Comparative study of SoxR activation by redox‐active compounds

SoxR from Escherichia coli and related enterobacteria is activated by a broad range of redox‐active compounds through oxidation or nitrosylation of its [2Fe–2S] cluster. Activated SoxR then induces SoxS, which subsequently activates more than 100 genes in response. In contrast, non‐enteric SoxRs directly activate their target genes in response to redox‐active compounds that include endogenously produced metabolites. We compared the responsiveness of SoxRs from Streptomyces coelicolor (ScSoxR), Pseudomonas aeruginosa (PaSoxR) and E. coli (EcSoxR), all expressed in S. coelicolor, towards natural or synthetic redox‐active compounds. EcSoxR responded to all compounds examined, whereas ScSoxR was insensitive to oxidants such as paraquat (Eh ?440 mV) and menadione sodium bisulphite (Eh ?45 mV) and to NO generators. PaSoxR was insensitive only to some NO generators. Whole‐cell EPR analysis of SoxRs expressed in E. coli revealed that the [2Fe–2S]¹⁺ of ScSoxR was not oxidizable by paraquat, differing from EcSoxR and PaSoxR. The mid‐point redox potential of purified ScSoxR was determined to be ?185 ± 10 mV, higher by ～ 100 mV than those of EcSoxR and PaSoxR, supporting its limited response to paraquat. The overall sensitivity profile indicates that both redox potential and kinetic reactivity determine the differential responses of SoxRs towards various oxidants.     

Cupryphans,metal‐binding,redox‐active,redesigned conopeptides

Contryphans are bioactive peptides, isolated from the venom of marine snails of the genus Conus, which are characterized by the short length of the polypeptide chain and the high degree of unusual post‐translational modifications. The cyclization of the polypeptide chain through a single disulphide bond, the presence of two conserved Pro residues, and the epimerization of a Trp/Leu residue confer to Contryphans a stable and well‐defined structure in solution, conserved in all members of the family, and tolerant to multiple substitutions. The potential of Contryphans as scaffolds for the design of redox‐active (macro)molecules was tested by engineering a copper‐binding site on two different variants of the natural peptide Contryphan‐Vn. The binding site was designed by computational modeling, and the redesigned peptides were synthesized and characterized by optical, fluorescence, electron spin resonance, and nuclear magnetic resonance spectroscopy. The novel peptides, named Cupryphan and Arg–Cupryphan, bind Cu²⁺ ions with a 1:1 stoichiometry and a K_d in the 100 nM range. Other divalent metals (e.g., Zn²⁺ and Mg²⁺) are bound with much lower affinity. In addition, Cupryphans catalyze the dismutation of superoxide anions with an activity comparable to other nonpeptidic superoxide dismutase mimics. We conclude that the Contryphan motif represents a natural robust scaffold which can be engineered to perform different functions, providing additional means for the design of catalytically active mini metalloproteins.     

A redox‐active isopropylmalate dehydrogenase functions in the biosynthesis of glucosinolates and leucine in Arabidopsis

We report a detailed functional characterization of an Arabidopsis isopropylmalate dehydrogenase (AtIPMDH1) that is involved in both glucosinolate biosynthesis and leucine biosynthesis. AtIPMDH1 shares high homology with enzymes from bacteria and yeast that are known to function in leucine biosynthesis. In plants, AtIPMDH1 is co‐expressed with nearly all the genes known to be involved in aliphatic glucosinolate biosynthesis. Mutation of AtIPMDH1 leads to a significant reduction in the levels of free leucine and of glucosinolates with side chains of four or more carbons. Complementation of the mutant phenotype by ectopic expression of AtIPMDH1, together with the enzyme’s substrate specificity, implicates AtIPMDH1 in both glucosinolate and leucine biosynthesis. This functional assignment is substantiated by subcellular localization of the protein in the chloroplast stroma, and the gene expression patterns in various tissues. Interestingly, AtIPMDH1 activity is regulated by a thiol‐based redox modification. This work characterized an enzyme in plants that catalyzes the oxidative decarboxylation step in both leucine biosynthesis (primary metabolism) and methionine chain elongation of glucosinolates (specialized metabolism). It provides evidence for the hypothesis that the two pathways share a common origin, and suggests a role for redox regulation of glucosinolate and leucine synthesis in plants.     

