The second coordination sphere of FIH controls hydroxylation

The factor inhibiting HIF (FIH) is a proximate oxygen sensor for human cells, hydroxylating Asn(803) within the α-subunit of the hypoxia inducible factor (HIF). FIH is an α-ketoglutatrate (αKG)-dependent, non-heme Fe(II) dioxygenase, in which Fe(II) is coordinated by a (His(2)Asp) facial triad, αKG, and H(2)O. Hydrogen bonding among the facial triad, the HIF-Asn(803) side chain, and various second-sphere residues suggests a functional role for the second coordination sphere in tuning the chemistry of the Fe(II) center. Point mutants of FIH were prepared to test the functional role of the αKG-centered (Asn(205) and Asn(294)) or HIF-Asn(803)-centered (Arg(238) and Gln(239)) second-sphere residues. The second sphere was tested for local effects on priming Fe(II) to react with O(2), oxidative decarboxylation, and substrate positioning. Steady-sate kinetics were used to test for overall catalytic effects; autohydroxylation rates were used to test for priming and positioning, and electronic spectroscopy was used to assess the primary coordination sphere and the electrophilicity of αKG. Asn(205) → Ala and Asn(294) → Ala mutants exhibited diminished rates of steady-state turnover, while minimally affecting autohydroxylation, consistent with impaired oxidative decarboxylation. Blue-shifted metal to ligand charge transfer transitions for (Fe+αKG)FIH indicated that these point mutations destabilized the π* orbitals of αKG, further supporting a slowed rate of oxidative decarboxylation. The Arg(238) → Met mutant exhibited steady-state rates too low to measure and diminished product yields, suggesting impaired substrate positioning or priming; the Arg(238) → Met mutant was capable of O(2) activation for the autohydroxylation reaction. The Gln(239) → Asn mutant exhibited significantly slowed steady-state kinetics and diminished product yields, suggesting impaired substrate positioning or priming. As HIF binding to the Gln(239) → Asn mutant stimulated autohydroxylation, it is more likely that this point mutant simply mispositions the HIF-Asn(803) side chain. This work combines kinetics and spectroscopy to show that these second-sphere hydrogen bonds play roles in promoting oxidative decarboxylation, priming Fe(II) to bind O(2), and positioning HIF-Asn(803).     

Melatonin reverses the oxidative stress and mitochondrial dysfunction caused by LETM1 silencing

LETM1 is a mitochondrial inner‐membrane protein, which is encoded by a gene present in a locus of 4p, which, in turn, is deleted in the Wolf–Hirschhorn Syndrome, and is assumed to be related to its pathogenesis. The cellular damage caused by the deletion is presumably related to oxidative stress. Melatonin has many beneficial roles in protecting mitochondria by scavenging reactive oxygen species, maintaining membrane potential, and improving functions. The aim of this study was to investigate the effects of melatonin administration to LETM1‐silenced mouse embryonic fibroblast cells as a cellular model for LETM1 deficiency. We transfected mouse embryonic fibroblast cells with a pair of siRNA against LETM1 and monitored the oxidative stress and mitochondrial functions with or without melatonin addition. MnSOD expression and aconitase activity decreased and oxidized protein levels increased in LETM1‐silenced cells. LETM1 suppression did not alter the expression of OXPHOS complexes, but the oxygen consumption rates decreased significantly; however, this change was not related to complex I but instead involved complex IV and complex II. Melatonin supplementation effectively normalized the parameters studied, including the oxygen consumption rate. Our findings identified a novel effect of LETM1 deficiency on cellular respiration via complex II as well as a potential beneficial role of melatonin treatment. On the other hand, these effects may be specific to the cell line used and need to be verified in other cell lines.     

Continuous flow membrane-less air cathode microbial fuel cell with spunbonded olefin diffusion layer

The power production performance of a membrane-less air-cathode microbial fuel cell was evaluated for 53 days. Anode and cathode electrodes and the micro-fiber cloth separator were configured by sandwiching the separator between two electrodes. In addition, the air-facing side of the cathode was covered with a spunbonded olefin sheet instead of polytetrafluoroethylene (PTFE) coating to control oxygen diffusion and water loss. The configuration resulted in a low resistance of about 4Ω and a maximum power density of 750 mW/m2. However, as a result of a gradual decrease in the cathode potential, maximum power density decreased to 280 mW/m2. The declining power output was attributed to loss of platinum catalyst (8.26%) and biomass growth (38.44%) on the cathode. Coulombic efficiencies over 55% and no water leakage showed that the spunbonded olefin sheet covering the air-facing side of the cathode can be a cost-effective alternative to PTFE coating.     

