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Mazzoli R, Pescarolo S, Gilli G, Gilardi G, Valetti F. Hydrogen production pathways in Clostridia and their improvement by metabolic engineering. Biotechnol Adv 2024; 73:108379. [PMID: 38754796 DOI: 10.1016/j.biotechadv.2024.108379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
Biological production of hydrogen has a tremendous potential as an environmentally sustainable technology to generate a clean fuel. Among the different available methods to produce biohydrogen, dark fermentation features the highest productivity and can be used as a means to dispose of organic waste biomass. Within this approach, Clostridia have the highest theoretical H2 production yield. Nonetheless, most strains show actual yields far lower than the theoretical maximum: improving their efficiency becomes necessary for achieving cost-effective fermentation processes. This review aims at providing a survey of the metabolic network involved in H2 generation in Clostridia and strategies used to improve it through metabolic engineering. Together with current achievements, a number of future perspectives to implement these results will be illustrated.
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Affiliation(s)
- Roberto Mazzoli
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123 Torino, Italy.
| | - Simone Pescarolo
- Biology applied to the environment, Laboratories of microbiology and ecotoxicology, Ecobioqual, Environment Park. Via Livorno 60, 10144 Torino, Italy
| | - Giorgio Gilli
- Department of Sciences of Public Health and Pediatrics, School of Medicine, University of Torino, Via Santena 5 bis, 10126 Torino, Italy
| | - Gianfranco Gilardi
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123 Torino, Italy
| | - Francesca Valetti
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123 Torino, Italy.
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2
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Kisgeropoulos EC, Artz JH, Blahut M, Peters JW, King PW, Mulder DW. Properties of the iron-sulfur cluster electron transfer relay in an [FeFe]-hydrogenase that is tuned for H 2 oxidation catalysis. J Biol Chem 2024; 300:107292. [PMID: 38636659 PMCID: PMC11126806 DOI: 10.1016/j.jbc.2024.107292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/20/2024] Open
Abstract
[FeFe]-hydrogenases catalyze the reversible oxidation of H2 from electrons and protons at an organometallic active site cofactor named the H-cluster. In addition to the H-cluster, most [FeFe]-hydrogenases possess accessory FeS cluster (F-cluster) relays that function in mediating electron transfer with catalysis. There is significant variation in the structural properties of F-cluster relays among the [FeFe]-hydrogenases; however, it is unknown how this variation relates to the electronic and thermodynamic properties, and thus the electron transfer properties, of enzymes. Clostridium pasteurianum [FeFe]-hydrogenase II (CpII) exhibits a large catalytic bias for H2 oxidation (compared to H2 production), making it a notable system for examining if F-cluster properties contribute to the overall function and efficiency of the enzyme. By applying a combination of multifrequency and potentiometric electron paramagnetic resonance, we resolved two electron paramagnetic resonance signals with distinct power- and temperature-dependent properties at g = 2.058 1.931 1.891 (F2.058) and g = 2.061 1.920 1.887 (F2.061), with assigned midpoint potentials of -140 ± 18 mV and -406 ± 12 mV versus normal hydrogen electrode, respectively. Spectral analysis revealed features consistent with spin-spin coupling between the two [4Fe-4S] F-clusters, and possible functional models are discussed that account for the contribution of coupling to the electron transfer landscape. The results signify the interplay of electronic coupling and free energy properties and parameters of the FeS clusters to the electron transfer mechanism through the relay and provide new insight as to how relays functionally complement the catalytic directionality of active sites to achieve highly efficient catalysis.
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Affiliation(s)
| | - Jacob H Artz
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Matthew Blahut
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - John W Peters
- Department of Chemistry and Biochemistry, The University of Oklahoma, Norman, Oklahoma, USA
| | - Paul W King
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA; Renewable and Sustainable Energy Institute, National Renewable Energy Laboratory and University of Colorado Boulder, Boulder, Colorado, USA
| | - David W Mulder
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA.
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Alleman AB, Peters JW. Mechanisms for Generating Low Potential Electrons across the Metabolic Diversity of Nitrogen-Fixing Bacteria. Appl Environ Microbiol 2023; 89:e0037823. [PMID: 37154716 PMCID: PMC10231201 DOI: 10.1128/aem.00378-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
The availability of fixed nitrogen is a limiting factor in the net primary production of all ecosystems. Diazotrophs overcome this limit through the conversion of atmospheric dinitrogen to ammonia. Diazotrophs are phylogenetically diverse bacteria and archaea that exhibit a wide range of lifestyles and metabolisms, including obligate anaerobes and aerobes that generate energy through heterotrophic or autotrophic metabolisms. Despite the diversity of metabolisms, all diazotrophs use the same enzyme, nitrogenase, to reduce N2. Nitrogenase is an O2-sensitive enzyme that requires a high amount of energy in the form of ATP and low potential electrons carried by ferredoxin (Fd) or flavodoxin (Fld). This review summarizes how the diverse metabolisms of diazotrophs utilize different enzymes to generate low potential reducing equivalents for nitrogenase catalysis. These enzymes include substrate-level Fd oxidoreductases, hydrogenases, photosystem I or other light-driven reaction centers, electron bifurcating Fix complexes, proton motive force-driven Rnf complexes, and Fd:NAD(P)H oxidoreductases. Each of these enzymes is critical for generating low potential electrons while simultaneously integrating the native metabolism to balance nitrogenase's overall energy needs. Understanding the diversity of electron transport systems to nitrogenase in various diazotrophs will be essential to guide future engineering strategies aimed at expanding the contributions of biological nitrogen fixation in agriculture.
