AccScience Publishing / MI / Online First / DOI: 10.36922/mi.4544
ORIGINAL RESEARCH ARTICLE

Investigation of hydrogenase enzymes and the presence of orthologs in the human proteome

Grace Russell1,2*
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1 Department of Research and Development, Water Fuel Engineering, Wakefield, Yorkshire, United Kingdom
2 School of Applied Science, College of Health and Social Sciences, University of the West of England (UWE), Bristol, United Kingdom
Submitted: 15 August 2024 | Accepted: 10 October 2024 | Published: 18 November 2024
(This article belongs to the Special Issue Hydrogen and the Human Microbiome)
© 2024 by the Author(s). This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution 4.0 International License ( https://creativecommons.org/licenses/by/4.0/ )
Abstract

Hydrogenase enzymes catalyze the reversible oxidation/reduction of hydrogen (H2) and play a crucial role in microbial energy metabolism, with significant implications for human immunity. H2, produced by gut microbes during fermentation or administered exogenously, is vital in modulating oxidative stress and inflammation. In the gastrointestinal tract, microbial H2 production can reach up to 13 L/day, with approximately 71% of commensal bacteria capable of metabolizing H2. By interacting with complex I, particularly the NDUFS7 subunit, H₂ may reduce mitochondrial electron leakage and limit the generation of reactive oxygen species (ROS). Excessive ROS can trigger pro-inflammatory signaling and impair immune responses. This study investigated the presence of hydrogenase orthologs in the human proteome, particularly within mitochondrial complex I, and their potential role in immune function. This novel research highlights a possible evolutionary link between microbial hydrogenases and human immunity, suggesting that microbial-derived H2 may support immune homeostasis by mitigating oxidative stress and inflammation. Although human homologs of nickel/iron hydrogenases, such as NDUFS2 and NDUFS7, likely lack classical hydrogenase activity, sequence similarities between NDUFS7 and hydrogenase subunits in Asgard archaea and δ-proteobacteria indicate the conservation of potential redox-active sites. Redox activity, occurring at the N2 iron-sulfur cluster in NDUFS7, may influence mitochondrial oxidative stress responses, which are integral to immune regulation. These findings open new avenues for exploring the therapeutic potential of H₂ in immune regulation.

Keywords
Complex I
Evolution
Hydrogen
Hydrogenases
Redox activity
NDUFS7
Oxidative stress
Funding
This research was co-funded by Water Fuel Engineering and the University of the West of England. Funding identification number 7096050. Project code: RDAS0184.
Conflict of interest
This work was part-funded by Water Fuel Engineering, a manufacturer of oxy-hydrogen inhalation devices. Grace Russell is the Guest Editor of this special issue but was not involved in the editorial or peer-review processes for this paper, either directly or indirectly.
References
  1. Campbell C, Kandalgaonkar MR, Golonka RM, Yeoh BS, Vijay-Kumar M, Saha P. Crosstalk between gut microbiota and host immunity: Impact on inflammation and immunotherapy. Biomedicines. 2023;11(2):294. doi: 10.3390/biomedicines11020294

 

  1. Mann ER, Lam Y K, Uhlig HH. Short-chain fatty acids: Linking diet, the microbiome and immunity. Nat Revs Immunol. 2024;24:577-595. doi: 10.1038/s41577-024-01014-8

 

  1. Kim CH. Complex regulatory effects of gut microbial short-chain fatty acids on immune tolerance and autoimmunity. Cell Mol Immunol. 2023;20(4):341-350. doi: 10.1038/s41423-023-00987-1

 

  1. Checa J, Aran JM. Reactive oxygen species: Drivers of physiological and pathological processes. J Inflamm Res. 2020;13:1057-1073. doi: 10.2147/JIR.S275595

 

  1. Ohta S. Molecular hydrogen may activate the transcription factor Nrf2 to alleviate oxidative stress through the hydrogen-targeted porphyrin. Aging Pathobiol Ther. 2023;5(1):25-32. doi: 10.31491/APT.2023.03.104

 

