Cyclic voltammetry, square wave voltammetry or electrochemical impedance spectroscopy? Interrogating electrochemical approaches for the determination of electron transfer rates of immobilized redox proteins

In this article, we cross-examine three well-established electrochemical approaches, namely cyclic voltammetry (CV), cyclic square-wave voltammetry (SWV) and electrochemical impedance spectroscopy (EIS) to dissect the electron transfer (ET) rate of electrostatically immobilized cytochrome c on Ag electrodes. A detailed analysis supported by simulations of redox transition provided three distinct values for the heterogeneous electron transfer (HET) rate constant of cyt c interfaced on COOH-terminated C₁₀-long alkanethiol, i.e., k_HET= 47.8 (±2,91) s^-1 in CV, k_HET= 64.8 (±1,27) s^-1 in SWV, and k_HET= 26.5 s^-1 in EIS. We discuss the obtained discrepancies obtained from electrochemical methods and compare them with the data from spectro-electrochemical experiments. A comprehensive selection list is created from which the most applicable approach can be chosen for studying proteins of interest. CV is most applicable to study the interfaced proteins exhibiting k_HET of ca. 0.5 - 70 s^-1, SWV is suitable for a broader range of k_HET of 5 - 120 s^-1 and EIS for k_HET of 0.5 to 5 s^-1 if alkanethiols are used as immobilization strategy.

ENOX2 NADH Oxidase: A BCR-ABL1-Dependent Cell Surface and Secreted Redox Protein in Chronic Myeloid Leukemia

Objective

Chronic myeloid leukemia (CML) is a disease caused by the acquisition of BCR-ABL1 fusion in hematopoietic stem cells. In this study, we focus on the oncofetal ENOX2 protein as a potential secretable biomarker in CML.

Materials and Methods

We used cell culture, western blot, quantitative RT-PCR, ELISA, transcriptome analyses, and bioinformatics techniques to investigate ENOX2 mRNA and protein expression.

Results

Western blot analyses of UT-7 and TET-inducible Ba/F3 cell lines demonstrated the upregulation of the ENOX2 protein. BCR-ABL1 was found to induce ENOX2 overexpression in a kinase-dependent manner. We confirmed increased ENOX2 mRNA expression in a cohort of CML patients at diagnosis. In a series of CML patients, ELISA assays showed a highly significant increase of ENOX2 protein levels in the plasma of patients with CML compared to controls. Reanalyzing the transcriptomic dataset confirmed ENOX2 mRNA overexpression in the chronic phase of the disease. Bioinformatic analyses identified several genes whose mRNA expressions were positively correlated with ENOX2 in the context of BCR-ABL1. Some of them encode proteins involved in cellular functions compatible with the growth deregulation observed in CML.

Conclusion

Our results highlight the upregulation of a secreted redox protein in a BCR-ABL1-dependent manner in CML. The data presented here suggest that ENOX2, through its transcriptional mechanism, plays a significant role in BCR-ABL1 leukemogenesis.

Coupling of membrane-based bubbleless micro-aeration for 2,4-dinitrophenol degradation in a hydrolysis acidification reactor

Micro-aeration hydrolysis acidification (HA) is an effective method to enhance the removal of toxic and refractory organic matter, but the difficulty in stable dosing control of trace oxygen limits its wide application. Membrane-based bubbleless aeration has been proved as an ideal aeration method because of its higher oxygen transfer rate, more uniform mass transfer, and lower cost than HA. However, the available information on its application in HA is limited. In this study, membrane-based bubbleless micro-aeration coupled with hydrolysis acidification (MBL-MHA) was exploited to investigate the performance of 2,4-dinitrophenol (2,4-DNP) degradation via comparing it with bubble micro-aeration HA (MHA) and anaerobic HA. The results indicated that the performances in MBL-MHA and MHA were higher than those in HA during the experiment. 2,4-DNP degradation rates under redox microenvironments caused by counter-diffusion in MBL-MHA (84.43∼97.28%) were higher than those caused by co-diffusion in MHA (82.41∼94.71%) under micro-aeration of 0.5-5.0 mL air/min. The 2,4-DNP degradation pathways in MBL-MHA were nitroreduction, deamination, aromatic ring cleavage, and fermentation, while those in MHA were hydroxylation, aromatic ring cleavage, and fermentation. Reduction/oxidation-related, interspecific electron transfer-related species, and fermentative species in MBL-MHA were more abundant than that in MHA. Ultimately, more reducing/oxidizing forces formed by more redox proteins/enzymes from these rich species could enhance 2,4-DNP degradation in MBL-MHA.

