Stefan Frielingsdorf
Constanze Pinske
Francesca Valetti
Chris Greening- 1Institute of Chemistry, Biophysical Chemistry, Technische Universität Berlin, Berlin, Germany
- 2Institute for Biology, Microbiology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
- 3Department of Life Sciences and Systems Biology, University of Torino, Turin, Italy
- 4Department of Microbiology, Monash University, Clayton, VIC, Australia
Editorial on the Research Topic
Hydrogenase: structure, function, maturation, and application
Molecular hydrogen (H2) is an important molecule in the metabolism of diverse microorganisms (Greening et al., 2015). Many microorganisms use H2 as an electron donor to support aerobic respiration, anaerobic respiration, and carbon fixation. Others produce H2 as a means to dispose reducing equivalents through fermentative and photobiological processes. Furthermore, exchange of H2 between different species shapes the ecology and biogeochemistry of diverse ecosystems globally (Schwartz et al., 2013). The enzymes that split or evolve H2 are called hydrogenases and these metalloproteins can be divided into three phylogenetically unrelated classes distinguishable by the metal composition of their active sites, namely [Fe]-, [FeFe]-, and [NiFe]-hydrogenases (Lubitz et al., 2014). Following a century of hydrogenase research, it is now possible to isolate, handle, and investigate these fragile enzymes. There have been numerous advances in understanding the regulation, function, structures, and maturation of these enzymes, as well as their involvement in important processes such as microbial pathogenesis and greenhouse gas cycling (Lubitz and Tumas, 2007; Greening et al., 2019; Benoit et al., 2020; Ehhalt and Rohrer, 2022). The employment of hydrogenases and hydrogenase-based applications could also potentially facilitate the world's transition to a sustainable H2-based energy economy in the future.
Hydrogenases mediate a seemingly simple reaction, i.e., the splitting of H2 into a proton and a hydride, followed by the complete separation of protons and electrons. However, the reaction mechanisms of the different enzyme types are not yet fully understood. Likewise, the intricate maturation of the metal cofactors is a constant resource of unprecedented biological chemistry (Bortolus et al., 2018; Britt et al., 2020; Schulz et al., 2020; Arlt et al., 2021; Stripp et al., 2021; Pagnier et al., 2022; Arriaza-Gallardo et al., 2023; Caserta et al., 2023). Additionally, features such as the frequent membrane association and O2 sensitivity of hydrogenases has so far hindered in vitro harnessing of their function. New structural, spectroscopic, and electrochemical data and methods will enable new insights into their maturation and reactions. In addition, the discovery and characterization of diverse hydrogenases occurring in different microorganisms provide opportunities to discover new physiological roles, structural adaptations, and potential applications of these enzymes (Peters et al., 2015; Dragomirova et al., 2018; Schuchmann et al., 2018; Pinske, 2019; Winkler et al., 2021). Attempts to employ hydrogenases for industrial purposes have been made, however, there is presumably still a long way to go until processes involving hydrogenases (biological H2 production or biological fuel cells) will become economically feasible (Rögner, 2015; Ji et al., 2023; Xuan et al., 2023).
This Research Topic comprises 11 articles that aimed to bring together recent advances in hydrogenase research, including structure, function, maturation, and application. In terms of structural investigation, Dragelj et al. theoretically and experimentally analyzed an isolated large subunit of a [NiFe]-hydrogenase. They confirmed that [NiFe] large subunits dimerize in the absence of their small subunit (Hartmann et al., 2018; Kwon et al., 2018; Caserta et al., 2020), and showed that the [NiFe]-cofactor is stabilized by the dimerization. In the realm of structure-function relationships, Kisgeropoulos et al. investigated the effect of amino acid exchanges of the primary proteinaceous proton acceptor in [FeFe]-hydrogenase. The data expand previous work (Cornish et al., 2011; Morra et al., 2012; Duan et al., 2018; Artz et al., 2020), demonstrating that the pKa of the proton acceptor is one factor controlling the catalytic bias of the enzyme. Three further articles dealt with functional aspects of hydrogenases. Morra reviewed the identification and characterization of novel [FeFe]-hydrogenases, described their functional roles, and recent findings regarding their O2 tolerance. Kpebe et al. reported on the essential role of a bifurcating [FeFe]-hydrogenase in the sulfate reducer Solidesulfovibrio fructosivorans, showing that during ethanol oxidation, the hydrogenase confurcates electrons from NADH and reduced ferredoxin to produce H2, which is later on used for energy conservation using sulfate as electron acceptor. The function of a bidirectional [NiFe]-hydrogenase in Synechocystis sp. PCC 6803 was investigated by Burgstaller et al.. They showed that this hydrogenase is essential for growth on arginine and glucose in the presence of light and O2, and interestingly this function seems to be unrelated to H2 catalysis. Instead, an H2-independent role for the transfer of electrons into the photosynthetic electron transfer chain is proposed, which is an important hypothesis that may also be relevant for certain multisubunit hydrogenases in other species.