  1. Shim JA, Ryu JH, Jo Y, Hong C. The role of gut microbiota in T cell immunity and immune mediated disorders. Int J Biol Sci. 2023;19(4):1178-1191. doi: 10.7150/ijbs.79430

 

  1. Wolf PG, Biswas A, Morales SE, Greening C, Gaskins HR. H2 metabolism is widespread and diverse among human colonic microbes. Gut Microbes. 2016;7(3):235-245. doi: 10.1080/19490976.2016.1182288

 

  1. Campbell A, Gdanetz K, Schmidt AW, Schmidt TM. H2 generated by fermentation in the human gut microbiome influences metabolism and competitive fitness of gut butyrate producers. Microbiome. 2023;11(1):133. doi: 10.1186/s40168-023-01565-3

 

  1. Sharma P, Parakh SK, Tsui TH, et al. Synergetic anaerobic digestion of food waste for enhanced production of biogas and value-added products: Strategies, challenges, and techno-economic analysis. Crit Rev Biotechnol. 2024;44(6):1040-1060. doi: 10.1080/07388551.2023.2241112

 

  1. Ohta S. Molecular hydrogen is a novel antioxidant to efficiently reduce oxidative stress with potential for the improvement of mitochondrial diseases. Biochim Biophys Acta. 2012;1820(5):586-594. doi: 10.1016/j.bbagen.2011.05.006

 

  1. LeBaron TW, Kura B, Kalocayova B, Tribulova N, Slezak J. A new approach for the prevention and treatment of cardiovascular disorders. Molecular hydrogen significantly reduces the effects of oxidative stress. Molecules. 2019;24(11):2076. doi: 10.3390/molecules24112076

 

  1. Alharbi AAD, Ebine N, Nakae S, Hojo T, Fukuoka Y. Application of molecular hydrogen as an antioxidant in responses to ventilatory and ergogenic adjustments during incremental exercise in humans. Nutrients. 2021;13(2):459. doi: 10.3390/nu13020459

 

  1. Artamonov MY, Martusevich AK, Pyatakovich FA, Minenko IA, Dlin SV, LeBaron TW. Molecular hydrogen: From molecular effects to stem cells management and tissue regeneration. Antioxidants. 2023;12(3):636. doi: 10.3390/antiox12030636

 

  1. Singh RB, Sumbalova Z, Fatima G, et al. Effects of molecular hydrogen in the pathophysiology and management of cardiovascular and metabolic diseases. Rev Cardiovasc Med. 2024;25(1):33. doi: 10.31083/j.rcm2501033

 

  1. Kucharská J, Gvozdjáková A, Kura B, Rausová Z, Slezák J. Effect of molecular hydrogen on coenzyme Q in plasma, myocardial tissue and mitochondria of rats. J Nutr Health Food Eng. 2018;8:362-364. doi: 10.15406/jnhfe.2018.08.00296

 

  1. Iuchi K, Nishimaki K, Kamimura N, Ohta S. Molecular hydrogen suppresses free-radical-induced cell death by mitigating fatty acid peroxidation and mitochondrial dysfunction. Can J Phys Pharm. 2019;97(10):999-1005. doi: 10.1139/cjpp-2018-0741

 

  1. Zhao N, Sun R, Cui Y, et al. High concentration hydrogen mitigates sepsis-induced acute lung injury in mice by alleviating mitochondrial fission and dysfunction. J. Pers Med. 2023;13(2):244. doi: 10.3390/jpm13020244

 

  1. Yang YX, Fei WY, Liu MS, et al. Molecular hydrogen promotes adipose-derived stem cell myogenic differentiation via regulation of mitochondria. Curr Stem Cell Res Ther. 2023;18(6):864-875. doi: 10.2174/1574888X17666220926115240

 

  1. Song L, Zhang Y, Zhu C, Ding X, Yang L, Yan H. Hydrogen-rich water partially alleviate inflammation, oxidative stress and intestinal flora dysbiosis in DSS-induced chronic ulcerative colitis mice. Adv Med Sci. 2022;67(1):29-38. doi: 10.1016/j.advms.2021.10.002

