9. Coulter ED, Shenvi NV, Kurtz DM (1999) NADH peroxidase activity of rubrerythrin. Biochemical and Biophysical Research Communications 255: 317–323. 10. Coulter ED, Kurtz DM Jr. (2001) A role for rubredoxin in oxidative stress protection in Desulfovibrio vulgaris: catalytic electron transfer to rubrerythrin and two-iron superoxide reductase. Arch Biochem Biophys 394: 76–86. 11. Kurtz DM Jr. (2006) Avoiding high-valent iron intermediates: superoxide reductase and rubrerythrin. J Inorg Biochem 100: 679–693. 12. Kawasaki S, Ono M, Watamura Y, Sakai Y, Satoh T, et al. (2007) An O2- inducible rubrerythrin-like protein, rubperoxin, is functional as a H2O2 reductase in an obligatory anaerobe Clostridium acetobutylicum. FEBS Lett 581: 2460–2464. 13. Wakagi T (2003) Sulerythrin, the smallest member of the rubrerythrin family, from a strictly aerobic and thermoacidophilic archaeon, Sulfolobus tokodaii strain 7. FEMS Microbiol Lett 222: 33–37. 14. Iyer RB, Silaghi-Dumitrescu R, Kurtz DM Jr., Lanzilotta WN (2005) High- resolution crystal structures of Desulfovibrio vulgaris (Hildenborough) nigerythrin: facile, redox-dependent iron movement, domain interface variability, and peroxidase activity in the rubrerythrins. J Biol Inorg Chem 10: 407–416. 15. Shiba H, Igarashi Y, Kodama T, Minoda Y (1982) The deficient carbohydrate metabolic pathways and the incomplete tricarboxylic acid cycle in an obligately autotrophic hydrogen-oxidizing bacterium. Agricultural and Biological Chem- istry 46: 2341–2345. 16. Pitulle C, Yang Y, Marchiani M, Moore ER, Siefert JL, et al. (1994) Phylogenetic position of the genus Hydrogenobacter. Int J Syst Bacteriol 44: 620–626. 17. Shiba H, Igarashi Y, Kodama T, Minoda Y (1985) The CO2 assimilation via the reductive tricarboxylic acid cycle in an obligately autotrophic, aerobic hydrogen-oxidizing bacterium, Hydrogenobacter thermophilus. Archives of Microbi- ology 141: 198–203. 18. Schauder R, Widdel F, Fuchs G (1987) Carbon Assimilation Pathways in Sulfate-Reducing Bacteria II. Enzymes of a Reductive Citric-Acid Cycle in the Autotrophic Desulfobacter-Hydrogenophilus. Archives of Microbiology 148: 218–225. 19. Beh M, Strauss G, Huber R, Stetter KO, Fuchs G (1993) Enzymes of the Reductive Citric-Acid Cycle in the Autotrophic Eubacterium Aquifex-Pyrophilus and in the Archaebacterium Thermoproteus-Neutrophilus. Archives of Microbiology 160: 306–311. 20. Wahlund TM, Tabita FR (1997) The reductive tricarboxylic acid cycle of carbon dioxide assimilation: initial studies and purification of ATP-citrate lyase from the green sulfur bacterium Chlorobium tepidum. J Bacteriol 179: 4859–4867. 21. Berg IA (2011) Ecological aspects of the distribution of different autotrophic CO2 fixation pathways. Appl Environ Microbiol 77: 1925–1936. 22. Arai H, Kanbe H, Ishii M, Igarashi Y (2010) Complete genome sequence of the thermophilic, obligately chemolithoautotrophic hydrogen-oxidizing bacterium Hydrogenobacter thermophilus TK-6. J Bacteriol 192: 2651–2652. 23. Fushinobu S, Shoun H, Wakagi T (2003) Crystal structure of sulerythrin, a rubrerythrin-like protein from a strictly aerobic archaeon, Sulfolobus tokodaii strain 7, shows unexpected domain swapping. Biochemistry 42: 11707–11715. 24. Tempel W, Liu ZJ, Schubot FD, Shah A, Weinberg MV, et al. (2004) Structural genomics of Pyrococcus furiosus: X-ray crystallography reveals 3D domain swapping in rubrerythrin. Proteins 57: 878–882. 25. Zhao W, Ye Z, Zhao J (2007) RbrA, a cyanobacterial rubrerythrin, functions as a FNR-dependent peroxidase in heterocysts in protection of nitrogenase from An Essential Antioxidant in H. thermophilus damage by hydrogen peroxide in Anabaena sp. PCC 7120. Mol Microbiol 66: 1219–1230. 