Efficacy of tar oil recovered during slow pyrolysis of macadamia nut shells

Decay and termite resistance of wood treated with tar oil obtained from a commercial pyrolysis process of macadamia nut shells was evaluated. Vacuum-treated pinewood specimens were subjected to two brown- and two white-rot fungi based on the soil-block test method specified by the American Wood Protection Association after a 10-day-leaching process. Treated specimens were also subjected to the subterranean termite attack according to Japanese Industrial Standards (JIS) for 3 weeks under laboratory conditions. In the study, growth inhibition of selected fungi with the tar oil was also tested in vitro. Treated wood specimens at a retention level of 460 kg m⁻³ showed good protection against all the fungi tested. Mass losses in leached specimens were less than those observed in unleached specimens. Similar results were seen when the specimens were subjected to termite attack. Inhibition tests showed that higher concentrations of the tar oil are critical for inhibition of the brown-rot fungi compared to the concentrations required to impede the white-rot and sap-staining fungi tested.     

Cell wall-degrading enzymes and pectin solubility and depolymerization in immature and ripe watermelon (Citrullus lanatus) fruit in response to exogenous ethylene

Watermelon fruit have been shown to be extremely sensitive to exogenous ethylene, exhibiting acute symptoms of whole-fruit softening and placental-tissue water-soaking following short periods of exposure to the gas. This study addressed the firmness, specific activities of cell wall hydrolases, and solubility and molecular mass properties of polyuronides in placental tissue in response to treatment of intact fruit with ethylene. Watermelon fruit were harvested at the immature and full-ripe stages and exposed to 50 µl l⁻¹ ethylene for 6 days at 20°C. The firmness of placental tissue from ethylene-treated ripe and immature fruit decreased nearly 80% during 6 days of ethylene exposure, whereas the firmness of placental tissue from fruit maintained in air remained relatively constant up to day 3 and then decreased slightly (12%) during the following 3 days of storage. Although ethylene treatment in some cases influenced the levels of extractable placental-tissue polygalacturonase (EC 3.2.1.15), pectinmethylesterase (EC 3.2.1.11), and α -(EC 3.2.1.22) and β -galactosidase (EC 3.2.1.23) specific activities, these effects were not observed for fruit of both developmental stages and appeared not to be directly involved in the water–soaking syndrome. Symptoms of water-soaking were accompanied by increases in the levels of water- and CDTA ( trans -1,2-cyclohexanediamine- N,N,N',N' -tetraacetic acid)-soluble polyuronides and significant molecular mass downshifts in polyuronides in both immature and ripe watermelon fruit. Polyuronide depolymerization in ethylene-treated ripe fruit was extensive. The parallel trends of enzyme changes in ethylene- compared with air-treated fruit indicate that extractable enzyme levels are not associated with development of the water-soaking disorder. The potential involvement of membrane dysfunction in the water-soaking phenomenon is discussed.     

Purification and characterization of a highly thermostable α-<Emphasis Type="SmallCaps">l</Emphasis>-Arabinofuranosidase from <Emphasis Type="Italic">Geobacillus caldoxylolyticus</Emphasis> TK4