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Affiliation(s)
- Alexander B. Alleman
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - John W. Peters
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
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Genome-Scale Mining of Acetogens of the Genus Clostridium Unveils Distinctive Traits in [FeFe]- and [NiFe]-Hydrogenase Content and Maturation. Microbiol Spectr 2022; 10:e0101922. [PMID: 35735976 PMCID: PMC9431212 DOI: 10.1128/spectrum.01019-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Knowledge of the organizational and functional properties of hydrogen metabolism is pivotal to the construction of a framework supportive of a hydrogen-fueled low-carbon economy. Hydrogen metabolism relies on the mechanism of action of hydrogenases. In this study, we investigated the genomes of several industrially relevant acetogens of the genus Clostridium (C. autoethanogenum, C. ljungdahlii, C. carboxidivorans, C. drakei, C. scatologenes, C. coskatii, C. ragsdalei, C. sp. AWRP) to systematically identify their intriguingly diversified hydrogenases’ repertoire. An entirely computational annotation pipeline unveiled common and strain-specific traits in the functional content of [NiFe]- and [FeFe]-hydrogenases. Hydrogenases were identified and categorized into functionally distinct classes by the combination of sequence homology, with respect to a database of curated nonredundant hydrogenases, with the analysis of sequence patterns characteristic of the mode of action of [FeFe]- and [NiFe]-hydrogenases. The inspection of the genes in the neighborhood of the catalytic subunits unveiled a wide agreement between their genomic arrangement and the gene organization templates previously developed for the predicted hydrogenase classes. Subunits’ characterization of the identified hydrogenases allowed us to glean some insights on the redox cofactor-binding determinants in the diaphorase subunits of the electron-bifurcating [FeFe]-hydrogenases. Finally, the reliability of the inferred hydrogenases was corroborated by the punctual analysis of the maturation proteins necessary for the biosynthesis of [NiFe]- and [FeFe]-hydrogenases. IMPORTANCE Mastering hydrogen metabolism can support a sustainable carbon-neutral economy. Of the many microorganisms metabolizing hydrogen, acetogens of the genus Clostridium are appealing, with some of them already in usage as industrial workhorses. Having provided detailed information on the hydrogenase content of an unprecedented number of clostridial acetogens at the gene level, our study represents a valuable knowledge base to deepen our understanding of hydrogenases’ functional specificity and/or redundancy and to develop a large array of biotechnological processes. We also believe our study could serve as a basis for future strain-engineering approaches, acting at the hydrogenases’ level or at the level of their maturation proteins. On the other side, the wealth of functional elements discussed in relation to the identified hydrogenases is worthy of further investigation by biochemical and structural studies to ultimately lead to the usage of these enzymes as valuable catalysts.
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Morra S. Fantastic [FeFe]-Hydrogenases and Where to Find Them. Front Microbiol 2022; 13:853626. [PMID: 35308355 PMCID: PMC8924675 DOI: 10.3389/fmicb.2022.853626] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/10/2022] [Indexed: 01/01/2023] Open
Abstract
[FeFe]-hydrogenases are complex metalloenzymes, key to microbial energy metabolism in numerous organisms. During anaerobic metabolism, they dissipate excess reducing equivalents by using protons from water as terminal electron acceptors, leading to hydrogen production. This reaction is coupled to reoxidation of specific redox partners [ferredoxins, NAD(P)H or cytochrome c3], that can be used either individually or simultaneously (via flavin-based electron bifurcation). [FeFe]-hydrogenases also serve additional physiological functions such as H2 uptake (oxidation), H2 sensing, and CO2 fixation. This broad functional spectrum is enabled by a modular architecture and vast genetic diversity, which is not fully explored and understood. This Mini Review summarises recent advancements in identifying and characterising novel [FeFe]-hydrogenases, which has led to expanding our understanding of their multiple roles in metabolism and functional mechanisms. For example, while numerous well-known [FeFe]-hydrogenases are irreversibly damaged by oxygen, some newly discovered enzymes display intrinsic tolerance. These findings demonstrate that oxygen sensitivity varies between different [FeFe]-hydrogenases: in some cases, protection requires the presence of exogenous compounds such as carbon monoxide or sulphide, while in other cases it is a spontaneous built-in mechanism that relies on a reversible conformational change. Overall, it emerges that additional research is needed to characterise new [FeFe]-hydrogenases as this will reveal further details on the physiology and mechanisms of these enzymes that will enable potential impactful applications.
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Affiliation(s)
- Simone Morra
- Faculty of Engineering, University of Nottingham, Nottingham, United Kingdom
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ACETONE-BUTYL FERMENTATION PECULIARITIES OF THE BUTANOL STRAINS -PRODUCER. BIOTECHNOLOGIA ACTA 2022. [DOI: 10.15407/biotech15.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The aim of this review was to generalize and analyze the features of acetone-butyl fermentation as a type of butyric acid fermentation in the process of obtaining butanol as an alternative biofuel. Methods. The methods of analysis and generalization of analytical information and literature sources were used in the review. The results were obtained using the following methods such as microbiological (morphological properties of strains), chromatographic (determination of solvent concentration), spectrophotometric (determination of bacterial concentration), and molecular genetic (phylogenetic analysis of strains). Results. The process of acetone-butyl fermentation was analyzed, the main producer strains were considered, the features of the relationship between alcohol formation and sporulation were described, the possibility of butanol obtaining from synthesis gas was shown, and the features of the industrial production of butanol were considered. Conclusions. The features of the mechanism of acetone-butyl fermentation (the relationships between alcohol formation and sporulation, the duration of the acid-forming and alcohol-forming stages during batch fermentation depending on the change in the concentration of H2, CO, partial pressure, organic acids and mineral additives) and obtaining an enrichment culture during the production of butanol as an alternative fuel were shown. The possibility of using synthesis gas as a substrate for reducing atmospheric emissions during the fermentation process was shown. The direction of increasing the productivity of butanol-producing strains to create a competitive industrial biofuel technology was proposed.
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Fasano A, Land H, Fourmond V, Berggren G, Léger C. Reversible or Irreversible Catalysis of H +/H 2 Conversion by FeFe Hydrogenases. J Am Chem Soc 2021; 143:20320-20325. [PMID: 34813699 DOI: 10.1021/jacs.1c09554] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Studies of molecular catalysts traditionally aim at understanding how a certain mechanism allows the reaction to be fast. A distinct question, which has only recently received attention in the case of bidirectional molecular catalysts, is how much thermodynamic driving force is required to achieve fast catalysis in either direction of the reaction. "Reversible" catalysts are bidirectional catalysts that work either way in response to even a small departure from equilibrium and thus do not waste input free energy as heat; conversely, "irreversible" catalysts require a large driving force to proceed at an appreciable rate [Fourmond et al. Nat. Rev. Chem. 2021, 5, 348-360]. Numerous mechanistic rationales for these contrasting behaviors have been proposed. To understand the determinants of catalytic (ir)reversibility, we examined the steady-state, direct electron transfer voltammetry of a particular FeFe hydrogenase, from Thermoanaerobacter mathranii, which is very unusual in that it irreversibly catalyzes H2 oxidation and production: a large overpotential is required for the reaction to proceed in either direction [Land et al. Chem. Sci. 2020, 11, 12789-12801]. In contrast to previous hypotheses, we demonstrate that in this particular enzyme catalytic irreversibility can be explained without invoking slow interfacial electron transfer or variations in the mechanism: the observed kinetics is fully consistent with the same catalytic pathway being used in both directions of the reaction.
