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Synthesis, Properties, and Electrochemical Proton Reduction of a Homoleptic Tetrathiolato Ni-Site Model of [NiFe]-Hydrogenase

[NiFe]-hydrogenase enzymes process H 2 at a nonplanar tetracysteinato-Ni site, the sole participator in proton binding/redox chemistry during turnover. With the objective of assessing whether a simple tetrahedral/ tetrathiolato-Ni 2+ core could promote H 2 evolution reaction (HER), we synthesized (Et 4 N) 2 [Ni(S-p-CF 3 −Ph) 4 ] (1) employing para-trifluoromethylbenzenethiolate ( − S-p-CF 3 −Ph) as a Ni-site analog of [NiFe]-hydrogenase. Spectroscopic measurements and X-ray crystallography confirm the distorted tetrahedral geometry of 1. Dissolution of 1 results in partial thiolate dissociation and formation of S,S-bridged complexes such as (Et 4 N) 2 [Ni 2 (S-p-CF 3 −Ph) 6 ] (3) among other ill-defined species. Dissociation is further accelerated in the presence of Brønsted acids, complicating the assessment of 1 for proton reduction. However, this dissociation/proton instability is suppressed in the presence of additional thiolate ligand to ensure tetrahedral/tetrathiolato 1 persists in solution. Electrochemical HER activity was evaluated by monitoring the current response of an MeCN solution of 1/ excess thiolate after sequential titration with a weak Brønsted acid (acetic acid). The results suggest that 1 is a modest electrocatalyst for the HER with a turnover frequency of 14.5 ± 3.6 s −1 and an overpotential of 0.72 ± 0.02 V. Control experiments and supplementary DFT computations indicate that 1, or a species derived from 1, is responsible for the HER and suggest an ECCE-type mechanism.

Evolution reactions

Functional roles of the [2Fe-2S] clusters in Synechocystis PCC 6803 Hox [NiFe]-hydrogenase reactivity with ferredoxins

The HoxEFUYH complex of Synechocystis PCC 6803 (S. 6803) consists of a HoxEFU ferredoxin:NAD(P)H oxidoreductase subcomplex and a HoxYH [NiFe]-hydrogenase subcomplex that catalyzes reversible H2 oxidation. Prior studies have suggested that the presence of HoxE is required for reactivity with ferredoxin; however, it is unknown how HoxE is functionally integrated into the electron transfer network of the HoxEFU:ferredoxin complex. Deciphering electron transfer pathways is challenged by the rich iron-sulfur cluster content of HoxEFU, which includes a [2Fe-2S] cluster in each subunit, along with multiple [4Fe-4S] clusters and a flavin cofactor. To resolve the role of HoxE, we determined the biophysical and thermodynamic properties of each [2Fe-2S] cluster in HoxEFU using steady-state and potentiometric EPR analysis in combination with square wave voltammetry (SWV). The temperature-dependence of the EPR signal for HoxE confirmed the coordination of a single [2Fe-2S] cluster that was shown by SWV to have an E m = -424 mV (versus SHE). Strikingly, when the E m of the HoxE [2Fe-2S] cluster was analyzed in HoxEFU titrations, it was shifted by >100 mV to an E m < -525 mV (versus SHE). EPR titrations of HoxEFU gave an E m value for the [2Fe-2S] cluster of HoxF, E m = -419 mV and HoxU, E m = -349 mV. These values were used to re-analyze the diaphorase kinetics in reactions performed with ferredoxins with varying E m 's. The results are formulated into a model of HoxEFU:ferredoxin reactivity and the role of HoxE in mediating electron transfer within the HoxEFU:ferredoxin complex.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

The HypA and HypB metallochaperones from Methanococcus maripaludis have unique metal-binding properties and a distinct nickel transfer mechanism

[NiFe] hydrogenases are widespread microbial metalloenzymes that catalyze the reversible conversion of hydrogen (H2) to protons and electrons, playing key roles in energy metabolism. The biosynthesis of the NiFe(CN) 2 CO cofactor involves a suite of maturation proteins, including the HypA and HypB nickel metallochaperones. Here, we define the metal-binding properties, nucleotide-dependent behavior, and functional interplay of HypA and HypB from the hydrogenotrophic methanogenic archaeon, Methanococcus maripaludis . Methanogens have multiple essential nickel-dependent enzymes, so they require efficient systems for nickel delivery that remain largely unexplored. Purified M. maripaludis HypA binds zinc or mononuclear iron at the C-terminal metal binding site, the latter of which has not been reported in other HypA proteins and may serve a unique regulatory role in methanogens. The G-protein metallochaperone HypB binds nickel at the G-domain, which stimulates GTPase activity. Size exclusion chromatography experiments reveal that HypA and HypB form complexes in the presence of nickel, and zinc-bound HypA is optimized for nickel transfer from HypB. The identity of the nucleotide bound to HypB (GDP or GTP) alters the oligomeric state of HypA-HypB complexes, supporting a GTPase-mediated nickel delivery pathway. The HypA-HypB 2 complex configuration is enriched and stable in the presence of GDP and nickel, indicating that this complex delivers nickel to the hydrogenase as opposed to HypA alone. Interestingly, affinity purification-mass spectrometry revealed that HypB interacts with several nickel-dependent proteins, suggesting that HypB may play a broader role in nickel homeostasis in M. maripaludis . Together, this work establishes a biochemical framework for HypAB-mediated nickel trafficking in methanogens.