Electrochemical and phylogenetic comparisons of oxygen-reducing electroautotrophic communities

The mechanisms of extracellular electron transfer and the microbial taxa associated with the observed electroactivity are fundamental to oxygen-reducing microbial cathodes. Here we confirmed the apparent 'electroautotrophic' behavior of electroactive biofilms (EABs) grown on carbon electrodes at + 0.20V vs. Ag/AgCl under air. The EABs catalyzed O₂ electroreduction into water ─ as demonstrated by a rotating ring disc experiment ─ and performed quasi-reversible heterogeneous electron transfer (HET). By using electrodes of low surface capacitance, we report for the first time nonturnover redox peaks that are very likely intrinsic to the redox protein(s) performing the HET. Because the formal potential of redox proteins is pH-dependent, we investigated the evolution of characteristic potentials of the EABs with the solution pH: (i) open circuit potential, (ii) half-wave potential, and (iii) averaged peak potential of nonturnover cyclic voltammograms, which is presumably the formal potential of the primary electron acceptor(s) for the community. In addition to describing the redox thermodynamics behind HET, we suggest that the corresponding data provides an electrochemical fingerprint that could help in comparing the electroactivity of diverse microbial communities. The taxon with the highest relative abundance in our EABs was an unclassified member of the Gammaproteobacteria that was phylogenetically closely related to most other abundant unclassified Gammaproteobacteria commonly reported in EABs reducing O₂ at high potentials, further suggesting that those taxa are responsible for the bioelectroactivity. Phylogenetic and electrochemical similarities between reported EABs jointly support the hypothesis that similar biomolecular mechanisms may be responsible for this highly probable electroautotrophic metabolism.

Molecular mechanisms of electron transfer employed by native proteins and biological-inorganic hybrid systems

Recent advances in enzymatic electrosynthesis of desired chemicals in biological-inorganic hybrid systems has generated interest because it can use renewable energy inputs and employs highly specific catalysts that are active at ambient conditions. However, the development of such innovative processes is currently limited by a deficient understanding of the molecular mechanisms involved in electrode-based electron transfer and biocatalysis. Mechanistic studies of non-electrosynthetic electron transferring proteins have provided a fundamental understanding of the processes that take place during enzymatic electrosynthesis. Thus, they may help explain how redox proteins stringently control the reduction potential of the transferred electron and efficiently transfer it to a specific electron acceptor. The redox sites at which electron donor oxidation and electron acceptor reduction take place are typically located in distant regions of the redox protein complex and are electrically connected by an array of closely spaced cofactors. These groups function as electron relay centers and are shielded from the surrounding environment by the electrically insulating apoporotein. In this matrix, electrons travel via electron tunneling, i.e. hopping between neighboring cofactors, over impressive distances of upto several nanometers and, as in the case of the Shewanella oneidensis Mtr electron conduit, traverse the bacterial cell wall to extracellular electron acceptors such as solid ferrihydrite. Here, the biochemical strategies of protein-based electron transfer are presented in order to provide a basis for future studies on the basis of which a more comprehensive understanding of the structural biology of enzymatic electrosynthesis may be attained.