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Affiliation(s)
- Andrea Fasano
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, Aix Marseille Université, 31 ch. Joseph Aiguier, 13009 Marseille, France
| | - Henrik Land
- Molecular Biomimetics, Department of Chemistry-Ångström, Uppsala University, Box-523, Uppsala 751 20, Sweden
| | - Vincent Fourmond
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, Aix Marseille Université, 31 ch. Joseph Aiguier, 13009 Marseille, France
| | - Gustav Berggren
- Molecular Biomimetics, Department of Chemistry-Ångström, Uppsala University, Box-523, Uppsala 751 20, Sweden
| | - Christophe Léger
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, Aix Marseille Université, 31 ch. Joseph Aiguier, 13009 Marseille, France
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8
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Arizzi M, Morra S, Gilardi G, Pugliese M, Gullino ML, Valetti F. Improving sustainable hydrogen production from green waste: [FeFe]-hydrogenases quantitative gene expression RT-qPCR analysis in presence of autochthonous consortia. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:182. [PMID: 34530890 PMCID: PMC8444407 DOI: 10.1186/s13068-021-02028-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 08/28/2021] [Indexed: 06/01/2023]
Abstract
BACKGROUND Bio-hydrogen production via dark fermentation of low-value waste is a potent and simple mean of recovering energy, maximising the harvesting of reducing equivalents to produce the cleanest fuel amongst renewables. Following several position papers from companies and public bodies, the hydrogen economy is regaining interest, especially in combination with circular economy and the environmental benefits of short local supply chains, aiming at zero net emission of greenhouse gases (GHG). The biomasses attracting the largest interest are agricultural and urban green wastes (pruning of trees, collected leaves, grass clippings from public parks and boulevards), which are usually employed in compost production, with some concerns over the GHG emission during the process. Here, an alternative application of green wastes, low-value compost and intermediate products (partially composted but unsuitable for completing the process) is studied, pointing at the autochthonous microbial consortium as an already selected source of implementation for biomass degradation and hydrogen production. The biocatalysts investigated as mainly relevant for hydrogen production were the [FeFe]-hydrogenases expressed in Clostridia, given their very high turnover rates. RESULTS Bio-hydrogen accumulation was related to the modulation of gene expression of multiple [FeFe]-hydrogenases from two strains (Clostridium beijerinckii AM2 and Clostridium tyrobutyricum AM6) isolated from the same waste. Reverse Transcriptase quantitative PCR (RT-qPCR) was applied over a period of 288 h and the RT-qPCR results showed that C. beijerinckii AM2 prevailed over C. tyrobutyricum AM6 and a high expression modulation of the 6 different [FeFe]-hydrogenase genes of C. beijerinckii in the first 23 h was observed, sustaining cumulative hydrogen production of 0.6 to 1.2 ml H2/g VS (volatile solids). These results are promising in terms of hydrogen yields, given that no pre-treatment was applied, and suggested a complex cellular regulation, linking the performance of dark fermentation with key functional genes involved in bio-H2 production in presence of the autochthonous consortium, with different roles, time, and mode of expression of the involved hydrogenases. CONCLUSIONS An applicative outcome of the hydrogenases genes quantitative expression analysis can be foreseen in optimising (on the basis of the acquired functional data) hydrogen production from a nutrient-poor green waste and/or low added value compost, in a perspective of circular bioeconomy.
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Affiliation(s)
- M Arizzi
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123, Torino, Italy
- Acea Engineering Laboratories Research Innovation SpA, Roma, Italy
| | - S Morra
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123, Torino, Italy
- Faculty of Engineering, University of Nottingham, Nottingham, UK
| | - G Gilardi
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123, Torino, Italy
| | - M Pugliese
- Centre of Competence for Innovation in Agro-Environmental Field (Agroinnova) and DiSAFA, University of Torino, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy
- AgriNewTech Srl, Via Livorno 60, 10140, Torino, Italy
| | - M L Gullino
- Centre of Competence for Innovation in Agro-Environmental Field (Agroinnova) and DiSAFA, University of Torino, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy
- AgriNewTech Srl, Via Livorno 60, 10140, Torino, Italy
| | - F Valetti
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123, Torino, Italy.
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Intasian P, Prakinee K, Phintha A, Trisrivirat D, Weeranoppanant N, Wongnate T, Chaiyen P. Enzymes, In Vivo Biocatalysis, and Metabolic Engineering for Enabling a Circular Economy and Sustainability. Chem Rev 2021; 121:10367-10451. [PMID: 34228428 DOI: 10.1021/acs.chemrev.1c00121] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Since the industrial revolution, the rapid growth and development of global industries have depended largely upon the utilization of coal-derived chemicals, and more recently, the utilization of petroleum-based chemicals. These developments have followed a linear economy model (produce, consume, and dispose). As the world is facing a serious threat from the climate change crisis, a more sustainable solution for manufacturing, i.e., circular economy in which waste from the same or different industries can be used as feedstocks or resources for production offers an attractive industrial/business model. In nature, biological systems, i.e., microorganisms routinely use their enzymes and metabolic pathways to convert organic and inorganic wastes to synthesize biochemicals and energy required for their growth. Therefore, an understanding of how selected enzymes convert biobased feedstocks into special (bio)chemicals serves as an important basis from which to build on for applications in biocatalysis, metabolic engineering, and synthetic biology to enable biobased processes that are greener and cleaner for the environment. This review article highlights the current state of knowledge regarding the enzymatic reactions used in converting biobased wastes (lignocellulosic biomass, sugar, phenolic acid, triglyceride, fatty acid, and glycerol) and greenhouse gases (CO2 and CH4) into value-added products and discusses the current progress made in their metabolic engineering. The commercial aspects and life cycle assessment of products from enzymatic and metabolic engineering are also discussed. Continued development in the field of metabolic engineering would offer diversified solutions which are sustainable and renewable for manufacturing valuable chemicals.
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Affiliation(s)
- Pattarawan Intasian
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Kridsadakorn Prakinee
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Aisaraphon Phintha
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand.,Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Duangthip Trisrivirat
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Nopphon Weeranoppanant
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand.,Department of Chemical Engineering, Faculty of Engineering, Burapha University, 169, Long-hard Bangsaen, Saensook, Muang, Chonburi 20131, Thailand
| | - Thanyaporn Wongnate
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
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Abstract
We describe as 'reversible' a bidirectional catalyst that allows a reaction to proceed at a significant rate in response to even a small departure from equilibrium, resulting in fast and energy-efficient chemical transformation. Examining the relation between reaction rate and thermodynamic driving force is the basis of electrochemical investigations of redox reactions, which can be catalysed by metallic surfaces and biological or synthetic molecular catalysts. This relation has also been discussed in the context of biological energy transduction, regarding the function of biological molecular machines that harness chemical reactions to do mechanical work. This Perspective describes mean-field kinetic modelling of these three types of systems - surface catalysts, molecular catalysts of redox reactions and molecular machines - with the goal of unifying concepts in these different fields. We emphasize that reversibility should be distinguished from other figures of merit, such as rate or directionality, before its design principles can be identified and used to engineer synthetic catalysts.