[NiFe] hydrogenase

Author Correction: Genome-guided isolation of the hyperthermophilic aerobe Fervidibacter sacchari reveals conserved polysaccharide metabolism in the Armatimonadota

Correction to: Nature Communicationshttps://doi.org/10.1038/s41467-024-53784-3, published online 4 November 2024 In the version of this article initially published, Table 1 did not include the properties of the taxa being proposed or refer directly to another location in the main manuscript describing the properties. As such, the original manuscript did not comply with Rule 27 (2)(c) of the ICNP. Also, Table 1 listed the order Fervidibacterales as the nomenclatural type for the class Fervidibacteria, which violates latest emended version of Rule 15 stating that the nomenclatural type for a class must be a genus. Below we provide a modification of Table 1 containing protologues with these errors corrected. We have also changed the order of the taxa in the table to meet the most common ordering. (Table presented.) Taxon names proposed under the ICNP Proposed taxon Etymology Description Genus Fervidibacter Fer.vi.di.bac’ter. L. masc. adj. fervidus, hot, steaming; N.L. masc. n. bacter, a rod; N.L. masc. n. Fervidibacter, a hot rod Thermophilic or hyperthermophilic inhabitants of freshwater thermal environments. All members are likely polysaccharide-degrading chemoheterotrophs with numerous carbohydrate-active enzymes encoded in their genomes. Aerobic, with high-affinity and/or low-affinity terminal oxidases present in the genomes. The oxidative pentose phosphate pathway and the tricarboxylic acid cycle are complete in genomes belonging to the genus. Gram-stain-negative and diderm cell envelope structure. Ovoid- to rod-shaped morphology. Spores are not formed. The genus is a distinct phylogenetic lineage in the family Fervidibacteraceae, the order Fervidibacterales, and the class Fervidibacteria in the phylum Armatimonadota. The type species is Fervidibacter sacchariT. Species Fervidibacter sacchari sac’cha.ri. N.L. gen. n. sacchari, of sugar Hyperthermophilic, microaerophilic, facultatively anaerobic, and grows chemoheterotrophically on monosaccharides and polysaccharides. Cells are ovoid- to rod-shaped, Gram-stain negative, and are 0.9–1.3 µm in width and 1.6–3.6 µm in length. Grows between 65 and 87.5 °C and an optimum temperature of 80 °C, and a pH range of 6.5–8.6 with an optimum pH of 7.5. Grows at an optimum O2 concentration of 5–10%. Grows on D-arabinose, D-galactose, D-glucose, D-rhamnose, D-ribose, D-xylose, chondroitin sulfate, colloidal chitin, galactan, gellan gum, guar gum, karaya gum, locust bean gum, xantham gum, xyloglucan, β-glucan, glycogen, starch, AFEX-pretreated corn stover, miscanthus, sugarcane bagasse, acetate and casamino acids. Grows weakly on xyloglucan under fermentation conditions. The major fatty acids (>10%) are C16:0, C18:0 and/or cyclo-C17:0, and iso-C16:0. The major respiratory quinones (>10%) are MK-8 and MK-9. The isolate and genomes of the species have been recovered from geothermal springs in the Great Basin, Nevada, USA. GC content of genomes range between 51–52%. Subunits for both the high-affinity and low-affinity terminal oxidases are encoded in the genomes. Genomes also encode a Group 3d [NiFe] hydrogenase, which produces hydrogen as an electron sink for NAD+ regeneration. The type strain PD1T (= JCM 39283T = DSM 113467T) was isolated from Great Boiling Spring in Nevada, USA. Family Fervidibacteraceae Fer.vi.di.bac.te.ra’ce.ae. N.L. masc. n. Fervidibacter type genus of the family; L. suff. -aceae ending to denote a family; N.L. fem. pl. n. Fervidibacteraceae the family of the genus Fervidibacter Thermophilic or hyperthermophilic inhabitants of freshwater thermal environments. All members are likely polysaccharide-degrading chemoheterotrophs with numerous carbohydrate-active enzymes encoded in their genomes. Aerobic, with high-affinity and/or low-affinity terminal oxidases present in the genomes. The oxidative pentose phosphate pathway and the tricarboxylic acid cycle are complete in genomes belonging to the family. The family is a distinct phylogenetic lineage in the order Fervidibacterales and the class Fervidibacteria in the phylum Armatimonadota. The type genus is Fervidibacter. Order Fervidibacterales Fer.vi.di.bac.te.ra’les. N.L. masc. n. Fervidibacter type genus of the order; L. suff. -ales ending to denote an order; N.L. fem. pl. n. Fervidibacterales the order of the genus Fervidibacter Thermophilic or hyperthermophilic inhabitants of freshwater thermal environments. All members are likely polysaccharide-degrading chemoheterotrophs with numerous carbohydrate-active enzymes encoded in their genomes. Aerobic or strictly anaerobic. Phylogenomic placement of this lineage within the Fervidibacteria and relative evolutionary divergence supports delineation of this lineage as an order within the class Fervidibacteria and phylum Armatimonadota. The type genus is Fervidibacter. Class Fervidibacteria Fer.vi.di.bac.te’ri.a. N.L. masc. n. Fervidibacter type genus of the type order of the class; L. suff. -ia ending to denote a class; N.L. neut. pl. n. Fervidibacteria the class of the order Fervidibacterales Thermophilic or hyperthermophilic inhabitants of freshwater thermal environments. All members are likely polysaccharide-degrading chemoheterotrophs with numerous carbohydrate-active enzymes encoded in their genomes. Aerobic or strictly anaerobic. Phylogenomic placement of this lineage within the Armatimonadota and relative evolutionary divergence supports delineation of this lineage as a class within the Armatimonadota. The type genus is Fervidibacter. 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Nou, Nancy O