A single mutation converts Alr5027 from cyanobacteria Nostoc sp. PCC 7120 to a heme-binding protein with heme-degrading ability

HutZ from Vibrio cholerae (VcHutZ) is a dimeric protein that catalyzes oxygen-dependent degradation of heme. The reaction mechanism is the same as that of canonical heme oxygenase (HO), but the structure of HutZ is quite different from that of HO. Thus, we postulate that HutZ has evolved via a different pathway from that of HO. The Alr5027 protein from cyanobacteria possessing proteins potentially related to ancestral proteins utilizing O₂ in enzymatic reactions is homologous to HutZ family proteins (67% similarity), but the heme axial ligand of HutZ is not conserved in Alr5027. To investigate whether Alr5027 can bind and degrade heme, we expressed Alr5027 in Escherichia coli and purified it. Although Alr5027 did not bind heme, replacement of Lys164, corresponding to the heme axial ligand of HutZ, with histidine conferred heme-binding capability. The K164H mutant produced verdoheme in the reaction with H₂O₂, indicating acquisition of heme-degradation ability. Among the mutants, the K164H mutant produced verdoheme most efficiently. Although the K164H mutant did not degrade heme through ascorbic acid, biliverdin, the final product of VcHutZ, was formed by treatment of verdoheme with ascorbic acid. An analysis of Trp103 fluorescence indicated elongation of the distance between protomers in this mutant compared with VcHutZ-the probable cause of the inefficiency of ascorbic acid-supported heme-degradation activity. Collectively, our findings indicate that a single lysine-to-histidine mutation converted Alr5027 to a heme-binding protein that can form verdoheme through H₂O₂, suggesting that HutZ family proteins have acquired the heme-degradation function through molecular evolution from an ancestor protein of Alr5027.

Regulation of thiol metabolism as a factor that influences the development and storage capacity of beech seeds

Seeds are the basis of propagation for the common beech (Fagus sylvatica L.), but the seed set of the beech is unsteady, with 5-10 years between abundant crops. Beech seeds are very difficult to store and lose their viability quickly even in optimum storage conditions. To date, it has not been possible to determine factors indicative of the aging process and the loss of viability of beech seeds during storage. To address this important economic challenge and interesting scientific problem, we analyzed the adjustment of the redox state during the development and storage of seeds. Many metabolic processes are based on reduction and oxidation reactions. Thiol proteins control and react to the redox state in the cells. The level of thiol proteins increased during seed maturation and decreased during storage. Gel-based redox proteomics identified 17 proteins in beech seeds during development. The proteins could be assigned to processes like metabolism and antioxidant functions. During storage, the number of proteins decreased to only six, i.e., oxidoreductases, peptidases, hydrolases and isomerases. The occurrence of peroxiredoxins (PRX) as thiol peroxidases and redox regulators indicates an important role of cytosolic 1CysPRX and PRXIIC, mitochondrial PRXIIF, and plastidic PRXIIE, 2CysPRX, and PRXQ in beech seeds during development and storage. Particularly, 2CysPRX was present in beech seeds during development and storage and may perform an important function in regulation of the redox state during both seed development and storage. The role of thiol proteins in the regulation of the redox state during the development and storage of beech seeds is discussed.

Taxonomic distribution, structure/function relationship and metabolic context of the two families of sulfide dehydrogenases: SQR and FCSD

Hydrogen sulfide (H₂S) is a versatile molecule with different functions in living organisms: it can work as a metabolite of sulfur and energetic metabolism or as a signaling molecule in higher Eukaryotes. H₂S is also highly toxic since it is able to inhibit heme cooper oxygen reductases, preventing oxidative phosphorylation. Due to the fact that it can both inhibit and feed the respiratory chain, the immediate role of H₂S on energy metabolism crucially relies on its bioavailability, meaning that studying the central players involved in the H₂S homeostasis is key for understanding sulfide metabolism. Two different enzymes with sulfide oxidation activity (sulfide dehydrogenases) are known: flavocytochrome c sulfide dehydrogenase (FCSD), a sulfide:cytochrome c oxidoreductase; and sulfide:quinone oxidoreductase (SQR). In this work we performed a thorough bioinformatic study of SQRs and FCSDs and integrated all published data. We systematized several properties of these proteins: (i) nature of flavin binding, (ii) capping loops and (iii) presence of key amino acid residues. We also propose an update to the SQR classification system and discuss the role of these proteins in sulfur metabolism.