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Li B, Steindel P, Haddad N, Elliott SJ. Maximizing (Electro)catalytic CO 2 Reduction with a Ferredoxin-Based Reduction Potential Gradient. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Bin Li
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Phillip Steindel
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Narmien Haddad
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Sean J. Elliott
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
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12
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Corrigan PS, Tirsch JL, Silakov A. Investigation of the Unusual Ability of the [FeFe] Hydrogenase from Clostridium beijerinckii to Access an O 2-Protected State. J Am Chem Soc 2020; 142:12409-12419. [PMID: 32580545 DOI: 10.1021/jacs.0c04964] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[FeFe] hydrogenases are enzymes capable of producing and oxidizing H2 at staggering submillisecond time scales. A major limitation in applying these enzymes for industrial hydrogen production is their irreversible inactivation by oxygen. Recently, an [FeFe] hydrogenase from Clostridium beijerinckii (CbHydA1) was reported to regain its catalytic activity after exposure to oxygen. In this report, we have determined that artificially matured CbHydA1 is indeed oxygen tolerant in the absence of reducing agents and sulfides by means of reaching an O2-protected state (Hinact). We were also able to generate the Hinact state anaerobically via both chemical and electrochemical oxidation. We use a combination of spectroscopy, electrochemistry, and density functional theory (DFT) to uncover intrinsic properties of the active center of CbHydA1, leading to its unprecedented oxygen tolerance. We have observed that reversible, low-potential oxidation of the active center leads to the protection against O2-induced degradation. The transition between the active oxidized state (Hox) and the Hinact state appears to proceed without any detectable intermediates. We found that the Hinact state is stable for more than 40 h in air, highlighting the remarkable resilience of CbHydA1 to oxygen. Using a combination of DFT and FTIR, we also provide a hypothesis for the chemical identity of the Hinact state. These results demonstrate that CbHydA1 has remarkable stability in the presence of oxygen, which will drive future efforts to engineer more robust catalysts for biofuel production.
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Affiliation(s)
- Patrick S Corrigan
- The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802, United States
| | - Jonathan L Tirsch
- The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802, United States
| | - Alexey Silakov
- The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802, United States
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13
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Abstract
As the only enzyme currently known to reduce dinitrogen (N2) to ammonia (NH3), nitrogenase is of significant interest for bio-inspired catalyst design and for new biotechnologies aiming to produce NH3 from N2. In order to reduce N2, nitrogenase must also hydrolyze at least 16 equivalents of adenosine triphosphate (MgATP), representing the consumption of a significant quantity of energy available to biological systems. Here, we review natural and engineered electron transfer pathways to nitrogenase, including strategies to redirect or redistribute electron flow in vivo towards NH3 production. Further, we also review strategies to artificially reduce nitrogenase in vitro, where MgATP hydrolysis is necessary for turnover, in addition to strategies that are capable of bypassing the requirement of MgATP hydrolysis to achieve MgATP-independent N2 reduction.
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Alterations of the Predominant Fecal Microbiota and Disruption of the Gut Mucosal Barrier in Patients with Early-Stage Colorectal Cancer. BIOMED RESEARCH INTERNATIONAL 2020; 2020:2948282. [PMID: 32280686 PMCID: PMC7114766 DOI: 10.1155/2020/2948282] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/18/2020] [Accepted: 03/09/2020] [Indexed: 12/16/2022]
Abstract
Growing evidence indicated that the gut microbiota was the intrinsic and essential component of the cancer microenvironment, which played vital roles in the development and progression of colorectal cancer (CRC). In our present study, we investigated the alterations of fecal abundant microbiota with real-time quantitative PCR and the changes of indicators of gut mucosal barrier from 53 early-stage CRC patients and 45 matched healthy controls. We found that the traditional beneficial bacteria such as Lactobacillus and Bifidobacterium decreased significantly and the carcinogenic bacteria such as Enterobacteriaceae and Fusobacterium nucleatum were significantly increased in CRC patients. We also found gut mucosal barrier dysfunction in CRC patients with increased levels of endotoxin (LPS), D-lactate, and diamine oxidase (DAO). With Pearson's correlation analysis, D-lactate, LPS, and DAO were correlated negatively with Lactobacillus and Bifidobacterium and positively with Enterobacteriaceae and F. nucleatum. Our present study found dysbiosis of the fecal microbiota and dysfunction of the gut mucosal barrier in patients with early-stage CRC, which implicated that fecal abundant bacteria and gut mucosal barrier indicators could be used as targets to monitor the development and progression of CRC in a noninvasive and dynamic manner.
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Benoit SL, Maier RJ, Sawers RG, Greening C. Molecular Hydrogen Metabolism: a Widespread Trait of Pathogenic Bacteria and Protists. Microbiol Mol Biol Rev 2020; 84:e00092-19. [PMID: 31996394 PMCID: PMC7167206 DOI: 10.1128/mmbr.00092-19] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Pathogenic microorganisms use various mechanisms to conserve energy in host tissues and environmental reservoirs. One widespread but often overlooked means of energy conservation is through the consumption or production of molecular hydrogen (H2). Here, we comprehensively review the distribution, biochemistry, and physiology of H2 metabolism in pathogens. Over 200 pathogens and pathobionts carry genes for hydrogenases, the enzymes responsible for H2 oxidation and/or production. Furthermore, at least 46 of these species have been experimentally shown to consume or produce H2 Several major human pathogens use the large amounts of H2 produced by colonic microbiota as an energy source for aerobic or anaerobic respiration. This process has been shown to be critical for growth and virulence of the gastrointestinal bacteria Salmonella enterica serovar Typhimurium, Campylobacter jejuni, Campylobacter concisus, and Helicobacter pylori (including carcinogenic strains). H2 oxidation is generally a facultative trait controlled by central regulators in response to energy and oxidant availability. Other bacterial and protist pathogens produce H2 as a diffusible end product of fermentation processes. These include facultative anaerobes such as Escherichia coli, S Typhimurium, and Giardia intestinalis, which persist by fermentation when limited for respiratory electron acceptors, as well as obligate anaerobes, such as Clostridium perfringens, Clostridioides difficile, and Trichomonas vaginalis, that produce large amounts of H2 during growth. Overall, there is a rich literature on hydrogenases in growth, survival, and virulence in some pathogens. However, we lack a detailed understanding of H2 metabolism in most pathogens, especially obligately anaerobic bacteria, as well as a holistic understanding of gastrointestinal H2 transactions overall. Based on these findings, we also evaluate H2 metabolism as a possible target for drug development or other therapies.
