Chromogenic assessment of the three molybdo-selenoprotein formate dehydrogenases in Escherichia coli

Tungsten Enzyme Using Hydrogen as an Electron Donor to Reduce Carboxylic Acids and NAD. ACS Catal 2022;12:8707-8717. [PMID: 35874620 PMCID: PMC9295118 DOI: 10.1021/acscatal.2c02147]

Tungsten-dependent aldehyde oxidoreductases (AORs) catalyze the oxidation of aldehydes to acids and are the only known enzymes reducing non-activated acids using electron donors with low redox potentials. We report here that AOR from Aromatoleum aromaticum (AOR_Aa) catalyzes the reduction of organic acids not only with low-potential Eu(II) or Ti(III) complexes but also with H₂ as an electron donor. Additionally, AOR_Aa catalyzes the H₂-dependent reduction of NAD⁺ or benzyl viologen. The rate of H₂-dependent NAD⁺ reduction equals to 10% of that of aldehyde oxidation, representing the highest H₂ turnover rate observed among the Mo/W enzymes. As AOR_Aa simultaneously catalyzes the reduction of acids and NAD⁺, we designed a cascade reaction utilizing a NAD(P)H-dependent alcohol dehydrogenase to reduce organic acids to the corresponding alcohols with H₂ as the only reductant. The newly discovered W-hydrogenase side activity of AOR_Aa may find applications in either NADH recycling or conversion of carboxylic acids to more useful biochemicals.

Use of Transposon Directed Insertion-Site Sequencing to Probe the Antibacterial Mechanism of a Model Honey on E. coli K-12

Antimicrobial resistance is an ever-growing health concern worldwide that has created renewed interest in the use of traditional anti-microbial treatments, including honey. However, understanding the underlying mechanism of the anti-microbial action of honey has been hampered due to the complexity of its composition. High throughput genetic tools could assist in understanding this mechanism. In this study, the anti-bacterial mechanism of a model honey, made of sugars, hydrogen peroxide, and gluconic acid, was investigated using genome-wide transposon mutagenesis combined with high-throughput sequencing (TraDIS), with the strain Escherichia coli K-12 MG1655 as the target organism. We identified a number of genes which when mutated caused a severe loss of fitness when cells were exposed to the model honey. These genes encode membrane proteins including those involved in uptake of essential molecules, and components of the electron transport chain. They are enriched for pathways involved in intracellular homeostasis and redox activity. Genes involved in assembly and activity of formate dehydrogenase O (FDH-O) were of particular note. The phenotypes of mutants in a subset of the genes identified were confirmed by phenotypic screening of deletion strains. We also found some genes which when mutated led to enhanced resistance to treatment with the model honey. This study identifies potential synergies between the main honey stressors and provides insights into the global antibacterial mechanism of this natural product.

Mechanisms of Energy Transduction by Charge Translocating Membrane Proteins

Life relies on the constant exchange of different forms of energy, i.e., on energy transduction. Therefore, organisms have evolved in a way to be able to harvest the energy made available by external sources (such as light or chemical compounds) and convert these into biological useable energy forms, such as the transmembrane difference of electrochemical potential (Δμ̃). Membrane proteins contribute to the establishment of Δμ̃ by coupling exergonic catalytic reactions to the translocation of charges (electrons/ions) across the membrane. Irrespectively of the energy source and consequent type of reaction, all charge-translocating proteins follow two molecular coupling mechanisms: direct- or indirect-coupling, depending on whether the translocated charge is involved in the driving reaction. In this review, we explore these two coupling mechanisms by thoroughly examining the different types of charge-translocating membrane proteins. For each protein, we analyze the respective reaction thermodynamics, electron transfer/catalytic processes, charge-translocating pathways, and ion/substrate stoichiometries.

Enhancement of Gluconobacter oxydans Resistance to Lignocellulosic-Derived Inhibitors in Xylonic Acid Production by Overexpressing Thioredoxin

Efficient utilization of lignocellulose is an economically relevant practice for improving the financial prospects of biorefineries. Lignocellulose contains significant levels of xylose that can be converted into valuable xylonic acid. However, some inhibitors of bioconversion processes are produced after pretreatment. Xylonic acid production in bacteria, such as Gluconobacter oxydans, is hindered by poor bacterial tolerance to contaminants. Therefore, in order to enhance bacterial resistance to inhibitors, a recombinant strain of G. oxydans was created by the introduction of the thioredoxin gene. Thioredoxin is a key protein responsible for maintaining cellular redox potential and is critical to the conversion of xylose to xylonate. Overexpression of thioredoxin was confirmed at the enzymatic level, while the recombinant strain showed increased catalytic activity when inhibitors, such as formic acid or p-hydroxybenzaldehyde (PHBA), were added to the synthetic xylose medium (17% and 7% improvement in xylonic acid yield, respectively). To probe the molecular mechanism behind the recombinant strain response to inhibitors, the expression levels of various genes were analyzed by qRT-PCR, which revealed five differentially expressed genes (DEGs) upon exposure to formic acid or PHBA.

Insights Into the Redox Sensitivity of Chloroflexi Hup-Hydrogenase Derived From Studies in Escherichia coli: Merits and Pitfalls of Heterologous [NiFe]-Hydrogenase Synthesis

The highly oxygen-sensitive hydrogen uptake (Hup) hydrogenase from Dehalococcoides mccartyi forms part of a protein-based respiratory chain coupling hydrogen oxidation with organohalide reduction on the outside of the cell. The HupXSL proteins were previously shown to be synthesized and enzymatically active in Escherichia coli. Here we examined the growth conditions that deliver active Hup enzyme that couples H₂ oxidation to benzyl viologen (BV) reduction, and identified host factors important for this process. In a genetic background lacking the three main hydrogenases of E. coli we could show that additional deletion of genes necessary for selenocysteine biosynthesis resulted in inactive Hup enzyme, suggesting requirement of a formate dehydrogenase for Hup activity. Hup activity proved to be dependent on the presence of formate dehydrogenase (Fdh-H), which is typically associated with the H₂-evolving formate hydrogenlyase (FHL) complex in the cytoplasm. Further analyses revealed that heterologous Hup activity could be recovered if the genes encoding the ferredoxin-like electron-transfer protein HupX, as well as the related HycB small subunit of Fdh-H were also deleted. These findings indicated that the catalytic HupL and electron-transferring HupS subunits were sufficient for enzyme activity with BV. The presence of the HupX or HycB proteins in the absence of Fdh-H therefore appears to cause inactivation of the HupSL enzyme. This is possibly because HupX or HycB aided transfer of electrons to the quinone pool or other oxidoreductase complexes, thus maintaining the HupSL heterodimer in a continuously oxidized state causing its inactivation. This proposal was supported by the observation that growth under either aerobic or anaerobic respiratory conditions did not yield an active HupSL. These studies thus provide a system to understand the redox sensitivity of this heterologously synthesized hydrogenase.