredoxins at their active site. Journal of Biological Chemistry 277: 19396–19401.
[80]
Bae YS, Kang SW, Seo MS, Baines IC, Tekle E, et al. (1997) Epidermal growth factor (EGF)-induced generation of hydrogen peroxide - Role in EGF receptor-mediated tyrosine phosphorylation. Journal of Biological Chemistry 272: 217–221.
[81]
Hao Q, Rutherford SA, Low B, Tang H (2006) Suppression of the phosphorylation of receptor tyrosine phosphatase-alpha on the Src-independent site tyrosine 789 by reactive oxygen species. Molecular Pharmacology 69: 1938–1944.
[82]
Hu YY, Wang XY, Zeng L, Cai DY, Sabapathy K, et al. (2005) ERK phosphorylates p66shcA on Ser36 and subsequently regulates p27(kip1) expression via the Akt-FOXO3a pathway: Implication of p27(kip1) in cell response to oxidative stress. Molecular Biology of the Cell 16: 3705–3718.
[83]
Schulenberg B, Goodman TN, Aggeler R, Capaldi RA, Patton WF (2004) Characterization of dynamic and steady-state protein phosphorylation using a fluorescent phosphoprotein gel stain and mass spectrometry. Electrophoresis 25: 2526–2532.
[84]
Lower BH, Potters MB, Kennelly PJ (2004) A phosphoprotein from the archaeon Sulfolobus solfataricus with protein-serine/threonine kinase activity. J Bacteriol 186: 463–472.
[85]
Ray WK, Keith SM, DeSantis AM, Hunt JP, Larson TJ, et al. (2005) A phosphohexomutase from the archaeon Sulfolobus solfataricus is covalently modified by phosphorylation on serine. J Bacteriol 187: 4270–4275.
[86]
Kim S, Lee SB (2005) Identification and characterization of Sulfolobus solfataricus D-gluconate dehydratase: a key enzyme in the non-phosphorylated Entner-Doudoroff pathway. Biochem J 387: 271–280.
[87]
Ferrer-Navarro M, Gomez A, Yanes O, Planell R, Aviles FX, et al. (2006) Proteome of the bacterium Mycoplasma penetrans. Journal of Proteome Research 5: 688–694.
[88]
Liu JF, Cai Y, Wang JL, Zhou Q, Yang B, et al. (2007) Phosphoproteome profile of human liver Chang's cell based on 2-DE with fluorescence staining and MALDI-TOF/TOF-MS. Electrophoresis 28: 4348–4358.
[89]
Morales MA, Watanabe R, Laurent C, Lenormand P, Rousselle JC, et al. (2008) Phosphoproteomic analysis of Leishmania donovani pro- and amastigote stages. Proteomics 8: 350–363.
[90]
Ma MY, Guo XJ, Wang FQ, Zhao C, Liu ZC, et al. (2008) Protein Expression Profile of the Mouse Metaphase-II Oocyte. Journal of Proteome Research 7: 4821–4830.
[91]
Eymann C, Becher D, Bernhardt J, Gronau K, Klutzny A, et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in Bacillus subtilis. Proteomics 7: 3509–3526.
[92]
Leichert LI, Jakob U (2004) Protein thiol modifications visualized in vivo. Plos Biology 2: 1723–1737.
[93]
Nie L, Wu G, Culley DE, Scholten JCM, Zhang W (2007) Integrative analysis of transcriptomic and proteomic data: Challenges, solutions and applications. Critical Reviews in Biotechnology 27: 63–75.
[94]
Williamson AJK, Smith DL, Blinco D, Unwin RD, Pearson S, et al. (2008) Quantitative proteomics analysis demonstrates post-transcriptional regulation of embryonic stem cell differentiation to hematopoiesis. Molecular & Cellular Proteomics 7: 459–472.
[95]
Nissom PM, Sanny A, Kok YJ, Hiang YT, Chuah SH, et al. (2006) Transcriptome and proteome profiling to understanding the biology of high productivity CHO cells. Molecular Biotechnology 34: 125–140.
[96]
Nie L, Wu G, Zhang WW (2006) Correlation of mRNA expression and protein abundance affected by multiple sequence features related to translational efficiency in Desulfovibrio vulgaris: A quantitative analysis. Genetics 174: 2229–2243.
[97]
Fricke WF, Seedorf H, Henne A, Kruer M, Liesegang H, et al. (2006) The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H-2 for methane formation and ATP synthesis. Journal of Bacteriology 188: 642–658.
[98]
Vergauwen B, De Vos D, Van Beeumen JJ (2006) Characterization of the bifunctional gamma-glutamate-cysteine ligase/glutathione synthetase (GshF) of Pasteurella multocida. Journal of Biological Chemistry 281: 4380–4394.
[99]
Janowiak BE, Griffith OW (2005) Glutathione synthesis in Streptococcus agalactiae - One protein accounts for gamma-glutamylcysteine synthetase and glutathione synthetase activities. Journal of Biological Chemistry 280: 11829–11839.
[100]
Boucher Y, Douady CJ, Papke RT, Walsh DA, Boudreau MER, et al. (2003) Lateral gene transfer and the origins of prokaryotic groups. Annual Review of Genetics 37: 283–328.
[101]
Marles-Wright J, Grant T, Delumeau O, van Duinen G, Firbank SJ, et al. (2008) Molecular architecture of the “stressosome,” a signal integration and transduction hub. Science 322: 92–96.