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Affiliation(s)
- Stéphane L Benoit
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Robert J Maier
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - R Gary Sawers
- Institute of Microbiology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton, VIC, Australia
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16
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Artz JH, Zadvornyy OA, Mulder DW, Keable SM, Cohen AE, Ratzloff MW, Williams SG, Ginovska B, Kumar N, Song J, McPhillips SE, Davidson CM, Lyubimov AY, Pence N, Schut GJ, Jones AK, Soltis SM, Adams MWW, Raugei S, King PW, Peters JW. Tuning Catalytic Bias of Hydrogen Gas Producing Hydrogenases. J Am Chem Soc 2019; 142:1227-1235. [PMID: 31816235 PMCID: PMC8653774 DOI: 10.1021/jacs.9b08756] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogenases display a wide range of catalytic rates and biases in reversible hydrogen gas oxidation catalysis. The interactions of the iron-sulfur-containing catalytic site with the local protein environment are thought to contribute to differences in catalytic reactivity, but this has not been demonstrated. The microbe Clostridium pasteurianum produces three [FeFe]-hydrogenases that differ in "catalytic bias" by exerting a disproportionate rate acceleration in one direction or the other that spans a remarkable 6 orders of magnitude. The combination of high-resolution structural work, biochemical analyses, and computational modeling indicates that protein secondary interactions directly influence the relative stabilization/destabilization of different oxidation states of the active site metal cluster. This selective stabilization or destabilization of oxidation states can preferentially promote hydrogen oxidation or proton reduction and represents a simple yet elegant model by which a protein catalytic site can confer catalytic bias.
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Affiliation(s)
- Jacob H. Artz
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, United States
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Oleg A. Zadvornyy
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - David W. Mulder
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Stephen M. Keable
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Michael W. Ratzloff
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - S. Garrett Williams
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Bojana Ginovska
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Neeraj Kumar
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jinhu Song
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Scott E. McPhillips
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Catherine M. Davidson
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Artem Y. Lyubimov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Natasha Pence
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Gerrit J. Schut
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Anne K. Jones
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - S. Michael Soltis
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Michael W. W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Simone Raugei
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, United States
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Paul W. King
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - John W. Peters
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, United States
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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17
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Mus F, Colman DR, Peters JW, Boyd ES. Geobiological feedbacks, oxygen, and the evolution of nitrogenase. Free Radic Biol Med 2019; 140:250-259. [PMID: 30735835 DOI: 10.1016/j.freeradbiomed.2019.01.050] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/31/2019] [Indexed: 12/21/2022]
Abstract
Biological nitrogen fixation via the activity of nitrogenase is one of the most important biological innovations, allowing for an increase in global productivity that eventually permitted the emergence of higher forms of life. The complex metalloenzyme termed nitrogenase contains complex iron-sulfur cofactors. Three versions of nitrogenase exist that differ mainly by the presence or absence of a heterometal at the active site metal cluster (either Mo or V). Mo-dependent nitrogenase is the most common while V-dependent or heterometal independent (Fe-only) versions are often termed alternative nitrogenases since they have apparent lower activities for N2 reduction and are expressed in the absence of Mo. Phylogenetic data indicates that biological nitrogen fixation emerged in an anaerobic, thermophilic ancestor of hydrogenotrophic methanogens and later diversified via lateral gene transfer into anaerobic bacteria, and eventually aerobic bacteria including Cyanobacteria. Isotopic evidence suggests that nitrogenase activity existed at 3.2 Ga, prior to the advent of oxygenic photosynthesis and rise of oxygen in the atmosphere, implying the presence of favorable environmental conditions for oxygen-sensitive nitrogenase to evolve. Following the proliferation of oxygenic phototrophs, diazotrophic organisms had to develop strategies to protect nitrogenase from oxygen inactivation and generate the right balance of low potential reducing equivalents and cellular energy for growth and nitrogen fixation activity. Here we review the fundamental advances in our understanding of biological nitrogen fixation in the context of the emergence, evolution, and taxonomic distribution of nitrogenase, with an emphasis placed on key events associated with its emergence and diversification from anoxic to oxic environments.
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Affiliation(s)
- Florence Mus
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Daniel R Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA.
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA.
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18
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Lindsay MR, Colman DR, Amenabar MJ, Fristad KE, Fecteau KM, Debes RV, Spear JR, Shock EL, Hoehler TM, Boyd ES. Probing the geological source and biological fate of hydrogen in Yellowstone hot springs. Environ Microbiol 2019; 21:3816-3830. [PMID: 31276280 DOI: 10.1111/1462-2920.14730] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 07/01/2019] [Indexed: 12/01/2022]
Abstract
Hydrogen (H2 ) is enriched in hot springs and can support microbial primary production. Using a series of geochemical proxies, a model to describe variable H2 concentrations in Yellowstone National Park (YNP) hot springs is presented. Interaction between water and crustal iron minerals yields H2 that partition into the vapour phase during decompressional boiling of ascending hydrothermal fluids. Variable vapour input leads to differences in H2 concentration among springs. Analysis of 50 metagenomes from a variety of YNP springs reveals that genes encoding oxidative hydrogenases are enriched in communities inhabiting springs sourced with vapour-phase gas. Three springs in the Smokejumper (SJ) area of YNP that are sourced with vapour-phase gas and with the most H2 in YNP were examined to determine the fate of H2 . SJ3 had the most H2 , the most 16S rRNA gene templates and the greatest abundance of culturable hydrogenotrophic and autotrophic cells of the three springs. Metagenomics and transcriptomics of SJ3 reveal a diverse community comprised of abundant populations expressing genes involved in H2 oxidation and carbon dioxide fixation. These observations suggest a link between geologic processes that generate and source H2 to hot springs and the distribution of organisms that use H2 to generate energy.