26. Kawasaki S, Sakai Y, Takahashi T, Suzuki I, Niimura Y (2009) O2 and reactive oxygen species detoxification complex, composed of O2-responsive NADH:ru- bredoxin oxidoreductase-flavoprotein A2-desulfoferrodoxin operon enzymes, rubperoxin, and rubredoxin, in Clostridium acetobutylicum. Appl Environ Microbiol 75: 1021–1029. 27. McCord JM, Fridovich I (1969) The utility of superoxide dismutase in studying free radical reactions. I. Radicals generated by the interaction of sulfite, dimethyl sulfoxide, and oxygen. J Biol Chem 244: 6056–6063. 28. Keele BB Jr., McCord JM, Fridovich I (1970) Superoxide dismutase from Escherichia coli B. A new manganese-containing enzyme. J Biol Chem 245: 6176–6181. 29. Peschek GA, Wastyn M, Trnka M, Molitor V, Fry IV, et al. (1989) Characterization of the cytochrome c oxidase in isolated and purified plasma membranes from the cyanobacterium Anacystis nidulans. Biochemistry 28: 3057–3063. 30. Richter OM, Tao JS, Turba A, Ludwig B (1994) A cytochrome ba3 functions as a quinol oxidase in Paracoccus denitrificans. Purification, cloning, and sequence comparison. J Biol Chem 269: 23079–23086. 31. Yamamoto M, Arai H, Ishii M, Igarashi Y (2006) Role of two 2- oxoglutarate:ferredoxin oxidoreductases in Hydrogenobacter thermophilus under aerobic and anaerobic conditions. FEMS Microbiol Lett 263: 189–193. 32. Lanzilotta WN, Dillard BD, Demick JM, Adams MWW (2011) A cryo- crystallographic time course for peroxide reduction by rubrerythrin from Pyrococcus furiosus. Journal of Biological Inorganic Chemistry 16: 949–959. 33. Kawasaki S, Ishikura J, Watamura Y, Niimura Y (2004) Identification of O2- induced peptides in an obligatory anaerobe, Clostridium acetobutylicum. FEBS Lett 571: 21–25. 34. Jacob F (1977) Evolution and tinkering. Science 196: 1161–1166. 35. Andrews SC (2010) The Ferritin-like superfamily: Evolution of the biological iron storeman from a rubrerythrin-like ancestor. Biochim Biophys Acta 1800: 691–705. pp 691–705. 36. Cooley RB, Rhoads TW, Arp DJ, Karplus PA (2011) A diiron protein autogenerates a valine-phenylalanine cross-link. Science 332: 929. 37. Cooley RB, Arp DJ, Karplus PA (2011) Symerythrin Structures at Atomic Resolution and the Origins of Rubrerythrins and the Ferritin-Like Superfamily. J Mol Biol. 38. Ishii M, Kawasumi T, Igarashi Y, Kodama T, Minoda Y (1987) 2-Methylthio- 1,4-naphthoquinone, a unique sulfur-containing quinone from a thermophilic hydrogen-oxidizing bacterium, Hydrogenobacter thermophilus. J Bacteriol 169: 2380–2384. 39. Hoseki J, Yano T, Koyama Y, Kuramitsu S, Kagamiyama H (1999) Directed evolution of thermostable kanamycin-resistance gene: a convenient selection marker for Thermus thermophilus. J Biochem 126: 951–956. 40. Wolff SP (1994) Ferrous Ion Oxidation in Presence of Ferric Ion Indicator Xylenol Orange for Measurement of Hydroperoxides. Methods in Enzymology 233: 182–189. 41. Ikeda T, Nakamura M, Arai H, Ishii M, Igarashi Y (2009) Ferredoxin-NADP reductase from the thermophilic hydrogen-oxidizing bacterium, Hydrogenobacter thermophilus TK-6. FEMS Microbiol Lett 297: 124–130. 42. Ukeda H, Maeda S, Ishii T, Sawamura M (1997) Spectrophotometric assay for superoxide dismutase based on tetrazolium salt 39–1– (phenylamino)-carbonyl– 3, 4-tetrazolium]-bis(4-methoxy-6-nitro)benzenesulfonic acid hydrate reduction by xanthine-xanthine oxidase. Anal Biochem 251: 206–209. PLoS ONE | www.plosone.org 9 April 2012 | Volume 7 | Issue 4 | e34825