Direct electrochemical study of the multiple redox centers of hydrogenase from Desulfovibrio gigas

Selenium-More than Just a Fortuitous Sulfur Substitute in Redox Biology

Living organisms use selenium mainly in the form of selenocysteine in the active site of oxidoreductases. Here, selenium's unique chemistry is believed to modulate the reaction mechanism and enhance the catalytic efficiency of specific enzymes in ways not achievable with a sulfur-containing cysteine. However, despite the fact that selenium/sulfur have different physicochemical properties, several selenoproteins have fully functional cysteine-containing homologues and some organisms do not use selenocysteine at all. In this review, selected selenocysteine-containing proteins will be discussed to showcase both situations: (i) selenium as an obligatory element for the protein's physiological function, and (ii) selenium presenting no clear advantage over sulfur (functional proteins with either selenium or sulfur). Selenium's physiological roles in antioxidant defence (to maintain cellular redox status/hinder oxidative stress), hormone metabolism, DNA synthesis, and repair (maintain genetic stability) will be also highlighted, as well as selenium's role in human health. Formate dehydrogenases, hydrogenases, glutathione peroxidases, thioredoxin reductases, and iodothyronine deiodinases will be herein featured.

Carbon dioxide reduction to high-value chemicals in microbial electrosynthesis system: Biological conversion and regulation strategies

Large emissions of atmospheric carbon dioxide (CO2) are causing climatic and environmental problems. It is crucial to capture and utilize the excess CO2 through diverse methods, among which the microbial electrosynthesis (MES) system has become an attractive and promising technology to mitigate greenhouse effects while reducing CO2 to high-value chemicals. However, the biological conversion and metabolic pathways through microbial catalysis have not been clearly elucidated. This review first introduces the main acetogenic bacteria for CO2 reduction and extracellular electron transfer mechanisms in MES. It then intensively analyzes the CO2 bioconversion pathways and carbon chain elongation processes in MES, together with energy supply and utilization. The factors affecting MES performance, including physical, chemical, and biological aspects, are summarized, and the strategies to promote and regulate bioconversion in MES are explored. Finally, challenges and perspectives concerning microbial electrochemical carbon sequestration are proposed, and suggestions for future research are also provided. This review provides theoretical foundation and technical support for further development and industrial application of MES for CO2 reduction.

Text-Mining to Identify Gene Sets Involved in Biocorrosion by Sulfate-Reducing Bacteria: A Semi-Automated Workflow

A significant amount of literature is available on biocorrosion, which makes manual extraction of crucial information such as genes and proteins a laborious task. Despite the fast growth of biology related corrosion studies, there is a limited number of gene collections relating to the corrosion process (biocorrosion). Text mining offers a potential solution by automatically extracting the essential information from unstructured text. We present a text mining workflow that extracts biocorrosion associated genes/proteins in sulfate-reducing bacteria (SRB) from literature databases (e.g., PubMed and PMC). This semi-automatic workflow is built with the Named Entity Recognition (NER) method and Convolutional Neural Network (CNN) model. With PubMed and PMCID as inputs, the workflow identified 227 genes belonging to several Desulfovibrio species. To validate their functions, Gene Ontology (GO) enrichment and biological network analysis was performed using UniprotKB and STRING-DB, respectively. The GO analysis showed that metal ion binding, sulfur binding, and electron transport were among the principal molecular functions. Furthermore, the biological network analysis generated three interlinked clusters containing genes involved in metal ion binding, cellular respiration, and electron transfer, which suggests the involvement of the extracted gene set in biocorrosion. Finally, the dataset was validated through manual curation, yielding a similar set of genes as our workflow; among these, hysB and hydA, and sat and dsrB were identified as the metal ion binding and sulfur metabolism genes, respectively. The identified genes were mapped with the pangenome of 63 SRB genomes that yielded the distribution of these genes across 63 SRB based on the amino acid sequence similarity and were further categorized as core and accessory gene families. SRB's role in biocorrosion involves the transfer of electrons from the metal surface via a hydrogen medium to the sulfate reduction pathway. Therefore, genes encoding hydrogenases and cytochromes might be participating in removing hydrogen from the metals through electron transfer. Moreover, the production of corrosive sulfide from the sulfur metabolism indirectly contributes to the localized pitting of the metals. After the corroboration of text mining results with SRB biocorrosion mechanisms, we suggest that the text mining framework could be utilized for genes/proteins extraction and significantly reduce the manual curation time.