Actinorhodin is a redox‐active antibiotic with a complex mode of action against Gram‐positive cells

Actinorhodin is a blue‐pigmented, redox‐active secondary metabolite that is produced by the bacterium Streptomyces coelicolor. Although actinorhodin has been used as a model compound for studying secondary metabolism, its biological activity is not well understood. Indeed, redox‐active antibiotics in general have not been widely investigated at the mechanistic level. In this work, we have conducted a comprehensive chemical genetic investigation of actinorhodin's antibacterial effect on target organisms. We find that actinorhodin is a potent, bacteriostatic, pH‐responsive antibiotic. Cells activate at least three stress responses in the presence of actinorhodin, including those responsible for managing oxidative damage, protein damage and selected forms of DNA damage. We find that mutations in the Staphylococcus aureus walRKHI operon can confer low‐level resistance to actinorhodin, indicating possible targeting of the cell envelope. Our study indicates a complex mechanism of action, involving multiple molecular targets, that is distinct from other antibiotics.     

Factors affecting sensitivity of Staphylococcus aureus 196E to polyphosphates

The effect of polyphosphates (eight compounds) on growth of Staphylococcus aureus 196E in brain heart infusion broth was studied. The organism was sensitive (in decreasing order) to chain polyphosphates with 21, 3, 13, and 15 PO4 groups, and bactericidal effects were observed with 0.5% of these compounds. No inhibition was effected by PPi or a metaphosphate. The inhibitory effects were pH dependent, and bacterial sensitivity was highest at pH greater than 7.4. Initial populations affected the number of survivors. No growth was observed after 24 h at 35 degrees C when the initial cell population was less than 10(4) CFU/ml, and a 100- to 1,000-fold decline in cell numbers occurred when initial populations were higher than 10(4) CFU/ml. Sodium tripolyphosphate produced less inhibition after heat sterilization (15 min, 121 degrees C) than after filter sterilization, whereas sodium hexametaphosphate (n = 21) retained most of its antimicrobial activity after heat sterilization. Supplementation of broth with Mg2+ was effective in overcoming inhibition by 0.5% sodium tripolyphosphate, and an addition of 0.25 to 1.0 mM cation restored most of the growth. Inhibition was partially eliminated by Ca2+ and Fe2+, but not by Zn2+ or Mn2+.     

Factors affecting sensitivity of Staphylococcus aureus 196E to polyphosphates.

The effect of polyphosphates (eight compounds) on growth of Staphylococcus aureus 196E in brain heart infusion broth was studied. The organism was sensitive (in decreasing order) to chain polyphosphates with 21, 3, 13, and 15 PO4 groups, and bactericidal effects were observed with 0.5% of these compounds. No inhibition was effected by PPi or a metaphosphate. The inhibitory effects were pH dependent, and bacterial sensitivity was highest at pH greater than 7.4. Initial populations affected the number of survivors. No growth was observed after 24 h at 35 degrees C when the initial cell population was less than 10(4) CFU/ml, and a 100- to 1,000-fold decline in cell numbers occurred when initial populations were higher than 10(4) CFU/ml. Sodium tripolyphosphate produced less inhibition after heat sterilization (15 min, 121 degrees C) than after filter sterilization, whereas sodium hexametaphosphate (n = 21) retained most of its antimicrobial activity after heat sterilization. Supplementation of broth with Mg2+ was effective in overcoming inhibition by 0.5% sodium tripolyphosphate, and an addition of 0.25 to 1.0 mM cation restored most of the growth. Inhibition was partially eliminated by Ca2+ and Fe2+, but not by Zn2+ or Mn2+.     

Factors affecting the redox state of bovine epididymal spermatozoa.

The oxidation-reduction state of bovine epididymal spermatozoa was determined in vitro by fluorescence spectroscopy and by direct chemical analysis. Enhanced NADH fluorescence in sperm was observed with the onset of anaerobiosis in the sample cuvette. However, part of this increased fluorescence was temporary and a stable pyridine nucleotide fluorescence was not reached until 25 min after the onset of anaerobiosis. The transient was not paralleled by an equivalent increase in cellular NADH as measured by absorption spectroscopy. Hypotonic treatment of sperm, which removed the plasma membrane, liberated greater than 50% of the cellular NAD and that remaining was reduced by rotenone addition, indicating its mitochondrial location. Hypotonically treated sperm did not demonstrate a transient fluorescence above that due to the increases in NADH from anaerobiosis. Addition of pyruvate to anaerobic sperm resulted in a rapid decrease in fluorescence that corresponded to NADH oxidation coupled with the reduction of pyruvate to lactate. The duration of this oxidized state was dependent on the amount of pyruvate added. Analysis of cellular NAD under similar conditions confirmed this result. The pyridine nucleotides of hypotonically treated cells were also oxidized by pyruvate but were not reduced by added glucose as in untreated sperm. These results indicate that pyruvate reduction served to balance reducing equivalents and temporarily reoxidized the intracellular milieu of the anaerobic spermatozoon. The data also support the hypothesis that pyruvate and lactate can serve as reducing equivalent carriers between cytosol and mitochondria.     