 

  1. Guo L, Liu M, Duan T. Hydrogen suppresses oxidative stress by inhibiting the p38 MAPK signaling pathway in preeclampsia. Adv Clin Exp Med. 2023;32(3):357-367. doi: 10.17219/acem/154623

 

  1. Begum R, Kim CS, Fadriquela A, et al. Molecular hydrogen protects against oxidative stress-induced RAW 264.7 macrophage cells through the activation of Nrf2 and inhibition of MAPK signaling pathway. Mol Cell Toxicol. 2020;16:103-118. doi: 10.1007/s13273-020-00074-w

 

  1. Lane N. Why are cells powered by proton gradients? Nat Educ. 2010;3(9):2. doi: 10.1038/46903

 

  1. White LM, Bhartia R, Stucky GD, Kanik I, Russell MJ. Mackinawite and greigite in ancient alkaline hydrothermal chimneys: Identifying potential key catalysts for emergent life. Earth Planet Sci Lett. 2015;100(430):105-114. doi: 10.1016/j.epsl.2015.08.013

 

  1. Piché-Choquette S, Constant P. Molecular hydrogen, a neglected key driver of soil biogeochemical processes. Appl Envirin Microbiol. 2019;85(6):e02418-18. doi: 10.1128/AEM.02418-18

 

  1. Russell MJ, Ponce A. Six “must-have” minerals for life’s emergence: Olivine, pyrrhotite, bridgmanite, serpentine, fougerite and mackinawite. Life (Basel). 2020;10(11):291. doi: 10.3390/life10110291

 

  1. Duval S, Zuchan K, Baymann F, et al. Minerals and the emergence of life. In: Kroneck P, Sosa Torres ME, editors. Metals in Life Sciences. Berlin: Springer; 2021. p. 135-157. doi: 10.1515/9783110589771-011

 

  1. Preiner M, Xavier JC, Vieira ADN, Kleinermanns K, Allen JF, Martin WF. Catalysts, autocatalysis and the origin of metabolism. Interface Focus. 2019;9(6):20190072. doi: 10.1098/rsfs.2019.0072

 

  1. Marreiros BC, Batista AP, Duarte AM, Pereira MM. A missing link between complex I and group 4 membrane-bound [NiFe] hydrogenases. Biochim Biophys Acta. 2013;1827(2):198-209. doi: 10.1016/j.bbabio.2012.09.012

 

  1. Read AD, Bentley RE, Archer SL, Dunham-Snary KJ. Mitochondrial iron-sulfur clusters: Structure, function, and an emerging role in vascular biology. Redox Biol. 2021;47:102164. doi: 10.1016/j.redox.2021.102164

 

  1. Greening C, Biswas A, Carere CR, et al. Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival. ISME J. 2016;10(3):761-777. doi: 10.1038/ismej.2015.153

 

  1. Lu F. Hypothetical hydrogenase activity of human mitochondrial Complex I and its role in preventing cancer transformation. Explor Res Hypothesis Med. 2023;8(3): 280-285. doi: 10.14218/ERHM.2022.00083

 

  1. López-García P, Moreira D. The syntrophy hypothesis for the origin of eukaryotes. In: Symbiosis: Mechanisms and Model Systems. Dordrecht: Springer Netherlands; 2001. p. 131-146. doi: 10.1007/0-306-48173-1_8

 

  1. López-García P, Moreira D. The syntrophy hypothesis for the origin of eukaryotes revisited. Nat Microbiol. 2020;5(5):655-667. doi: 10.1038/s41564-020-0710-4

 

  1. Ensembl Genome Browser 112. Available from: https://www. ensembl.org/index.html?redirect=no [Last accessed on 2023 Nov 13].

 

  1. EMBOSS Dotmatcher EMBL-EBI. Available from: https:// www.ebi.ac.uk/jdispatcher/seqstats/emboss_dotmatcher [Last accessed on 2023 Nov 14].

 

  1. Clustal Omega EMBL-EBI. Available from: https://www. ebi.ac.uk/jdispatcher/msa/clustalo [Last accessed on 2023 Nov 15].

