1、Anaerobic Microbes: Oxygen Detoxification Without Superoxide Dismutase,Presented by J. Spencer King and Seth I. Berger,Before we begin a few questions,Why dont pure anaerobes use SOD to remove superoxide, and Catalase to remove Peroxides?SOR in p. furiosus functions efficiently 75 C below the optima
2、l growth temperature of p. furiosus. Why do the authors of the paper believe this is so?,Berger-King 9.17.03,Verbosity to obscure ignorance,will not be tolerated.,Before we begin a few questions,Why dont pure anaerobes use SOD to remove superoxide, and Catalase to remove Peroxides?SOR in p. furiosus
3、 functions efficiently 75 C below the optimal growth temperature of p. furiosus. Why do the authors of the paper believe this is so?,Berger-King 9.17.03,Answers,Because SOD and Catalase both produce Oxygen.The only time that p. furiosus is exposed to oxygen is when the deep sea vent waters mix with
4、the surrounding cold seawater.,Brief Synopsis of Anaerobes,Aerotolerant Anaerobes O2 not Toxic O2 independent metabolism Facultative Anaerobes Can grow with or without O2 Change metabolism depending on O2 concentration Strict Anaerobes O2 is Toxic,Berger-King 9.17.03,Berger-King 9.17.03,About Pyroco
5、ccus furiosus,Archea Strict Anaerobe Hyperthermophilic Deep sea vents 70 to 100 C Up to 200 atm Irregular cocci shape Polar flagella group Hydrogen important in metabolism,Phylogenetic location,Berger-King 9.17.03,Superoxide O2-,Present in all aerobic environments Molecular oxygen has strong reducti
6、on activity Unstable free radical very toxic Reacts with H2O2 to from hydroxyl radicals Anaerobic organisms need protection too Exposure to oxygen sometime during life cycle is possible especially for microbes living in water, like Pyrococcus furiosus,Berger-King 9.17.03,Superoxide Dismutase and Cat
7、alase,Aerobic organism defense superoxide removal enzyme. SOD removes O2- Catalase then processes the H2O2 productIn some instances, non-specific peroxidases process the H2O2,Berger-King 9.17.03,SOD and catalase genes not present in completed anaerobic genomes circa 1999 Why?,SOD and Catalase in Ana
8、erobes,Berger-King 9.17.03,Strict Anaerobes need some other method of removing toxic oxygen species,Both produce Oxygen!,Requirements for SOD replacement,Remove superoxide before it becomes toxic Do not produce oxygen Be active under the conditions required by Pyrococcus furiosusData suggests the me
9、chanism for oxygen metabolism in Pyrococcus furiosus is Superoxide Reductase (SOR),Preliminary Steps,Select model organism P. furiosis: a strictly anaerobic hyperthermophile Isolate Putative Superoxide Dismutase(SOD) Multistep Column Chromatography Denaturing Gel Electrophoresis 14,000 Daltons Direc
10、t Chemical Analysis Contains Iron ( 0.5 atoms/mol) found using a inductively coupled argon plasma spectrometer (ICAP),Preliminary Steps,Clone gene NH2-terminal amino acid sequence information Locate in known genome 124 amino acid protein(14,323 Da) 14 bp downstream of rubredoxin (5895 Da) Previously
11、 purified iron-containing redox protein,Sequence Homologies,40% identity to desulfoferrodoxins iron containing COOH-terminal region 50% identity to neelaredoxinBoth are redox proteins and have been shown to posses SOD activity.,Detecting SOD Activity,Standard SOD Assay Steady-state generation of sup
12、eroxide Bovine Xanthine Oxidase + Xanthine Superoxide reduces Cytochrome C directly Measure A550 increase rate One unit of Activity is amount of protein needed to inhibit rate by 50%,Differences Between SOD and SOR,SOR does not oxidize Cytochrome C when it was initially reduced with Sodium Dithionit
13、e. It will subsequently oxidize it when a superoxide source is added. No Oxygen is generated Different behaviors in Assays,Bovine SOD vs P. furiosus SOR,Figure 1. Pyrococcus furiosus superoxide reductase is not a superoxide dismutase. Reactions were performed as described (18) in 1-ml cuvettes under
14、 aerobic conditions. Superoxide produced by xanthine (0.2 mM) and xanthine oxidase (3.4 g) directly reduced horse heart cytochrome c (20 M), as shown by the increase in absorbance at 550 nm (A550) (A and B, trace 1). Addition of bovine SOD (3.4 g, 1 U) inhibited the rate of reduction (A), trace 2. E
15、xcess SOD (40 U) prevented reduction completely (A), trace 3, and additional SOD (60 U) had no further effect (A), trace 4. P. furiosus SOR (2.5 g or 17 nM) also resulted in inhibition of reduction (B), trace 2, and more SOR (6.2 g) completely prevented reduction (B), trace 3. Addition of excess SOR
16、 (15 g) caused oxidation of the reduced cytochrome c that was present before SOR addition (B), trace 4. Time zero is when SOR or SOD was added to the cuvettes (approximately 90 s after addition of xanthine oxidase). Under these conditions, A550 = 0.178 for fully oxidized cytochrome c.,SOD behavior,S