Systems biology defines the biological significance of redox‐active proteins during cellulose degradation in an aerobic bacterium

Microbial depolymerization of plant cell walls contributes to global carbon balance and is a critical component of renewable energy. The genomes of lignocellulose degrading microorganisms encode diverse classes of carbohydrate modifying enzymes, although currently there is a paucity of knowledge on the role of these proteins in vivo. We report the comprehensive analysis of the cellulose degradation system in the saprophytic bacterium Cellvibrio japonicus. Gene expression profiling of C. japonicus demonstrated that three of the 12 predicted β‐1,4 endoglucanases (cel5A, cel5B, and cel45A) and the sole predicted cellobiohydrolase (cel6A) showed elevated expression during growth on cellulose. Targeted gene disruptions of all 13 predicted cellulase genes showed that only cel5B and cel6A were required for optimal growth on cellulose. Our analysis also identified three additional genes required for cellulose degradation: lpmo10B encodes a lytic polysaccharide monooxygenase (LPMO), while cbp2D and cbp2E encode proteins containing carbohydrate binding modules and predicted cytochrome domains for electron transfer. CjLPMO10B oxidized cellulose and Cbp2D demonstrated spectral properties consistent with redox function. Collectively, this report provides insight into the biological role of LPMOs and redox proteins in cellulose utilization and suggests that C. japonicus utilizes a combination of hydrolytic and oxidative cleavage mechanisms to degrade cellulose.     

Factors affecting sensitivity of group B streptococci to an exogenous murein hydrolase

Group B streptococci treated with cell wall synthesis inhibitors (penicillin or vancomycin) or by a variety of membrane-acting agents are sensitized to the lytic action of exogenous M1 muramidase. Muramidase without a sensitizing agent caused rupture of bacterial chains only, accompanied by the release of a small amount of cell wall peptidoglycan label and an increase of the number of colony-forming units. In combination with sensitizing agents the exogenous muramidase appeared to initiate hydrolysis of biosynthetically new peptidoglycan. Treatment of the cells with chloramphenicol or starvation for nutritionally required amino acids suppressed the rate of cell lysis and peptidoglycan hydrolysis during subsequent sensitization and muramidase treatment of the bacteria. Purified cell walls prepared from the amino acid starved cells were also hydrolyzed with a slower rate by muramidase. It is suggested that agents sensitizing the bacteria to the exogenous muramidase act by perturbing or removing some nonmurein components of the cell envelope which protect the peptidoglycan from the activity of exogenous enzyme. Agents increasing resistance against exogenous muramidase may also cause some alteration in peptidoglycan structure.     

Factors affecting catalase level and sensitivity to hydrogen peroxide in Escherichia coli.

Composition of the culture medium, growth phase, and temperature play important roles in the sensitivity of Escherichia coli to H2O2. The medium and growth phase affected the sensitivity of the cells to H2O2 by modifying the amount of catalase synthesized by them, whereas the effect of temperature was due to the thermolability of the enzyme. Since catalase is unstable in the presence of its substrate, the correlation between the catalase level in the cells and their sensitivity to H2O2 could be observed only when the H2O2 concentration was not excessive in proportion to the amount of catalase.     

Generation of hydroxyl radicals and other redox active compounds in the sea water exposed to heat

The process of heat-induced generation of hydroxyl radicals in seawater was studied using coumarin-3-carboxylic acid as a fluorescent detector of .OH. The rate constants of .OH thermoproduction were determined in the temperature range of 40 to 60 degrees C. The activation energy for thermal production of .OH in seawater was 25 kcal/mol. It was found that this reaction is affected by .OH scavengers, additional oxygenation of solution, catalase, and iron chelators. Deferoxamine (desferal), an iron chelator used in therapy, enhanced the rate constant for this reaction many-fold. It was shown that heat-induced .OH production in seawater at 28 degrees C is about 1% of the .OH photochemical production caused by maximal daytime irradiation with natural sunlight. The rate of .OH thermoproduction at 28 degrees C was three orders of magnitude greater than the average rate of .OH production in water due to natural background radiation. The thermally induced generation of an unidentified reducing agent(s) in seawater was investigated by the use of Ellman's reagent. The kinetic parameters of the process were evaluated.     

Scale‐up of citric acid fermentation by redox potential control

To obtain high citric acid productivity in Aspergillus niger fermentation on beet molasses substrate, a certain redox potential profile with two maxima (260 and 280 mV) and two minima (180 and 80 mV) must be maintained. The most effective regulation of redox potential is by regulation of aeration and agitation. It has been shown that control of redox potential by aeration and agitation is a most successful method for scale‐up from 10‐L laboratory scale to the 100‐ and 1000‐L pilot‐plant scale, even in geometrically dissimilar stirred‐tank reactors. © 1999 John Wiley & Sons, Inc. Biotechnol Bioeng 64: 552–557, 1999.     