Electrochemical characterization of a family AA10 LPMO and the impact of residues shaping the copper site on reactivity

Research on enzymes for lignocellulose biomass degradation has progressively increased in recent years due to the interest in taking advantage of this natural resource. Among these enzymes are the lytic polysaccharide monooxygenases (LPMOs) that oxidatively depolymerize crystalline cellulose using a reactive oxygen species generated in a reduced mono‑copper active site. The copper site comprises of a highly conserved histidine-brace, providing three equatorial nitrogen ligands, whereas less conserved residues close to the copper contribute to shaping and confining the site. The catalytic copper site is exposed to the solvent and to the crystalline substrates, and as so, the influence of the copper environment on LPMO properties, including the redox potential, is of great interest. In the current work, a direct electrochemical study of an LPMO (ScLPMO10C) was conducted allowing to retrieve kinetic and thermodynamic data associated with the redox transition in the catalytic centre. Moreover, two residues that do not bind to the copper but shape the copper sites were mutated, and the properties of the mutants were compared with those of the wild-type enzyme. The direct electrochemical studies, using cyclic voltammetry, yielded redox potentials in the +200 mV range, well in line with LPMO redox potentials determined by other methods. Interestingly, while the mutations hardly affected the formal redox potential of the enzyme, they drastically affected the reactivity of the copper site and enzyme functionality.

Bacteria coated cathodes as an in-situ hydrogen evolving platform for microbial electrosynthesis

Hydrogen is a key intermediate element in microbial electrosynthesis as a mediator of the reduction of carbon dioxide (CO₂) into added value compounds. In the present work we aimed at studying the biological production of hydrogen in biocathodes operated at − 1.0 V vs. Ag/AgCl, using a highly comparable technology and CO₂ as carbon feedstock. Ten bacterial strains were chosen from genera Rhodobacter, Rhodopseudomonas, Rhodocyclus, Desulfovibrio and Sporomusa, all described as hydrogen producing candidates. Monospecific biofilms were formed on carbon cloth cathodes and hydrogen evolution was constantly monitored using a microsensor. Eight over ten bacteria strains showed electroactivity and H₂ production rates increased significantly (two to eightfold) compared to abiotic conditions for two of them (Desulfovibrio paquesii and Desulfovibrio desulfuricans). D. paquesii DSM 16681 exhibited the highest production rate (45.6 ± 18.8 µM min⁻¹) compared to abiotic conditions (5.5 ± 0.6 µM min⁻¹), although specific production rates (per 16S rRNA copy) were similar to those obtained for other strains. This study demonstrated that many microorganisms are suspected to participate in net hydrogen production but inherent differences among strains do occur, which are relevant for future developments of resilient biofilm coated cathodes as a stable hydrogen production platform in microbial electrosynthesis.

Linking bacterial metabolism to graphite cathodes: electrochemical insights into the H(2) -producing capability of Desulfovibrio sp

Microbial biocathodes allow converting and storing electricity produced from renewable sources in chemical fuels (e.g., H(2) ) and are, therefore, attracting considerable attention as alternative catalysts to more expensive and less available noble metals (notably Pt). Microbial biocathodes for H(2) production rely on the ability of hydrogenase-possessing microorganisms to catalyze proton reduction, with a solid electrode serving as direct electron donor. This study provides new chemical and electrochemical data on the bioelectrocatalytic activity of Desulfovibrio species. A combination of chronoamperometry, cyclic voltammetry, and impedance spectroscopy tests were used to assess the performance of the H(2) -producing microbial biocathode and to shed light on the involved electron transfer mechanisms. Cells attached onto a graphite electrode were found to catalyze H(2) production for cathode potentials more reducing than -900 mV vs. standard hydrogen electrode. The highest obtained H(2) production was 8 mmol L(-1) per day, with a Coulombic efficiency close to 100 %. The electrochemical performance of the biocathode changed over time probably due to the occurrence of enzyme activation processes induced by extended electrode polarization. Remarkably, H(2) (at least up to 20 % v/v) was not found to significantly inhibit its own production.