 

  1. ScanProsite - SIB Swiss Institute of Bioinformatics Expasy. Available from: https://www.expasy.org/resources/ scanprosite [Last accessed on 2024 Jan 21].

 

  1. Anderson I, Brass A. Searching DNA databases for similarities to DNA sequences: When is a match significant? Bioinformatics. 1998;14(4):349-356. doi: 10.1093/bioinformatics/14.4.349

 

  1. Ge L, Qi J, Shao B, et al. Microbial hydrogen economy alleviates colitis by reprogramming colonocyte metabolism and reinforcing intestinal barrier. Gut Microbes. 2022;14(1):2013764. doi: 10.1080/19490976.2021.2013764

 

  1. Smith NW, Shorten PR, Altermann EH, Roy NC, McNabb WC. Hydrogen cross-feeders of the human gastrointestinal tract. Gut Microbes. 2019;10(3):270-288. doi: 10.1080/19490976.2018.1546522

 

  1. Ostojic SM. Hydrogen-rich water as a modulator of gut microbiota? J Funct Foods. 2021;78:104360. doi: 10.1016/j.jff.2021.104360

 

  1. Tanaka Y, Kiuchi M, Higashimura Y, Naito Y, Koyama K. The effects of ingestion of hydrogen-dissolved alkaline electrolyzed water on stool consistency and gut microbiota: A double-blind randomized trial. Med Gas Res. 2021;11(4):138-144. doi: 10.4103/2045-9912.318858

 

  1. Ichikawa Y, Yamamoto H, Hirano SI, Sato B, Takefuji Y, Satoh F. The overlooked benefits of hydrogen-producing bacteria. Med Gas Res. 2023;13(3):108-111. doi: 10.4103/2045-9912.344977

 

  1. Yokoyama K, Sakamaki A, Takahashi K, et al. Hydrogen-producing small intestinal bacterial overgrowth is associated with hepatic encephalopathy and liver function. PLoS One. 2022;17(2):e0264459. doi: 10.1371/journal.pone.0264459

 

  1. Graham DB, Xavier RJ. Conditioning of the immune system by the microbiome. Trends Immunol. 2023;44(7):499-511. doi: 10.1016/j.it.2023.05.002

 

  1. Miyauchi E, Shimokawa C, Steimle A, Desai MS, Ohno H. The impact of the gut microbiome on extra-intestinal autoimmune diseases. Nat Rev Immunol. 2023;23(1):9-23. doi: 10.1038/s41577-022-00727-y

 

  1. Hu J, Chen J, Xu X, Hou Q, Ren J, Yan X. Gut microbiota-derived 3-phenylpropionic acid promotes intestinal epithelial barrier function via AhR signaling. Microbiome. 2023;11(1):102.

 

  1. Poto R, Fusco W, Rinninella E, et al. The role of gut microbiota and leaky gut in the pathogenesis of food allergy. Nutrients. 2023;16(1):92. doi: 10.3390/nu16010092

 

  1. Herb M, Schramm M. Functions of ROS in macrophages and antimicrobial immunity. Antioxidants. 2021;10(2):313. doi: 10.3390/antiox10020313

 

  1. Sun L, Wang X, Saredy J, Yuan Z, Yang X, Wang H. Innate-adaptive immunity interplay and redox regulation in immune response. Redox Biol. 2020;37:101759. doi: 10.1016/j.redox.2020.101759

 

  1. Youn GS, Lee KW, Choi SY, Park J. Overexpression of HDAC6 induces pro-inflammatory responses by regulating ROS-MAPK-NF-κB/AP-1 signaling pathways in macrophages. Free Radic Biol Med. 2016;97:14-23. doi: 10.1016/j.freeradbiomed.2016.05.014

 

  1. Kim NY, Kim S, Park HM, et al. Cinnamomum verum extract inhibits NOX2/ROS and PKCδ/JNK/AP-1/NF-κB pathway-mediated inflammatory response in PMA-stimulated THP-1 monocytes. Phytomedicine. 2023;112:154685. doi: 10.1016/j.phymed.2023.154685