17、OR behavior,Comparison of Different Assay Results,Other Genomes,Homologues are found in almost all complete genomes from anaerobes and a couple incomplete ones. 116 138 Residues with 20 70% identity Not found in any of the 16 available genomes of true aerobes (circa 1999),Rubredoxin,Adjacent to SOR
18、in P. Furiosus genome Known Electron Carrier Oxidized by Superoxide (opposed to cytochrome C which is reduced) Can be measured by A490 Also autooxidizes in air SOR increased rate of oxidation Effect of SOR required superoxide SOD decreased rate,Rubredoxin,Found in almost ever known anaerobic genome
19、despite function previously unknown. NADP-ruberedoxin oxioreductase reduced rubredoxin. Provides a mechanism for providing the reducing power for superoxide reduction. HOWEVER, still produces peroxide Must be removed, but not via O2 producing catalase,Bovine SOD vs P. furiosus SOR,Figure 2. Pyrococc
20、us furiosus SOR is a rubredoxin-superoxide oxidoreductase. Reactions were done as in Fig. 1, except that reduced rubredoxin replaced cytochrome c. Superoxide directly oxidized P. furiosus rubredoxin, as shown by the increase in A490. Rubredoxin (28 M) reduced by the addition of sodium dithionite (42
21、 M) slowly auto-oxidized upon exposure to air (A and B, trace 1). Addition of superoxide rapidly increased the rate of oxidation (A) and (B), trace 2. Catalase (10 U) had little effect (A), trace 5, whereas in a separate experiment, bovine SOD (1 U) abolished the effect of superoxide (A), trace 3, a
22、nd excess SOD (10 U) slowed down even the spontaneous oxidation of rubredoxin (A), trace 4. In contrast, addition of P. furiosus SOR (1.2 g) increased the rate of superoxide-dependent rubredoxin oxidation (B), trace 3, and the rate increased with additional SOR 1.2 g; (B), trace 4.,SOD behavior,SOR
23、behavior,Detoxification System,Figure 3. Model for detoxification of reactive oxygen species in anaerobes such as P. furiosus. Abbreviations are as follows: NROR, NAD(P)H-rubredoxin oxidoreductase; Rdred, reduced rubredoxin; Rdox, oxidized rubredoxin; XH2, unknown organic electron donor. Enzymes and
24、 proteins shown in bold were purified from P. furiosus; the others are hypothetical, based on genome sequence analyses.,Superoxide Reductase,SOR and NROR are both catalytically active and efficient at 25 C. 75 C cooler than P. furiosus growth temperature. Exposure to O2 in the deep sea vents is limi
25、ted to cold exposure to seawaterSOR and NROR together are a constitutively expressed defense mechanism which becomes active when the cell is exposed to a hostile environment.,Critiques,Sequence comparisons %-similarity is not shown. Sequence analysis methods not detailed What to do with the H2O2 ? O
26、nly hypothetical peroxidases Peroxidase activity at 25C? Formatting and layout Diagrams are informative but not attractive More detailed materials and methods Science publication requirements. Fortuitousness of Fig 1 line B,3,Bovine SOD vs P. furiosus SOR,Figure 1. Pyrococcus furiosus superoxide red
27、uctase is not a superoxide dismutase. Reactions were performed as described (18) in 1-ml cuvettes under aerobic conditions. Superoxide produced by xanthine (0.2 mM) and xanthine oxidase (3.4 g) directly reduced horse heart cytochrome c (20 M), as shown by the increase in absorbance at 550 nm (A550)
28、(A and B, trace 1). Addition of bovine SOD (3.4 g, 1 U) inhibited the rate of reduction (A), trace 2. Excess SOD (40 U) prevented reduction completely (A), trace 3, and additional SOD (60 U) had no further effect (A), trace 4. P. furiosus SOR (2.5 g or 17 nM) also resulted in inhibition of reduction
29、 (B), trace 2, and more SOR (6.2 g) completely prevented reduction (B), trace 3. Addition of excess SOR (15 g) caused oxidation of the reduced cytochrome c that was present before SOR addition (B), trace 4. Time zero is when SOR or SOD was added to the cuvettes (approximately 90 s after addition of
30、xanthine oxidase). Under these conditions, A550 = 0.178 for fully oxidized cytochrome c.,SOD behavior,SOR behavior,June 2002:“The evidence for superoxide reduction by SOR is now overwhelming and comes from a variety of anaerobic and microaerophilic species.”“The catalytic Fe site of SOR is structura
31、lly and electronically tuned to mediate superoxide reduction rather than oxidation.”“NAD(P)H, via rubredoxin and NAD(P)H:rubredoxin oxidoreductase is the source of reductant.”“What is still to be determined is the fate of the peroxide generated by the SOR reaction”Journal of Biological Inorganic Chemistry Issue: Volume 7, Number 6 Date: June 2002 Pages: 647 - 652,Follow up Article,