Potentials of Gene Therapy for Diabetic Retinopathy: The Use of Nucleic Acid Constructs Containing a TXNIP Promoter

Diabetic retinopathy (DR) is considered as a chronic eye disease leading to blindness. DR is associated with hyperglycemia-induced oxidative stress, chronic low-grade inflammation and premature cell death. DR affects retinal capillaries, neuroretina and the retinal pigment epithelium. Recently, the thioredoxin-interacting protein TXNIP has been shown as a pro-oxidative stress, pro-inflammatory and pro-apoptotic protein, highly induced by diabetes and high glucose in all cells examined including the retina. TXNIP's actions involve binding to and inhibition of anti-oxidant and thiol-reducing capacities of thioredoxins (Trx) causing cellular oxidative stress and apoptosis. Trx1 is found in the cytosol and nucleus while Trx2 is the mitochondrial isoform. Several studies provided evidence that knockdown of TXNIP by siRNA or chemical blockade ameliorates early abnormalities of DR including endothelial dysfunction, pericyte apoptosis, Müller cell gliosis and neurodegeneration. Therefore, TXNIP is considered a potential target for preventing or slowing down the progression of DR. We recently proposed that nucleic acid constructs containing a proximal TXNIP promoter linked to a redox gene or shRNA that reduces oxidative stress and inflammation may be used to treat DR. The TXNIP promoter is sensitive to hyperglycemia therefore can drive expression of the linked gene or shRNA under high glucose environment such as seen in diabetes while remaining unresponsive at physiological glucose levels. Such a TXNIP-promoter linked gene or shRNA construct can be delivered to the retina by using adeno-associated viral vectors including AAV2 and AAV2/8 or an appropriate carrier via the intravitreal or sub retinal delivery for long-term gene therapies in DR.

Biochemical and Biophysical Methods to Examine the Effects of Site-Directed Mutagenesis on Enzymatic Activities and Interprotein Interactions

Mutations in proteins often affect interactions with partner molecules, sequentially changing their activities and functions. In order to examine mutagenic effects, we herein describe practical and detailed protocols for enzymatic activity assays using ferredoxin (Fd)-NADP⁺ reductase (FNR) and sulfite reductase (SiR), which are electron-transferring enzymes for the Calvin cycle and sulfur assimilation in various organisms, respectively. Methods for isothermal titration calorimetry and nuclear magnetic resonance spectroscopy, which are very useful thermodynamically and mechanically for investigating the effects of mutations on intermolecular interactions, are also described with practical examples of the Fd-FNR binding system.

Characterization of the free energy dependence of an interprotein electron transfer reaction by variation of pH and site-directed mutagenesis

The interprotein electron transfer (ET) reactions of the cupredoxin amicyanin, which mediates ET from the tryptophan tryptophylquinone (TTQ) cofactor of methylamine dehydrogenase to cytochrome c-551i have been extensively studied. However, it was not possible to perform certain key experiments in that native system. This study examines the ET reaction from reduced amicyanin to an alternative electron acceptor, the diheme protein MauG. It was possible to vary the ΔG° for this ET reaction by simply changing pH to determine the dependence of kET on ΔG°. A P94A mutation of amicyanin significantly altered its oxidation-reduction midpoint potential value. It was not possible to study the ET from reduced P94A amicyanin to cytochrome c-551i in the native system because that reaction was kinetically coupled. However, the reaction from reduced P94A amicyanin to MauG was a true ET reaction and it was possible to determine values of reorganization energy (λ) and electronic coupling for the reactions of this variant as well as native amicyanin. Comparison of the λ values associated with the ET reactions between amicyanin and the TTQ of methylamine dehydrogenase, the diheme center of MauG and the single heme of cytochrome c-551i, provides insight into the factors that dictate the λ values for the respective reactions. These results demonstrate how study of ET reactions with alternative redox partner proteins can complement and enhance our understanding of the reactions with the natural redox partners, and further our understanding of mechanisms of protein ET reactions.