 

  1. Mazat JP, Devin A, Ransac S. Modelling mitochondrial ROS production by the respiratory chain. Cell Mol Life Sci. 2020;77(3):455-465. doi: 10.1007/s00018-019-03381-1

 

  1. Duong QV, Levitsky Y, Dessinger MJ, Strubbe-Rivera JO, Bazil JN. Identifying site-specific superoxide and hydrogen peroxide production rates from the mitochondrial electron transport system using a computational strategy. Function (Oxf). 2021;2(6):50. doi: 10.1093/function/zqab050

 

  1. Gvozdjáková A, Kucharská J, Kura B, et al. A new insight into the molecular hydrogen effect on coenzyme Q and mitochondrial function of rats. Can J Physiol Pharmacol. 2020;98(1):29-34. doi: 10.1139/cjpp-2019-0281

 

  1. Kishi S, Saito K, Kato Y, Ishikita H. Redox potentials of ubiquinone, menaquinone, phylloquinone, and plastoquinone in aqueous solution. Photosynth Res. 2017;134:193-200. doi: 10.1007/s11120-017-0433-4

 

  1. Wood PM. The two redox potentials for oxygen reduction to superoxide. Trends Biochem Sci. 1987;12:250-251.

 

  1. Jamialahmadi H, Khalili-Tanha G, Rezaei-Tavirani M, Nazari E. The effects of hydrogen-rich water on blood lipid profiles in metabolic disorders clinical trials: A systematic review and meta-analysis. Int J Endocrinol Metab. 2024;22(3):e148600. doi: 10.5812/ijem-148600

 

  1. Tian Y, Zhang Y, Wang Y, et al. Hydrogen, a novel therapeutic molecule, regulates oxidative stress, inflammation, and apoptosis. Front Physiol. 2021;12:789507. doi: 10.3389/fphys.2021.789507

 

  1. Niu Y, Nie Q, Dong L, et al. Hydrogen attenuates allergic inflammation by reversing energy metabolic pathway switch. Sci Rep. 2020;10(1):1962. doi: 10.1038/s41598-020-58999-0

 

  1. Hirano SI, Ichikawa Y, Sato B, Yamamoto H, Takefuji Y, Satoh F. Potential therapeutic applications of hydrogen in chronic inflammatory diseases: Possible inhibiting role on mitochondrial stress. Int J Mol Sci. 2021;22(5):2549. doi: 10.3390/ijms22052549

 

  1. Nogueira JE, Branco LG. Recent advances in molecular hydrogen research reducing exercise-induced oxidative stress and inflammation. Curr Pharm Des. 2021;27(5):731-736. doi: 10.2174/1381612826666201113100245

 

  1. Botek M, Krejčí J, McKune A, Valenta M, Sládečková B. Hydrogen rich water consumption positively affects muscle performance, lactate response, and alleviates delayed onset of muscle soreness after resistance training. J Strength Cond Res. 2022;36(10):2792-2799. doi: 10.1519/JSC.0000000000003979

 

  1. Lu KC, Shen MC, Wang RL, et al. Using oral molecular hydrogen supplements to combat microinflammation in humans: A pilot observational study. Int J Med Sci. 2024;21(12):2390-2401. doi: 10.7150/ijms.101114

 

  1. Tard C, Pickett CJ. Structural and functional analogues of the active sites of the [Fe]-, [NiFe]-, and [FeFe]-hydrogenases. Chem Rev. 2009;109(6):2245-2274. doi: 10.1021/cr800542q

 

  1. Ash PA, Kendall-Price SE, Vincent KA. Unifying activity, structure, and spectroscopy of [NiFe] hydrogenases: Combining techniques to clarify mechanistic understanding. Accounts Chem Res. 2019;52(11):3120-3131. doi: 10.1021/acs.accounts.9b00293

 

  1. Russell G, Zulfiqar F, Hancock JT. Hydrogenases and the role of molecular hydrogen in plants. Plants. 2020;9(9):1136. doi: 10.3390/plants9091136

 

