Comparative analysis of CO2 reduction by soluble Escherichia coli formate dehydrogenase H and its selenocysteine-to-cysteine substitution variant

Metal-dependent formate dehydrogenases (Me-FDHs) are highly active CO2-reducing enzymes operating at low redox potentials and employ either molybdenum or tungsten to reduce the bound substrate. This makes them suitable for electrochemical applications such as fossil-free production of commodity chemicals utilizing renewable energy. Electrocatalytic CO2 reduction by cathode-immobilized Me-FDHs has been recently demonstrated and rational protein engineering can be used to optimize Me-FDHs for various carbon reduction reactions. In the present study, CO2 reduction by soluble monomeric Escherichia coli formate dehydrogenase H (EcFDH-H) was demonstrated and the function of its nucleophilic selenocysteine residue as a transient ligand of a centrally bound molybdenum atom was investigated. Kinetic analysis of the wildtype enzyme revealed maximum CO2 reduction rates of 44 ± 6 s−1 at pH 5.8 that was decreased to 19% and 0% in the case of selenocysteine substitution with the structural homologues cysteine and serine, respectively. Further selenocysteine-to-cysteine substitution effects included an increased acid tolerance as well as stronger inhibition by nitrate and azide indicating a shift of the Mo oxidation state from IV to VI. Conversely, a destabilizing effect on the oxidized Mo(VI) center could be assigned to the native selenocysteine residue that may facilitate the observed efficient CO2 reduction by rapid transition between Mo oxidation states. Taken together, the performed characterization of EcFDH-H as a catalyst for CO2 reduction and the selenocysteine substitution analysis furthers the understanding of the active-site structure of Me-FDHs and thereby supports the development of more efficient biocatalysts for CO2 reduction

Comparative analysis of CO2 reduction by soluble Escherichia coli formate dehydrogenase H and its selenocysteine-to-cysteine substitution variant

Metal-dependent formate dehydrogenases (Me-FDHs) are highly active CO2-reducing enzymes operating at low redox potentials and employ either molybdenum or tungsten to reduce the bound substrate. This makes them suitable for electrochemical applications such as fossil-free production of commodity chemicals utilizing renewable energy. Electrocatalytic CO2 reduction by cathode-immobilized Me-FDHs has been recently demonstrated and rational protein engineering can be used to optimize Me-FDHs for various carbon reduction reactions. In the present study, CO2 reduction by soluble monomeric Escherichia coli formate dehydrogenase H (EcFDH-H) was demonstrated and the function of its nucleophilic selenocysteine residue as a transient ligand of a centrally bound molybdenum atom was investigated. Kinetic analysis of the wildtype enzyme revealed maximum CO2 reduction rates of 44 ± 6 s−1 at pH 5.8 that was decreased to 19% and 0% in the case of selenocysteine substitution with the structural homologues cysteine and serine, respectively. Further selenocysteine-to-cysteine substitution effects included an increased acid tolerance as well as stronger inhibition by nitrate and azide indicating a shift of the Mo oxidation state from IV to VI. Conversely, a destabilizing effect on the oxidized Mo(VI) center could be assigned to the native selenocysteine residue that may facilitate the observed efficient CO2 reduction by rapid transition between Mo oxidation states. Taken together, the performed characterization of EcFDH-H as a catalyst for CO2 reduction and the selenocysteine substitution analysis furthers the understanding of the active-site structure of Me-FDHs and thereby supports the development of more efficient biocatalysts for CO2 reduction

Artificial electron acceptors decouple archaeal methane oxidation from sulfate reduction

The oxidation of methane with sulfate is an important microbial metabolism in the global carbon cycle. In marine methane seeps, this process is mediated by consortia of anaerobic methanotrophic archaea (ANME) that live in syntrophy with sulfate-reducing bacteria (SRB). The underlying interdependencies within this uncultured symbiotic partnership are poorly understood. We used a combination of rate measurements and single-cell stable isotope probing to demonstrate that ANME in deep-sea sediments can be catabolically and anabolically decoupled from their syntrophic SRB partners using soluble artificial oxidants. The ANME still sustain high rates of methane oxidation in the absence of sulfate as the terminal oxidant, lending support to the hypothesis that interspecies extracellular electron transfer is the syntrophic mechanism for the anaerobic oxidation of methane

In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry

Here we describe the application of a new click chemistry method for fluorescent tracking of protein synthesis in individual microorganisms within environmental samples. This technique, termed bioorthogonal non-canonical amino acid tagging (BONCAT), is based on the in vivo incorporation of the non-canonical amino acid L-azidohomoalanine (AHA), a surrogate for L-methionine, followed by fluorescent labeling of AHA containing cellular proteins by azide-alkyne click chemistry. BONCAT was evaluated with a range of phylogenetically and physiologically diverse archaeal and bacterial pure cultures and enrichments, and used to visualize translationally active cells within complex environmental samples including an oral biofilm, freshwater, and anoxic sediment. We also developed combined assays that couple BONCAT with rRNA-targeted FISH, enabling a direct link between taxonomic identity and translational activity. Using a methanotrophic enrichment culture incubated under different conditions, we demonstrate the potential of BONCAT-FISH to study microbial physiology in situ. A direct comparison of anabolic activity using BONCAT and stable isotope labeling by nanoSIMS (^(15)NH_4^+ assimilation) for individual cells within a sediment sourced enrichment culture showed concordance between AHA positive cells and ^(15)N enrichment. BONCAT-FISH offers a fast, inexpensive, and straightforward fluorescence microscopy method for studying the in situ activity of environmental microbes on a single cell level

Comparative Genomics and Proteomic Analysis of Assimilatory Sulfate Reduction Pathways in Anaerobic Methanotrophic Archaea