On the subtopic of hydrogenase maturation, Haase and Sawers investigated residues that contribute to [NiFe]-hydrogenase maturation. They found a histidine residue in a HypC-type chaperone that is important for efficient binding to its maturation partner HypD (Blokesch and Böck, 2002). In addition, this residue is important for selectivity, ensuring that only the correct large [NiFe]-hydrogenase subunit is matured. It should be emphasized that understanding cofactor maturation and incorporation is of high importance for any future application of hydrogenases, which is demonstrated in the following article. In an interdisciplinary approach in the fields of maturation and application, Fan et al. significantly improved the [NiFe]-cofactor incorporation in the course of heterologous production of a [NiFe]-hydrogenase from Cupriavidus necator in Escherichia coli. Previously, cofactor insertion was not functional, resulting in production of inactive hydrogenases (Fan et al., 2021).
Another four articles explore the application of hydrogenases. Hogendoorn et al. isolated the novel strain “Candidatus Hydrogenisulfobacillus filiaventi” R50 gen. nov., sp., nov. which was characterized as a chemolithoautotrophic thermoacidophilic aerobic H2-oxidizing bacterium. This strain excretes about half of the fixed CO2 in the form of amino acids, which makes it a promising candidate for the industrial production of organic compounds from CO2, using H2 as energy source. H2 oxidation in this strain is facilitated by two [NiFe]-hydrogenases from the groups 1b and 1h, with the latter conferring high affinity toward H2 (Søndergaard et al., 2016). Kobayashi et al. engineered the acetogenic bacterium Moorella thermoacetica for enhanced acetate, ethanol and acetone production. They found that H2 supplementation under mixotrophic conditions increases NADH levels but can inhibit growth due to an unbalanced redox status. This study emphasized the role of a reversible electron-bifurcating group A3 [FeFe]-hydrogenase for balancing the cellular redox state. These observations may also be exploited for biohydrogen production by that strain. Another way to produce H2 was analyzed by Barahona et al.. In order to enhance nitrogenase-driven H2 production in Rhodobacter capsulatus, they used a sensory hydrogenase coupled to the production of a fluorescence signal. By inducing genome-wide mutations and using high-throughput fluorescence-activated cell sorting, they were able to generate mutants with elevated H2 evolution capabilities. Finally, Schumann et al. reviewed current state-of-the-art and future perspectives for efficient light-driven H2 production using phototrophic microorganisms. This technology potentially enables conversion of solar energy into a chemical compound that enables storage and transport. However, as discussed by the authors, extensive engineering is required for this technology to be efficient and scalable.
Taken together, the Research Topic advances our knowledge especially on the function and application of hydrogenases and provides important perspectives for future H2-based biologically green technologies.
Author contributions
SF: Writing—original draft, Writing—review and editing. CP: Writing—review and editing. FV: Writing—review and editing. CG: Writing—review and editing.
Funding
Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy—EXC 2008–390540038—UniSysCat (SF).
Acknowledgments
We thank the Frontiers in Microbiology editorial team for their support. Even more importantly, we thank all reviewers for their critical comments and constructive suggestions.
Conflict of interest
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Publisher's note
All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.