Factors affecting antibacterial activity of hop compounds and their derivatives

W.J. SIMPSON AND A.R.W. SMITH. 1992. The antibacterial effect of weak acids derived from the hop plant ( Humulus lupulus L.) increased with decreasing pH. Analysis of the minimum inhibitory concentration of such compounds against Lactobacillus brevis IFO 3960 over pH4–7 suggests that undissociated molecules were mainly responsible for inhibition of bacterial growth. The antibacterial activity of trans -isohumulone was ca 20 times greater than that of humulone, 11 times greater than that of colupulone and nine times greater than that of trans -humulinic acid when the degree of ionization was taken into account. Monovalent cations (K+, Na+, NH₄+, Rb+, Li+) stimulated antibacterial activity of trans -isohumulone but the effect was smaller than that observed with H+. The response to divalent cations varied: Ca2+ had little effect on antibacterial activity, whereas Mg2+ reduced activit. Lipid materials and β-cyclodextrin also antagonized the antibacterial action of trans -isohumulone.     

Plant‐based compounds with potential as push‐pull stimuli to manage behavior of leaf‐cutting ants

Leaf‐cutting ants are a serious pest of young forestry plantations. Currently, the main control method is the use of broad‐spectrum insecticides, which have a negative effect on non‐target organisms and the environment. In this work, plant‐based compounds were evaluated in laboratory assays with Acromyrmex ambiguus Emery (Hymenoptera: Formicidae) for their potential use as repellent and attractant stimuli to be used in a push‐pull strategy. Farnesol, a sesquiterpene present in many essential oils, was tested as a repellent at doses of 10, 50, and 100 mg. Its distance of action was studied by comparing the repellent effect of farnesol in a situation in which ants had to touch the farnesol in order to reach the food source in comparison to when ants could reach the food source without getting into direct contact with it. Different parts of the orange fruit (pulp and peel) were evaluated and compared as attractants, given that citrus‐based baits are among the most popular attractants used. Results from laboratory bioassays indicated that farnesol is repellent at doses of 50 mg and acts upon contact or at a very short distance. Furthermore, orange pulp was more attractive than the peel, and volatile compounds were highly responsible for the attraction. When both stimuli were tested simultaneously in a laboratory experiment, repellency of farnesol was enhanced in the presence of orange pulp odor. When tested in a field push‐pull experiment, the results also showed a good repellent effect of farnesol as well as an attractant effect of the orange pulp. These results encourage long‐term studies with these substances in a field setting and suggest that repellents can be enhanced by the use of attractants to manage leaf‐cutting ants behavior.     

Modeling conformational redox‐switch modulation of human succinic semialdehyde dehydrogenase

Succinic semialdehyde dehydrogenase (SSADH) converts succinic semialdehyde (SSA) to succinic acid in the mitochondrial matrix and is involved in the metabolism of the inhibitory neurotransmitter γ‐aminobutyric acid (GABA). The molecular structure of human SSADH revealed the intrinsic regulatory mechanism—redox‐switch modulation—by which large conformational changes are brought about in the catalytic loop through disulfide bonding. The crystal structures revealed two SSADH conformations, and computational modeling of transformation between them can provide substantial insights into detailed dynamic redox modulation. On the basis of these two clear crystal structures, we modeled the conformational motion between these structures in silico. For that purpose, we proposed and used a geometry‐based coarse‐grained mathematical model of long‐range protein motion and the related modeling algorithm. The algorithm is based on solving the special optimization problem, which is similar to the classical Monge–Kantorovich mass transportation problem. The modeled transformation was supported by another morphing method based on a completely different framework. The result of the modeling facilitates better interpretation and understanding of the SSADH biological role. Proteins 2015; 83:2217–2229. © 2015 Wiley Periodicals, Inc.     

Factors affecting antibacterial activity of hop compounds and their derivatives.

The antibacterial effect of weak acids derived from the hop plant (Humulus lupulus L.) increased with decreasing pH. Analysis of the minimum inhibitory concentration of such compounds against Lactobacillus brevis IFO 3960 over pH 4-7 suggests that undissociated molecules were mainly responsible for inhibition of bacterial growth. The antibacterial activity of trans-isohumulone was ca 20 times greater than that of humulone, 11 times greater than that of colupulone and nine times greater than that of trans-humulinic acid when the degree of ionization was taken into account. Monovalent cations (K+, Na+, NH4+, Rb+, Li+) stimulated antibacterial activity of trans-isohumulone but the effect was smaller than that observed with H+. The response to divalent cations varied: Ca2+ had little effect on antibacterial activity, whereas Mg2+ reduced activity. Lipid materials and beta-cyclodextrin also antagonized the antibacterial action of trans-isohumulone.