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Affiliation(s)
- Melody R Lindsay
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Daniel R Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | | | | | - Randall V Debes
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ, USA
| | - John R Spear
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CZ, USA
| | - Everett L Shock
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA.,School of Earth and Space Exploration, Arizona State University, Tempe, AZ, USA
| | | | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
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19
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Fourmond V, Wiedner ES, Shaw WJ, Léger C. Understanding and Design of Bidirectional and Reversible Catalysts of Multielectron, Multistep Reactions. J Am Chem Soc 2019; 141:11269-11285. [PMID: 31283209 DOI: 10.1021/jacs.9b04854] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Some enzymes, including those that are involved in the activation of small molecules such as H2 or CO2, can be wired to electrodes and function in either direction of the reaction depending on the electrochemical driving force and display a significant rate at very small deviations from the equilibrium potential. We call the former property "bidirectionality" and the latter "reversibility". This performance sets very high standards for chemists who aim at designing synthetic electrocatalysts. Only recently, in the particular case of the hydrogen production/evolution reaction, has it been possible to produce inorganic catalysts that function bidirectionally, with an even smaller number that also function reversibly. This raises the question of how to engineer such desirable properties in other synthetic catalysts. Here we introduce the kinetic modeling of bidirectional two-electron-redox reactions in the case of molecular catalysts and enzymes that are either attached to an electrode or diffusing in solution in the vicinity of an electrode. We emphasize that trying to discuss bidirectionality and reversibility in relation to a single redox potential leads to an impasse: the catalyst undergoes two redox transitions, and therefore two catalytic potentials must be defined, which may depart from the two potentials measured in the absence of catalysis. The difference between the two catalytic potentials defines the reversibility; the difference between their average value and the equilibrium potential defines the directionality (also called "preference", or "bias"). We describe how the sequence of events in the bidirectional catalytic cycle can be elucidated on the basis of the voltammetric responses. Further, we discuss the design principles of bidirectionality and reversibility in terms of thermodynamics and kinetics and conclude that neither bidirectionality nor reversibility requires that the catalytic energy landscape be flat. These theoretical findings are illustrated by previous results obtained with nickel diphosphine molecular catalysts and hydrogenases. In particular, analysis of the nickel catalysts highlights the fact that reversible catalysis can be achieved by catalysts that follow complex mechanisms with branched reaction pathways.
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Affiliation(s)
- Vincent Fourmond
- Aix Marseille Université , CNRS, BIP UMR 7281 , Marseille , France
| | - Eric S Wiedner
- Pacific Northwest National Laboratory , P.O. Box 999, K2-57, Richland , Washington 99352 , United States
| | - Wendy J Shaw
- Pacific Northwest National Laboratory , P.O. Box 999, K2-57, Richland , Washington 99352 , United States
| | - Christophe Léger
- Aix Marseille Université , CNRS, BIP UMR 7281 , Marseille , France
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20
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Baffert C, Kpebe A, Avilan L, Brugna M. Hydrogenases and H 2 metabolism in sulfate-reducing bacteria of the Desulfovibrio genus. Adv Microb Physiol 2019; 74:143-189. [PMID: 31126530 DOI: 10.1016/bs.ampbs.2019.03.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Hydrogen metabolism plays a central role in sulfate-reducing bacteria of the Desulfovibrio genus and is based on hydrogenases that catalyze the reversible conversion of protons into dihydrogen. These metabolically versatile microorganisms possess a complex hydrogenase system composed of several enzymes of both [FeFe]- and [NiFe]-type that can vary considerably from one Desulfovibrio species to another. This review covers the molecular and physiological aspects of hydrogenases and H2 metabolism in Desulfovibrio but focuses particularly on our model bacterium Desulfovibrio fructosovorans. The search of hydrogenase genes in more than 30 sequenced genomes provides an overview of the distribution of these enzymes in Desulfovibrio. Our discussion will consider the significance of the involvement of electron-bifurcation in H2 metabolism.
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Affiliation(s)
- Carole Baffert
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Arlette Kpebe
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Luisana Avilan
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Myriam Brugna
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
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21
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Utesch T, Sabra W, Prescher C, Baur J, Arbter P, Zeng A. Enhanced electron transfer of different mediators for strictly opposite shifting of metabolism inClostridium pasteurianumgrown on glycerol in a new electrochemical bioreactor. Biotechnol Bioeng 2019; 116:1627-1643. [DOI: 10.1002/bit.26963] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 02/08/2019] [Accepted: 02/28/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Tyll Utesch
- Institute of Bioprocess and Biosystems EngineeringHamburg University of Technology Denickestrasse Hamburg Germany
| | - Wael Sabra
- Institute of Bioprocess and Biosystems EngineeringHamburg University of Technology Denickestrasse Hamburg Germany
| | - Christin Prescher
- Institute of Bioprocess and Biosystems EngineeringHamburg University of Technology Denickestrasse Hamburg Germany
| | - Julian Baur
- Institute of Bioprocess and Biosystems EngineeringHamburg University of Technology Denickestrasse Hamburg Germany
| | - Philipp Arbter
- Institute of Bioprocess and Biosystems EngineeringHamburg University of Technology Denickestrasse Hamburg Germany
| | - An‐Ping Zeng
- Institute of Bioprocess and Biosystems EngineeringHamburg University of Technology Denickestrasse Hamburg Germany
- Beijing Advanced Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical Technology Chaoyang District Beijing China
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22
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Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria. Nat Commun 2019; 10:463. [PMID: 30692531 PMCID: PMC6349859 DOI: 10.1038/s41467-018-08246-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 12/18/2018] [Indexed: 01/06/2023] Open
Abstract
The evolution of aerobic respiration was likely linked to the origins of oxygenic Cyanobacteria. Close phylogenetic neighbors to Cyanobacteria, such as Margulisbacteria (RBX-1 and ZB3), Saganbacteria (WOR-1), Melainabacteria and Sericytochromatia, may constrain the metabolic platform in which aerobic respiration arose. Here, we analyze genomic sequences and predict that sediment-associated Margulisbacteria have a fermentation-based metabolism featuring a variety of hydrogenases, a streamlined nitrogenase, and electron bifurcating complexes involved in cycling of reducing equivalents. The genomes of ocean-associated Margulisbacteria encode an electron transport chain that may support aerobic growth. Some Saganbacteria genomes encode various hydrogenases, and others may be able to use O2 under certain conditions via a putative novel type of heme copper O2 reductase. Similarly, Melainabacteria have diverse energy metabolisms and are capable of fermentation and aerobic or anaerobic respiration. The ancestor of all these groups may have been an anaerobe in which fermentation and H2 metabolism were central metabolic features. The ability to use O2 as a terminal electron acceptor must have been subsequently acquired by these lineages. Most cyanobacteria are oxygenic photoautotrophs, and fermenters under dark anoxic conditions. Here, the authors analyse genomic sequences of related uncultivated bacteria, inferring their metabolic potential, and supporting that their common ancestor was an anaerobe capable of fermentation and H2 metabolism.