References
Arlt, C., Nutschan, K., Haase, A., Ihling, C., Tänzler, D., Sinz, A., et al. (2021). Native mass spectrometry identifies the HybG chaperone as carrier of the Fe(CN)2CO group during maturation of E. coli [NiFe]-hydrogenase 2. Sci. Rep. 11, 24362. doi: 10.1038/s41598-021-03900-w
Arriaza-Gallardo, F. J., Zheng, Y.-C., Gehl, M., Nomura, S., Fernandes Queiroz, J. P., and Shima, S. (2023). [Fe]-hydrogenase, cofactor biosynthesis and engineering. Chem. Bio. Chem. 2023:e202300330. doi: 10.1002/cbic.202300330
Artz, J., Mulder, D., Ratzloff, M., Peters, J., and King, P. (2020). The Hydricity and Reactivity Relationship in [FeFe]-Hydrogenases. doi: 10.21203/rs.3.rs-77874/v1
Benoit, S. L., Maier, R. J., Sawers, R. G., and Greening, C. (2020). Molecular hydrogen metabolism: a widespread trait of pathogenic bacteria and protists. Microbiol. Mol. Biol. Rev. 84, 19. doi: 10.1128/MMBR.00092-19
Blokesch, M., and Böck, A. (2002). Maturation of [NiFe]-hydrogenases in Escherichia coli: the HypC cycle. J. Mol. Biol. 324, 287–296. doi: 10.1016/S0022-2836(02)01070-7
Bortolus, M., Costantini, P., Doni, D., and Carbonera, D. (2018). Overview of the maturation machinery of the H-cluster of [FeFe]-hydrogenases with a focus on HydF. Int. J. Mol. Sci. 19. doi: 10.3390/ijms19103118
Britt, R. D., Rao, G., and Tao, L. (2020). Biosynthesis of the catalytic H-cluster of [FeFe] hydrogenase: the roles of the Fe-S maturase proteins HydE, HydF, and HydG. Chem. Sci. 11, 10313–10323. doi: 10.1039/D0SC04216A
Caserta, G., Hartmann, S., van Stappen, C., Karafoulidi-Retsou, C., Lorent, C., Yelin, S., et al. (2023). Stepwise assembly of the active site of [NiFe]-hydrogenase. Nat. Chem. Biol. 19, 498–506. doi: 10.1038/s41589-022-01226-w
Caserta, G., Lorent, C., Ciaccafava, A., Keck, M., Breglia, R., Greco, C., et al. (2020). The large subunit of the regulatory [NiFe]-hydrogenase from Ralstonia eutropha- a minimal hydrogenase? Chem. Sci. 11, 5453–5465. doi: 10.1039/D0SC01369B
Cornish, A. J., Gärtner, K., Yang, H., Peters, J. W., and Hegg, E. L. (2011). Mechanism of proton transfer in [FeFe]-hydrogenase from Clostridium pasteurianum. J. Biol. Chem. 286, 38341–38347. doi: 10.1074/jbc.M111.254664
Dragomirova, N., Rothe, P., Schwoch, S., Hartwig, S., Pinske, C., and Sawers, R. G. (2018). Insights into the redox sensitivity of chloroflexi Hup-hydrogenase derived from studies in Escherichia coli: merits and pitfalls of heterologous [NiFe]-hydrogenase synthesis. Front. Microbiol. 9, 2837. doi: 10.3389/fmicb.2018.02837
Duan, J., Senger, M., Esselborn, J., Engelbrecht, V., Wittkamp, F., Apfel, U.-P., et al. (2018). Crystallographic and spectroscopic assignment of the proton transfer pathway in [FeFe]-hydrogenases. Nat. Commun. 9, 4726. doi: 10.1038/s41467-018-07140-x
Ehhalt, D. H., and Rohrer, F. (2022). The tropospheric cycle of H2: a critical review. Tellus B Chem. Phys. Meteorol. 61, 500. doi: 10.1111/j.1600-0889.2009.00416.x
Fan, Q., Caserta, G., Lorent, C., Lenz, O., Neubauer, P., and Gimpel, M. (2021). Optimization of culture conditions for oxygen-tolerant regulatory [NiFe]-hydrogenase production from Ralstonia eutropha H16 in Escherichia coli. Microorganisms 9, 61195. doi: 10.3390/microorganisms9061195
Greening, C., Biswas, A., Carere, C. R., Jackson, C. J., Taylor, M. C., Stott, M. B., et al. (2015). Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival. ISME J. 10, 761–77. doi: 10.1038/ismej.2015.153
Greening, C., Geier, R., Wang, C., Woods, L. C., Morales, S. E., McDonald, M. J., et al. (2019). Diverse hydrogen production and consumption pathways influence methane production in ruminants. ISME J. 13, 2617–2632. doi: 10.1038/s41396-019-0464-2