The gene encoding an α-l-arabinofuranosidase from Geobacillus caldoxylolyticus TK4, AbfATK4, was isolated, cloned, and sequenced. The deduced protein had a molecular mass of about 58 kDa, and analysis of its amino acid sequence revealed significant homology and conservation of different catalytic residues with α-l-arabinofuranosidases belonging to family 51 of the glycoside hydrolases. A histidine tag was introduced at the N-terminal end of AbfATK4, and the recombinant protein was expressed in Escherichia coli BL21, under control of isopropyl-β-D-thiogalactopyranoside-inducible T7 promoter. The enzyme was purified by nickel affinity chromatography. The molecular mass of the native protein, as determined by gel filtration, was about 236 kDa, suggesting a homotetrameric structure. AbfATK4 was active at a broad pH range (pH 5.0–10.0) and at a broad temperature range (40–85°C), and it had an optimum pH of 6.0 and an optimum temperature of 75–80°C. The enzyme was more thermostable than previously described arabinofuranosidases and did not lose any activity after 48 h incubation at 70°C. The protein exhibited a high level of activity with p-nitrophenyl-α-l-arabinofuranoside, with apparent K _m and V _max values of 0.17 mM and 588.2 U/mg, respectively. AbfATK4 also exhibited a low level of activity with p-nitrophenyl-β-d-xylopyranoside, with apparent K _m and V _max values of 1.57 mM and 151.5 U/mg, respectively. AbfATK4 released l-arabinose only from arabinan and arabinooligosaccharides. No endoarabinanase activity was detected. These findings suggest that AbfATK4 is an exo-acting enzyme.     

Inhibitory effects of nitrogen oxides on a mixed methanogenic culture

The effect of nitrate, nitrite, nitric oxide (NO), and nitrous oxide on a mixed, mesophilic (35 degrees C) methanogenic culture was investigated. Short-term inhibition assays were conducted at a concentration range of 10-350 mg N/L nitrate, 17-500 mg N/L nitrite, 0.02-0.8 mg N/L aqueous NO, and 19-191 mg N/L aqueous nitrous oxide. Simultaneous methane production and N-oxide reduction was observed in 10 and 30 mg N/L nitrate and 0.02 mg N/L aqueous NO-amended cultures. However, addition of N-oxide resulted in immediate cessation of methanogenesis in all other cultures. Methanogenesis completely recovered subsequent to the complete reduction of N-oxides to nitrogen gas in all N-oxide-amended cultures, with the exception of the 500 mg N/L nitrite- and 0.8 mg N/L aqueous NO-amended cultures. Partial recovery of methanogenesis was observed in the 500 mg N/L nitrite-amended culture in contrast to complete inhibition of methanogenesis in the 0.8 mg N/L aqueous NO-amended culture. Accumulation of volatile fatty acids was observed in both cultures at the end of the incubation period. Among all N-oxides, NO exerted the most and nitrate exerted the least inhibitory effect on the fermentative/methanogenic consortia. The effect of multiple additions of nitrate (300 mg N/L) on the same methanogenic culture was also investigated. Long-term exposure of the methanogenic culture to nitrate resulted in an increase of N-oxide reduction rates and decrease of methane production rates, which was attributed to changes in the microbial community structure due to nitrate addition.     

Effect of sulfide on nitrate reduction in mixed methanogenic cultures

The effect of sulfide on nitrate reduction and methanogenesis was investigated in two mixed, mesophilic (35 degrees C) methanogenic cultures: sulfide-free and sulfide-acclimated (67 mg S/L total sulfide). A mixture of dextrin/peptone served as the carbon/electron donor source for the two stock cultures, as well as in all assays reported here. The sulfide-free enriched culture was amended with both nitrate (75-350 mg N/L) and sulfide (10-100 mg S/L). Denitrification was the predominant pathway at all sulfide levels tested and methanogenesis did not recover in any of the sulfide- and nitrate-amended cultures, except in the 10 mg S/L culture. Accumulation of denitrification intermediates such as NO and N(2)O took place, which irreversibly inhibited the methanogens and resulted in the complete cessation of methane production. In contrast, conversion of nitrate to nitrite and then to ammonia via dissimilatory nitrate reduction to ammonia (DNRA) prevented the accumulation of denitrification intermediates and led to the recovery of methanogenesis in the nitrate-amended, sulfide-acclimated, mixed methanogenic culture. The effect of the COD/N value on nitrate reduction was assessed with the sulfide-acclimated, methanogenic culture at COD/N values of 10, 20, and 60. As the COD/N value increased, the fraction of nitrate reduced through DNRA also increased. The results of this study have significant implications relative to the combined anaerobic treatment of carbon-, nitrogen-, and/or sulfur-bearing wastes.