The monofunctional CO dehydrogenase CooS is essential for growth of Thermoanaerobacter kivui on carbon monoxide

Thermoanaerobacter kivui is a thermophilic acetogen that can grow on carbon monoxide as sole carbon and energy source. To identify the gene(s) involved in CO oxidation, the genome sequence was analyzed. Two genes potentially encoding CO dehydrogenases were identified. One, cooS, potentially encodes a monofunctional CO dehydrogenase, whereas another, acsA, potentially encodes the CODH component of the CODH/ACS complex. Both genes were cloned, a His-tag encoding sequence was added, and the proteins were produced from a plasmid in T. kivui. His-AcsA copurified by affinity chromatography with AcsB, the acetyl-CoA synthase of the CO dehydrogenase/acetyl CoA synthase complex. His-CooS copurified with CooF1, a small iron-sulfur center containing protein likely involved in electron transport. Both protein complexes had CO:ferredoxin oxidoreductase as well as CO:methyl viologen oxidoreductase activity, but the activity of CooSF1 was 15-times and 231-times lower, respectively. To underline the importance of CooS, the gene was deleted in the CO-adapted strain. Interestingly, the ∆cooS deletion mutant did not grow on CO anymore. These experiments clearly demonstrated that CooS is essential for growth of T. kivui on CO. This is in line with the hypothesis that CooS is the CO-oxidizing enzyme in cells growing on CO.

Tunnel-redesigned O2-tolerant CO dehydrogenase for removal of CO in real flue gas

Carbon monoxide dehydrogenase (CODH)-catalyzed oxidation of CO to CO2 provides a promising means of removal of toxic and waste CO from industrial flue gas despite of the lack of active and stable enzymes in the atmosphere. Herein we present rationally and selectively redesigned ChCODH-II (Carboxydothermus hydrogenoformans) variants by engineering gas tunnels in order for O2-tolerant CODHs to catalyze efficient CO oxidation under oxygen (O2). Using the redesigned ChCODH-II A559W and A559H variants showing 42- and 128-fold elevation of O2 tolerance, respectively, complete CO removal was achieved under a near-atmospheric condition. Moreover, these variants efficiently removed CO from industrial flue gas (Linz–Donawiz converter Gas: LDG) discharged from a steel mill despite the high O2 level (13.4%) during successful and repeated reuse after immobilized on Ni-NTA agarose beads. Our study will provide insights into redesigning the transformation of O2-sensitive CODHs into tolerant enzymes for use as workhorses for conversion of toxic or waste gases into safe or value-added chemicals.

Tree phyllospheres are a habitat for diverse populations of CO-oxidising bacteria

BackgroundCarbon monoxide (CO) is a naturally occurring and ubiquitous trace gas in the atmosphere. As a product of combustion processes, it can reach concentrations in the mg/m3 range in urban areas, contributing to air pollution. Aerobic CO-degrading microorganisms have been identified previously and are thought to remove ~370 Tg of CO in soils and oceans per year. Based on the presence of genes encoding subunits of the enzyme carbon monoxide dehydrogenase in metagenomes, a large fraction of soil bacteria may have the potential for CO degradation. The activity and diversity of CO-degrading microorganisms in above ground habitats such as the phyllosphere has not been addressed, however, and their potential role in global CO cycling remains unknown.ResultsMonitoring of CO-degradation in leaf washes of two common British trees, Ilex aquifolium and Crataegus monogyna, demonstrated CO uptake in all samples investigated. Leaf washes of I. aquifolium had significantly higher CO oxidation rates than those of C. monogyna. A diverse range of bacterial taxa were identified as candidate CO-oxidising taxa based on high-throughput sequencing and multivariate statistical analysis of 16S rRNA amplicon data, as well as functional diversity analysis based on coxL, the gene encoding the large subunit of CO-dehydrogenase. Candidate CO-oxidising taxa included a range of Rhizobiales and Burkholderiales, of which the Burkholderiales OTUs were abundant colonisers of the phyllosphere at the time of sampling, as indicated by 16S rRNA gene sequencing. In addition, an estimated 12.4% of leaf OTUs in samples of this study contained coxL homologues, based on their predicted genomes. We also mined data of publicly available phyllosphere metagenomes for genes encoding subunits of CO-dehydrogenase which indicated that, on average, 25% of phyllosphere bacteria contained CO-dehydrogenase gene homologues. A CO-oxidising Phyllobacteriaceae strain was isolated from phyllosphere samples which contains genes encoding both CODH as well as a RuBisCO.ConclusionsThe phyllosphere, a vast microbial habitat, supports diverse and potentially abundant CO-oxidising bacteria. These findings identify tree phyllosphere bacteria as a potential sink for atmospheric CO and highlight the need for a more detailed assessment of phyllosphere microbial communities in the global cycle of CO.