  1. Kampjut D, Sazanov LA. The coupling mechanism of mammalian respiratory complex I. Science. 2020;370(6516):4209. doi: 10.1126/science.abc4209

 

  1. Kampjut D, Sazanov LA. Structure of respiratory complex I– an emerging blueprint for the mechanism. Curr Opin Struct Biol. 2022;74:102350. doi: 10.1016/j.sbi.2022.102350

 

  1. Pace CN, Horn G, Hebert EJ, et al. Tyrosine hydrogen bonds make a large contribution to protein stability. J Mol Biol. 2021;312(2):393-404. doi: 10.1006/jmbi.2001.4956

 

  1. Nicaise M, Valerio-Lepiniec M, Izadi-Pruneyre N, Adjadj E, Minard P, Desmadril M. Role of the tyrosine corner motif in the stability of neocarzinostatin. Protein Eng. 2003;16(10):733-738. doi: 10.1093/protein/gzg099

 

  1. Wirth C, Brandt U, Hunte C, Zickermann V. Structure and function of mitochondrial complex I. Biochim Biophys Acta. 2016;1857(7):902-914. doi: 10.1016/j.bbabio.2016.02.013

 

  1. Dunham-Snary KJ, Wu D, Potus F, et al. Ndufs2, a core subunit of mitochondrial complex I, is essential for acute oxygen-sensing and hypoxic pulmonary vasoconstriction. Circ Res. 2019;124(12):1727-1746. doi: 10.1161/CIRCRESAHA.118.31428

 

  1. Yoga EG, Angerer H, Parey K, Zickermann V. Respiratory complex I- mechanistic insights and advances in structure determination. Biochim Biophys Acta Bioenerg. 2020;1861(3):148153. doi: 10.1016/j.bbabio.2020.148153

 

  1. Ishihara G, Kawamoto K, Komori N, Ishibashi T. Molecular hydrogen suppresses superoxide generation in the mitochondrial complex I and reduced mitochondrial membrane potential. Biochem Biophys Res Commun. 2020;522(4):965-970. doi: 10.1016/j.bbrc.2019.11.135

 

  1. Shen K, Pender CL, Bar-Ziv R, et al. Mitochondria as cellular and organismal signaling hubs. Annu Rev Cell Dev Biol. 2022;38(1):179-218. doi: 10.1146/annurev-cellbio-120420-015303

 

  1. Wang B, Dai T, Sun W, et al. Protein N-myristoylation: Functions and mechanisms in control of innate immunity. Cell Mol Immunol. 2021;18(4):878-888. doi: 10.1038/s41423-021-00663-2

 

  1. Johnson JL, Yaron TM, Huntsman EM, et al. An atlas of substrate specificities for the human serine/threonine kinome. Nature. 2023;613(7945):759-766. doi: 10.1038/s41586-022-05575-3

 

  1. Fei W, Pang E, Hou L, et al. Synergistic effect of hydrogen and 5-Aza on myogenic differentiation through the p38 MAPK signaling pathway in adipose-derived mesenchymal stem cells. Int J Stem Cells. 2023;16(1):78-92. doi: 10.15283/ijsc21238

 

  1. Benjin X, Ling L. Developments, applications, and prospects of cryo-electron microscopy. Protein Sci. 2020;29(4):872-882. doi: 10.1002/pro.3805

 

  1. Murphy MP, Bayir H, Belousov V, et al. Guidelines for measuring reactive oxygen species and oxidative damage in cells and in vivo. Nat Metab. 2022;4(6):651-662. doi: 10.1038/s42255-022-00591-z

 

  1. Yoo JY, Groer M, Dutra SV, Sarkar A, McSkimming DI. Gut microbiota and immune system interactions. Microorganisms. 2020;8(10):1587. doi: 10.3390/microorganisms8101587

 

  1. Yang Y, Bin P, Tao S, et al. Evaluation of the mechanisms underlying amino acid and microbiota interactions in intestinal infections using germ-free animals. Infect Microbes Dis. 2021;3(2):79-86. doi: 10.1097/IM9.0000000000000060
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