Hartmann, S., Frielingsdorf, S., Ciaccafava, A., Lorent, C., Fritsch, J., Siebert, E., et al. (2018). O2-tolerant H2 activation by an isolated large subunit of a [NiFe] hydrogenase. Biochemistry 57, 5339–5349. doi: 10.1021/acs.biochem.8b00760
Ji, H., Wan, L., Gao, Y., Du, P., Li, W., Luo, H., et al. (2023). Hydrogenase as the basis for green hydrogen production and utilization. J. Energy Chem. 85, 348–362. doi: 10.1016/j.jechem.2023.06.018
Kwon, S., Watanabe, S., Nishitani, Y., Kawashima, T., Kanai, T., Atomi, H., et al. (2018). Crystal structures of a [NiFe] hydrogenase large subunit HyhL in an immature state in complex with a Ni chaperone HypA. Proc. Natl. Acad. Sci. U.S.A. 115, 7045–7070. doi: 10.1073/pnas.1801955115
Lubitz, W., Ogata, H., Rüdiger, O., and Reijerse, E. (2014). Hydrogenases. Chem. Rev. 114, 4081–4148. doi: 10.1021/cr4005814
Lubitz, W., and Tumas, W. (2007). Hydrogen: an overview. Chem. Rev. 107, 3900–3903. doi: 10.1021/cr050200z
Morra, S., Giraudo, A., Di Nardo, G., King, P. W., Gilardi, G., and Valetti, F. (2012). Site saturation mutagenesis demonstrates a central role for cysteine 298 as proton donor to the catalytic site in CaHydA [FeFe]-hydrogenase. PloS ONE 7, e48400. doi: 10.1371/journal.pone.0048400
Pagnier, A., Balci, B., Shepard, E. M., Broderick, W. E., and Broderick, J. B. (2022). [FeFe]-hydrogenase in vitro maturation. Angew. Chem. Int. Ed. 61, e202212074. doi: 10.1002/anie.202212074
Peters, J. W., Schut, G. J., Boyd, E. S., Mulder, D. W., Shepard, E. M., Broderick, J. B., et al. (2015). [FeFe]- and [NiFe]-hydrogenase diversity, mechanism, and maturation. BBA - Mol. Cell Res. 1853, 1350–1369. doi: 10.1016/j.bbamcr.2014.11.021
Pinske, C. (2019). Bioenergetic aspects of archaeal and bacterial hydrogen metabolism. Adv. Microb. Physiol. 74, 487–514. doi: 10.1016/bs.ampbs.2019.02.005
Schuchmann, K., Chowdhury, N. P., and Müller, V. (2018). Complex multimeric [FeFe] hydrogenases: biochemistry, physiology and new opportunities for the Hydrogen Economy. Front. Microbiol. 9, 2911. doi: 10.3389/fmicb.2018.02911
Schulz, A.-C., Frielingsdorf, S., Pommerening, P., Lauterbach, L., Bistoni, G., Neese, F., et al. (2020). Formyltetrahydrofolate decarbonylase synthesizes the active site CO ligand of O2-tolerant [NiFe] Hydrogenase. J. Am. Chem. Soc. 142, 1457–1464. doi: 10.1021/jacs.9b11506
Schwartz, E., Fritsch, J., and Friedrich, B. (2013). “H2-metabolizing prokaryotes,” in The Prokaryotes, eds. E. Rosenberg, E. F. DeLong, S. Lory, E. Stackebrandt, and F. Thompson (Berlin: Springer Berlin Heidelberg), 119–199.
Søndergaard, D., Pedersen, C. N. S., and Greening, C. (2016). HydDB: A web tool for hydrogenase classification and analysis. Sci. Rep. 6, 34212. doi: 10.1038/srep34212
Stripp, S. T., Oltmanns, J., Müller, C. S., Ehrenberg, D., Schlesinger, R., Heberle, J., et al. (2021). Electron inventory of the iron-sulfur scaffold complex HypCD essential in [NiFe]-hydrogenase cofactor assembly. Biochem. J. 478, 3281–3295. doi: 10.1042/BCJ20210224
Winkler, M., Duan, J., Rutz, A., Felbek, C., Scholtysek, L., Lampret, O., et al. (2021). A safety cap protects hydrogenase from oxygen attack. Nat. Commun. 12, 756. doi: 10.1038/s41467-020-20861-2
Keywords: hydrogenase, metalloenzyme, hydrogen, metabolism, biotechnology, metal cofactor maturation
Citation: Frielingsdorf S, Pinske C, Valetti F and Greening C (2023) Editorial: Hydrogenase: structure, function, maturation, and application. Front. Microbiol. 14:1284540. doi: 10.3389/fmicb.2023.1284540
Received: 28 August 2023; Accepted: 12 September 2023;
Published: 22 September 2023.
Edited and reviewed by: David Emerson, Bigelow Laboratory for Ocean Sciences, United States
Copyright © 2023 Frielingsdorf, Pinske, Valetti and Greening. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Stefan Frielingsdorf, stefan.frielingsdorf@tu-berlin.de