QM/MM study of the binding of H2 to MoCu CO dehydrogenase: development and applications of improved H2 van der Waals parameters

The MoCu CO dehydrogenase enzyme not only transforms CO into CO2 but it can also oxidise H2. Even if its hydrogenase activity has been known for decades, a debate is ongoing on the most plausible mode for the binding of H2 to the enzyme active site and the hydrogen oxidation mechanism. In the present work, we provide a new perspective on the MoCu-CODH hydrogenase activity by improving the in silico description of the enzyme. Energy refinement—by means of the BigQM approach—was performed on the intermediates involved in the dihydrogen oxidation catalysis reported in our previously published work (Rovaletti, et al. “Theoretical Insights into the Aerobic Hydrogenase Activity of Molybdenum–Copper CO Dehydrogenase.” Inorganics 7 (2019) 135). A suboptimal description of the H2–HN(backbone) interaction was observed when the van der Waals parameters described in previous literature for H2 were employed. Therefore, a new set of van der Waals parameters is developed here in order to better describe the hydrogen–backbone interaction. They give rise to improved binding modes of H2 in the active site of MoCu CO dehydrogenase. Implications of the resulting outcomes for a better understanding of hydrogen oxidation catalysis mechanisms are proposed and discussed.

Draft Genome Sequence of the Carboxydotrophic Alphaproteobacterium Aminobacter carboxidus Type Strain DSM 1086

ABSTRACT Aminobacter carboxidus is a soil Gram-negative alphaproteobacterium belonging to the physiological group of carboxydobacteria which aerobically oxidize CO to CO2. Here, we report the draft genome sequence of the A. carboxidus DSM 1086 type strain and the identification of both form I and form II CO dehydrogenase systems in this strain.

Thioester synthesis through geoelectrochemical CO2 fixation on Ni sulfides

Thioester synthesis by CO dehydrogenase/acetyl-CoA synthase is among the most ancient autotrophic metabolisms. Although the preceding prebiotic CO2 fixation routes to thioesters are often suggested, none has any experimentally supported evidence. Here we demonstrate that, under an electrochemical condition realizable in early ocean hydrothermal systems, nickel sulfide (NiS) gradually reduces to Ni0, while accumulating surface-bound CO due to CO2 electroreduction. The resultant partially reduced NiS facilitates thioester (S-methyl thioacetate) formation from CO and methanethiol even at room temperature and neutral pH. This thioester formation can further be enhanced up to a selectivity of 56% by NiS coprecipitating with FeS or CoS. Considering the central role of Ni in the enzymatic process mentioned above, our demonstrated thioester synthesis with the partially reduced NiS could have a direct implication to the autotrophic origin of life.

Thioester Synthesis through Geoelectrochemical CO2 Fixation on Ni Sulfides

Thioester synthesis by CO dehydrogenase/acetyl-CoA synthase is among the most ancient autotrophic metabolisms. Although the preceding prebiotic CO2 fixation routes to thioesters are often suggested, none has any experimentally supported evidence. Here we demonstrate that, under an electrochemical condition realizable in early ocean hydrothermal systems, nickel sulfide (NiS) gradually reduces to Ni0, while accumulating surface-bound CO due to CO2 electroreduction. The resultant partially reduced NiS facilitates thioester (S-methyl thioacetate) formation from CO and methanethiol even at room temperature and neutral pH. This thioester formation can further be enhanced up to a selectivity of 56% by NiS coprecipitating with FeS or CoS. Considering the central role of Ni in the enzymatic process mentioned above, our demonstrated thioester synthesis with the partially reduced NiS could have a direct implication to the autotrophic origin of life.<br>

Thioester Synthesis through Geoelectrochemical CO2 Fixation on Ni Sulfides

Thioester synthesis by CO dehydrogenase/acetyl-CoA synthase is among the most ancient autotrophic metabolisms. Although the preceding prebiotic CO2 fixation routes to thioesters are often suggested, none has any experimentally supported evidence. Here we demonstrate that, under an electrochemical condition realizable in early ocean hydrothermal systems, nickel sulfide (NiS) gradually reduces to Ni0, while accumulating surface-bound CO due to CO2 electroreduction. The resultant partially reduced NiS facilitates thioester (S-methyl thioacetate) formation from CO and methanethiol even at room temperature and neutral pH. This thioester formation can further be enhanced up to a selectivity of 56% by NiS coprecipitating with FeS or CoS. Considering the central role of Ni in the enzymatic process mentioned above, our demonstrated thioester synthesis with the partially reduced NiS could have a direct implication to the autotrophic origin of life.<br>