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23
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Clostridial whole cell and enzyme systems for hydrogen production: current state and perspectives. Appl Microbiol Biotechnol 2018; 103:567-575. [PMID: 30446778 DOI: 10.1007/s00253-018-9514-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/06/2018] [Accepted: 11/09/2018] [Indexed: 10/27/2022]
Abstract
Strictly anaerobic bacteria of the Clostridium genus have attracted great interest as potential cell factories for molecular hydrogen production purposes. In addition to being a useful approach to this process, dark fermentation has the advantage of using the degradation of cheap agricultural residues and industrial wastes for molecular hydrogen production. However, many improvements are still required before large-scale hydrogen production from clostridial metabolism is possible. Here we review the literature on the basic biological processes involved in clostridial hydrogen production, and present the main advances obtained so far in order to enhance the hydrogen productivity, as well as suggesting some possible future prospects.
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24
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Ratzloff MW, Artz JH, Mulder DW, Collins RT, Furtak TE, King PW. CO-Bridged H-Cluster Intermediates in the Catalytic Mechanism of [FeFe]-Hydrogenase CaI. J Am Chem Soc 2018; 140:7623-7628. [PMID: 29792026 DOI: 10.1021/jacs.8b03072] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The [FeFe]-hydrogenases ([FeFe] H2ases) catalyze reversible H2 activation at the H-cluster, which is composed of a [4Fe-4S]H subsite linked by a cysteine thiolate to a bridged, organometallic [2Fe-2S] ([2Fe]H) subsite. Profoundly different geometric models of the H-cluster redox states that orchestrate the electron/proton transfer steps of H2 bond activation have been proposed. We have examined this question in the [FeFe] H2ase I from Clostridium acetobutylicum (CaI) by Fourier-transform infrared (FTIR) spectroscopy with temperature annealing and H/D isotope exchange to identify the relevant redox states and define catalytic transitions. One-electron reduction of Hox led to formation of HredH+ ([4Fe-4S]H2+-FeI-FeI) and Hred' ([4Fe-4S]H1+-FeII-FeI), with both states characterized by low frequency μ-CO IR modes consistent with a fully bridged [2Fe]H. Similar μ-CO IR modes were also identified for HredH+ of the [FeFe] H2ase from Chlamydomonas reinhardtii (CrHydA1). The CaI proton-transfer variant C298S showed enrichment of an H/D isotope-sensitive μ-CO mode, a component of the hydride bound H-cluster IR signal, Hhyd. Equilibrating CaI with increasing amounts of NaDT, and probed at cryogenic temperatures, showed HredH+ was converted to Hhyd. Over an increasing temperature range from 10 to 260 K catalytic turnover led to loss of Hhyd and appearance of Hox, consistent with enzymatic turnover and H2 formation. The results show for CaI that the μ-CO of [2Fe]H remains bridging for all of the "Hred" states and that HredH+ is on pathway to Hhyd and H2 evolution in the catalytic mechanism. These results provide a blueprint for designing small molecule catalytic analogs.
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Affiliation(s)
- Michael W Ratzloff
- Biosciences Center , National Renewable Energy Laboratory , Golden , Colorado 80401 , United States
| | - Jacob H Artz
- Biosciences Center , National Renewable Energy Laboratory , Golden , Colorado 80401 , United States
| | - David W Mulder
- Biosciences Center , National Renewable Energy Laboratory , Golden , Colorado 80401 , United States
| | - Reuben T Collins
- Physics Department , Colorado School of Mines , Golden , Colorado 80401 , United States
| | - Thomas E Furtak
- Physics Department , Colorado School of Mines , Golden , Colorado 80401 , United States
| | - Paul W King
- Biosciences Center , National Renewable Energy Laboratory , Golden , Colorado 80401 , United States
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25
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Electron Transfer to Nitrogenase in Different Genomic and Metabolic Backgrounds. J Bacteriol 2018; 200:JB.00757-17. [PMID: 29483165 DOI: 10.1128/jb.00757-17] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 02/16/2018] [Indexed: 11/20/2022] Open
Abstract
Nitrogenase catalyzes the reduction of dinitrogen (N2) using low-potential electrons from ferredoxin (Fd) or flavodoxin (Fld) through an ATP-dependent process. Since its emergence in an anaerobic chemoautotroph, this oxygen (O2)-sensitive enzyme complex has evolved to operate in a variety of genomic and metabolic backgrounds, including those of aerobes, anaerobes, chemotrophs, and phototrophs. However, whether pathways of electron delivery to nitrogenase are influenced by these different metabolic backgrounds is not well understood. Here, we report the distribution of homologs of Fds, Flds, and Fd-/Fld-reducing enzymes in 359 genomes of putative N2 fixers (diazotrophs). Six distinct lineages of nitrogenase were identified, and their distributions largely corresponded to differences in the host cells' ability to integrate O2 or light into energy metabolism. The predicted pathways of electron transfer to nitrogenase in aerobes, facultative anaerobes, and phototrophs varied from those in anaerobes at the levels of Fds/Flds used to reduce nitrogenase, the enzymes that generate reduced Fds/Flds, and the putative substrates of these enzymes. Proteins that putatively reduce Fd with hydrogen or pyruvate were enriched in anaerobes, while those that reduce Fd with NADH/NADPH were enriched in aerobes, facultative anaerobes, and anoxygenic phototrophs. The energy metabolism of aerobic, facultatively anaerobic, and anoxygenic phototrophic diazotrophs often yields reduced NADH/NADPH that is not sufficiently reduced to drive N2 reduction. At least two mechanisms have been acquired by these taxa to overcome this limitation and to generate electrons with potentials capable of reducing Fd. These include the bifurcation of electrons or the coupling of Fd reduction to reverse ion translocation.IMPORTANCE Nitrogen fixation supplies fixed nitrogen to cells from a variety of genomic and metabolic backgrounds, including those of aerobes, facultative anaerobes, chemotrophs, and phototrophs. Here, using informatics approaches applied to genomic data, we show that pathways of electron transfer to nitrogenase in metabolically diverse diazotrophic taxa have diversified primarily in response to host cells' acquired ability to integrate O2 or light into their energy metabolism. The acquisition of two key enzyme complexes enabled aerobic and facultatively anaerobic phototrophic taxa to generate electrons of sufficiently low potential to reduce nitrogenase: the bifurcation of electrons via the Fix complex or the coupling of Fd reduction to reverse ion translocation via the Rhodobacter nitrogen fixation (Rnf) complex.
