Abstract[NiFe]-hydrogenases activate dihydrogen. Like all [NiFe]-hydrogenases, hydrogenase 2 of Escherichia coli has a bimetallic NiFe(CN)2CO cofactor in its catalytic subunit. Biosynthesis of the Fe(CN)2CO group of the [NiFe]-cofactor occurs on a distinct scaffold complex comprising the HybG and HypD accessory proteins. HybG is a member of the HypC-family of chaperones that confers specificity towards immature hydrogenase catalytic subunits during transfer of the Fe(CN)2CO group. Using native mass spectrometry of an anaerobically isolated HybG–HypD complex we show that HybG carries the Fe(CN)2CO group. Our results also reveal that only HybG, but not HypD, interacts with the apo-form of the catalytic subunit. Finally, HybG was shown to have two distinct, and apparently CO2-related, covalent modifications that depended on the presence of the N-terminal cysteine residue on the protein, possibly representing intermediates during Fe(CN)2CO group biosynthesis. Together, these findings suggest that the HybG chaperone is involved in both biosynthesis and delivery of the Fe(CN)2CO group to its target protein. HybG is thus suggested to shuttle between the assembly complex and the apo-catalytic subunit. This study provides new insights into our understanding of how organometallic cofactor components are assembled on a scaffold complex and transferred to their client proteins.

Spores have strongly reduced metabolic activity and are produced during the complex developmental cycle of the actinobacteriumStreptomyces coelicolor. Resting spores can remain viable for decades, yet little is known about how they conserve energy. It is known, however, that they can reduce either oxygen or nitrate using endogenous electron sources.S. coelicoloruses either a cytochromebdoxidase or a cytochromebcc-aa3oxidase supercomplex to reduce oxygen, while nitrate is reduced by Nar-type nitrate reductases, which typically oxidize quinol directly. Here, we show that in resting spores the Nar1 nitrate reductase requires a functionalbcc-aa3supercomplex to reduce nitrate. Mutants lacking the completeqcr-ctagenetic locus encoding thebcc-aa3supercomplex showed no Nar1-dependent nitrate reduction. Recovery of Nar1 activity was achieved by genetic complementation but only when the completeqcr-ctalocus was reintroduced to the mutant strain. We could exclude that the dependence on the supercomplex for nitrate reduction was via regulation of nitrate transport. Moreover, the catalytic subunit, NarG1, of Nar1 was synthesized in theqcr-ctamutant, ruling out transcriptional control. Constitutive synthesis of Nar1 in mycelium revealed that the enzyme was poorly active in this compartment, suggesting that the Nar1 enzyme cannot act as a typical quinol oxidase. Notably, nitrate reduction by the Nar2 enzyme, which is active in growing mycelium, was not wholly dependent on thebcc-aa3supercomplex for activity. Together, our data suggest that Nar1 functions together with the proton-translocatingbcc-aa3supercomplex to increase the efficiency of energy conservation in resting spores.IMPORTANCEStreptomyces coelicolorforms spores that respire with either oxygen or nitrate, using only endogenous electron donors. This helps maintain a membrane potential and, thus, viability. Respiratory nitrate reductase (Nar) usually receives electrons directly from reduced quinone species; however, we show that nitrate respiration in spores requires a respiratory supercomplex comprising cytochromebccoxidoreductase andaa3oxidase. Our findings suggest that the Nar1 enzyme in theS. coelicolorspore functions together with the proton-translocatingbcc-aa3supercomplex to help maintain the membrane potential more efficiently. Dissecting the mechanisms underlying this survival strategy is important for our general understanding of bacterial persistence during infection processes and of how bacteria might deal with nutrient limitation in the natural environment.

Four Hyp proteins build a scaffold complex upon which the Fe(CN)2CO group of the [NiFe]‐cofactor of hydrogenases (Hyd) is made. Two of these Hyp proteins, the redox‐active, [4Fe‐4S]‐containing HypD protein and the HypC chaperone, form the basis of this scaffold complex. Two different scaffold complexes exist in Escherichia coli, HypCD, and the paralogous HybG‐HypD complex, both of which exhibit ATPase activity. Apart from a Rossmann fold, there is no obvious ATP‐binding site in HypD. The aim of this study, therefore, was to identify amino acid motifs in HypD that are required for the ATPase activity of the HybG‐HypD scaffold complex. Amino acid‐exchange variants in three conserved motifs within HypD were generated. Variants in which individual cysteine residues coordinating the iron–sulfur ([4Fe‐4S]) cluster were exchanged abolished Hyd enzyme activity and reduced ATPase activity but also destabilized the complex. Two conserved cysteine residues, C69 and C72, form part of HypD's Rossmann fold and play a role in HypD's thiol‐disulfide exchange activity. Substitution of these two residues individually with alanine also abolished hydrogenase activity and strongly reduced ATPase activity, particularly the C72A exchange. Residues in a further conserved GFETT motif were exchanged, but neither hydrogenase enzyme activity nor ATPase activity of the isolated HybG‐HypD complexes was significantly affected. Together, our findings identify a strong correlation between the redox activity of HypD, ATPase activity, and the ability of the complex to mature Hyd enzymes. These results further highlight the important role of thiol residues in the HybG‐HypD scaffold complex during [NiFe]‐cofactor biosynthesis.

Streptomyces coelicolor A3(2), an obligately aerobic, oxidase-positive, and filamentous soil bacterium, lacks a soluble cytochrome c in its respiratory chain, having instead a membrane-associated diheme c-type cytochrome, QcrC. This necessitates complex formation to allow electron transfer between the cytochrome bcc and aa3 oxidase respiratory complexes. Combining genetic complementation studies with in-gel cytochrome oxidase activity staining, we demonstrate that the complete qcrCAB-ctaCDFE gene locus on the chromosome, encoding, respectively, the bcc and aa3 complexes, is required to manifest a cytochrome oxidase enzyme activity in both spores and mycelium of a qcr-cta deletion mutant. Blue-native-PAGE identified a cytochrome aa3 oxidase complex of approximately 270 kDa, which catalyzed oxygen-dependent diaminobenzidine oxidation without the requirement for exogenously supplied cytochrome c, indicating association with QcrC. Furthermore, higher molecular mass complexes were identified upon addition of soluble cytochrome c, suggesting the supercomplex is unstable and readily dissociates into subcomplexes lacking QcrC. Immunological and mass spectrometric analyses of active, high-molecular mass oxidase-containing complexes separated by clear-native PAGE identified key subunits of both the bcc complex and the aa3 oxidase, supporting supercomplex formation. Our data also indicate that the cytochrome b QcrB of the bcc complex is less abundant in spores compared with mycelium.

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