Sulfate is the predominant electron acceptor for anaerobic oxidation of methane (AOM) in marine sediments. This process is carried out by a syntrophic consortium of anaerobic methanotrophic archaea (ANME) and sulfate reducing bacteria (SRB) through an energy conservation mechanism that is still poorly understood. It was previously hypothesized that ANME alone could couple methane oxidation to dissimilatory sulfate reduction, but a genetic and biochemical basis for this proposal has not been identified. Using comparative genomic and phylogenetic analyses, we found the genetic capacity in ANME and related methanogenic archaea for sulfate reduction, including sulfate adenylyltransferase, APS kinase, APS/PAPS reductase and two different sulfite reductases. Based on characterized homologs and the lack of associated energy conserving complexes, the sulfate reduction pathways in ANME are likely used for assimilation but not dissimilation of sulfate. Environmental metaproteomic analysis confirmed the expression of 6 proteins in the sulfate assimilation pathway of ANME. The highest expressed proteins related to sulfate assimilation were two sulfite reductases, namely assimilatory-type low-molecular-weight sulfite reductase (alSir) and a divergent group of coenzyme F_(420)-dependent sulfite reductase (Group II Fsr). In methane seep sediment microcosm experiments, however, sulfite and zero-valent sulfur amendments were inhibitory to ANME-2a/2c while growth in their syntrophic SRB partner was not observed. Combined with our genomic and metaproteomic results, the passage of sulfur species by ANME as metabolic intermediates for their SRB partners is unlikely. Instead, our findings point to a possible niche for ANME to assimilate inorganic sulfur compounds more oxidized than sulfide in anoxic marine environments

Comparative Genomics and Proteomic Analysis of Assimilatory Sulfate Reduction Pathways in Anaerobic Methanotrophic Archaea

Sulfate is the predominant electron acceptor for anaerobic oxidation of methane (AOM) in marine sediments. This process is carried out by a syntrophic consortium of anaerobic methanotrophic archaea (ANME) and sulfate reducing bacteria (SRB) through an energy conservation mechanism that is still poorly understood. It was previously hypothesized that ANME alone could couple methane oxidation to dissimilatory sulfate reduction, but a genetic and biochemical basis for this proposal has not been identified. Using comparative genomic and phylogenetic analyses, we found the genetic capacity in ANME and related methanogenic archaea for sulfate reduction, including sulfate adenylyltransferase, APS kinase, APS/PAPS reductase and two different sulfite reductases. Based on characterized homologs and the lack of associated energy conserving complexes, the sulfate reduction pathways in ANME are likely used for assimilation but not dissimilation of sulfate. Environmental metaproteomic analysis confirmed the expression of 6 proteins in the sulfate assimilation pathway of ANME. The highest expressed proteins related to sulfate assimilation were two sulfite reductases, namely assimilatory-type low-molecular-weight sulfite reductase (alSir) and a divergent group of coenzyme F420-dependent sulfite reductase (Group II Fsr). In methane seep sediment microcosm experiments, however, sulfite and zero-valent sulfur amendments were inhibitory to ANME-2a/2c while growth in their syntrophic SRB partner was not observed. Combined with our genomic and metaproteomic results, the passage of sulfur species by ANME as metabolic intermediates for their SRB partners is unlikely. Instead, our findings point to a possible niche for ANME to assimilate inorganic sulfur compounds more oxidized than sulfide in anoxic marine environments

Application of the Fluorescence-Activating and Absorption-Shifting Tag (FAST) for Flow Cytometry in Methanogenic Archaea

We thank N. Buan for providing the plasmid pNB730 and W. Whitman for providing pMEV4. Furthermore, We thank Ingemar von Ossowski, Jichen Bao, and Thinh Nguyen for help finalizing this work. This project was supported by grants from Novo Nordisk Foundation and the Academy of Finland (grant NNF19OC0055464 to N.A. and grants NNF19OC0054329 and 326020 to S.S.).Methane-producing archaea play a crucial role in the global carbon cycle and are used for biotechnological fuel production. Methanogenic model organisms such as Methanococcus maripaludis and Methanosarcina acetivorans have been biochemically characterized and can be genetically engineered by using a variety of existing molecular tools. The anaerobic lifestyle and autofluorescence of methanogens, however, restrict the use of common fluorescent reporter proteins (e.g., GFP and derivatives), which require oxygen for chromophore maturation. Recently, the use of a novel oxygen-independent fluorescent activation and absorption-shifting tag (FAST) was demonstrated with M. maripaludis. Similarly, we now describe the use of the tandem activation and absorption-shifting tag protein 2 (tdFAST2), which fluoresces when the cell-permeable fluorescent ligand (fluorogen) 4-hydroxy-3,5-dimethoxybenzylidene rhodanine (HBR-3,5DOM) is present. Expression of tdFAST2 in M. acetivorans and M. maripaludis is noncytotoxic and tdFAST2:HBR-3,5DOM fluorescence is clearly distinguishable from the autofluorescence. In flow cytometry experiments, mixed methanogen cultures can be distinguished, thereby allowing for the possibility of high-throughput investigations of the characteristic dynamics within single and mixed cultures. IMPORTANCE Methane-producing archaea play an essential role in the global carbon cycle and demonstrate great potential for various biotechnological applications, e.g., biofuel production, carbon dioxide capture, and electrochemical systems. Oxygen sensitivity and high autofluorescence hinder the use of common fluorescent proteins for studying methanogens. By using tdFAST2:HBR-3,5DOM fluorescence, which functions under anaerobic conditions and is distinguishable from the autofluorescence, real-time reporter studies and high-throughput investigation of the mixed culture dynamics of methanogens via flow cytometry were made possible. This will further help accelerate the sustainable exploitation of methanogens.Peer reviewe