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26
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Caserta G, Papini C, Adamska-Venkatesh A, Pecqueur L, Sommer C, Reijerse E, Lubitz W, Gauquelin C, Meynial-Salles I, Pramanik D, Artero V, Atta M, Del Barrio M, Faivre B, Fourmond V, Léger C, Fontecave M. Engineering an [FeFe]-Hydrogenase: Do Accessory Clusters Influence O 2 Resistance and Catalytic Bias? J Am Chem Soc 2018; 140:5516-5526. [PMID: 29595965 DOI: 10.1021/jacs.8b01689] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[FeFe]-hydrogenases, HydAs, are unique biocatalysts for proton reduction to H2. However, they suffer from a number of drawbacks for biotechnological applications: size, number and diversity of metal cofactors, oxygen sensitivity. Here we show that HydA from Megasphaera elsdenii (MeHydA) displays significant resistance to O2. Furthermore, we produced a shorter version of this enzyme (MeH-HydA), lacking the N-terminal domain harboring the accessory FeS clusters. As shown by detailed spectroscopic and biochemical characterization, MeH-HydA displays the following interesting properties. First, a functional active site can be assembled in MeH-HydA in vitro, providing the enzyme with excellent hydrogenase activity. Second, the resistance of MeHydA to O2 is conserved in MeH-HydA. Third, MeH-HydA is more biased toward proton reduction than MeHydA, as the result of the truncation changing the rate limiting steps in catalysis. This work shows that it is possible to engineer HydA to generate an active hydrogenase that combines the resistance of the most resistant HydAs and the simplicity of algal HydAs, containing only the H-cluster.
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Affiliation(s)
- Giorgio Caserta
- Laboratoire de Chimie des Processus Biologiques , Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University , 11 place Marcelin Berthelot , 75005 Paris , France
| | - Cecilia Papini
- Laboratoire de Chimie des Processus Biologiques , Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University , 11 place Marcelin Berthelot , 75005 Paris , France
| | - Agnieszka Adamska-Venkatesh
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques , Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University , 11 place Marcelin Berthelot , 75005 Paris , France
| | - Constanze Sommer
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany
| | - Edward Reijerse
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany
| | - Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany
| | - Charles Gauquelin
- LISBP , Université de Toulouse, CNRS, INRA, INSA , Toulouse , France
| | | | - Debajyoti Pramanik
- Laboratoire de Chimie et Biologie des Métaux , Université Grenoble Alpes, CEA/BIG, CNRS , 17 rue des martyrs , 38000 Grenoble , France
| | - Vincent Artero
- Laboratoire de Chimie et Biologie des Métaux , Université Grenoble Alpes, CEA/BIG, CNRS , 17 rue des martyrs , 38000 Grenoble , France
| | - Mohamed Atta
- Laboratoire de Chimie et Biologie des Métaux , Université Grenoble Alpes, CEA/BIG, CNRS , 17 rue des martyrs , 38000 Grenoble , France
| | - Melisa Del Barrio
- Aix Marseille Université , CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines UMR 7281 , 13400 Marseille , France
| | - Bruno Faivre
- Laboratoire de Chimie des Processus Biologiques , Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University , 11 place Marcelin Berthelot , 75005 Paris , France
| | - Vincent Fourmond
- Aix Marseille Université , CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines UMR 7281 , 13400 Marseille , France
| | - Christophe Léger
- Aix Marseille Université , CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines UMR 7281 , 13400 Marseille , France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques , Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University , 11 place Marcelin Berthelot , 75005 Paris , France
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27
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Lampret O, Adamska-Venkatesh A, Konegger H, Wittkamp F, Apfel UP, Reijerse EJ, Lubitz W, Rüdiger O, Happe T, Winkler M. Interplay between CN - Ligands and the Secondary Coordination Sphere of the H-Cluster in [FeFe]-Hydrogenases. J Am Chem Soc 2017; 139:18222-18230. [PMID: 29179539 DOI: 10.1021/jacs.7b08735] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The catalytic cofactor of [FeFe]-hydrogenses (H-cluster) is composed of a generic cubane [4Fe-4S]-cluster (4FeH) linked to a binuclear iron-sulfur cluster (2FeH) that has an open coordination site at which the reversible conversion of protons to molecular hydrogen occurs. The (2FeH) subsite features a diatomic coordination sphere composed of three CO and two CN- ligands affecting its redox properties and providing excellent probes for FTIR spectroscopy. The CO stretch vibrations are very sensitive to the redox changes within the H-cluster occurring during the catalytic cycle, whereas the CN- signals seem to be relatively inert to these effects. This could be due to the more structural role of the CN- ligands tightly anchoring the (2FeH) unit to the protein environment through hydrogen bonding. In this work we explore the effects of structural changes within the secondary ligand sphere affecting the CN- ligands on FTIR spectroscopy and catalysis. By comparing the FTIR spectra of wild-type enzyme and two mutagenesis variants, we are able to assign the IR signals of the individual CN- ligands of the (2FeH) site for different redox states of the H-cluster. Moreover, protein film electrochemistry reveals that targeted manipulation of the secondary coordination sphere of the proximal CN- ligand (i.e., closest to the (4FeH) site) can affect the catalytic bias. These findings highlight the importance of the protein environment for re-adjusting the catalytic features of the H-cluster in individual enzymes and provide valuable information for the design of artificial hydrogenase mimics.
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Affiliation(s)
- Oliver Lampret
- Fakultät für Biologie und Biotechnologie, Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie, Ruhr Universität Bochum , Universitätsstraße 150, 44801 Bochum, Germany
| | - Agnieszka Adamska-Venkatesh
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Hannes Konegger
- Fakultät für Biologie und Biotechnologie, Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie, Ruhr Universität Bochum , Universitätsstraße 150, 44801 Bochum, Germany
| | - Florian Wittkamp
- Fakultät für Chemie und Biochemie, Lehrstuhl für Anorganische Chemie I-Bioanorganische Chemie, Ruhr Universität Bochum , Universitätsstraße 150, 44801 Bochum, Germany
| | - Ulf-Peter Apfel
- Fakultät für Chemie und Biochemie, Lehrstuhl für Anorganische Chemie I-Bioanorganische Chemie, Ruhr Universität Bochum , Universitätsstraße 150, 44801 Bochum, Germany
| | - Edward J Reijerse
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Olaf Rüdiger
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Thomas Happe
- Fakultät für Biologie und Biotechnologie, Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie, Ruhr Universität Bochum , Universitätsstraße 150, 44801 Bochum, Germany
| | - Martin Winkler
- Fakultät für Biologie und Biotechnologie, Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie, Ruhr Universität Bochum , Universitätsstraße 150, 44801 Bochum, Germany
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