1
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Wang L, Cheng X, Guo Y, Cao J, Sun M, Hwang JS, Liu R, Fang J. Novel isolates of hydrogen-oxidizing chemolithoautotrophic Sulfurospirillum provide insight to the functions and adaptation mechanisms of Campylobacteria in shallow-water hydrothermal vents. mSystems 2024:e0014824. [PMID: 39166872 DOI: 10.1128/msystems.00148-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 07/24/2024] [Indexed: 08/23/2024] Open
Abstract
Enhancing the availability of representative isolates from hydrothermal vents (HTVs) is imperative for comprehending the microbial processes that propel the vent ecosystem. In recent years, Campylobacteria have emerged as the predominant and ubiquitous taxon across both shallow and deep-sea vent systems. Nevertheless, only a few isolates have been cultured, primarily originating from deep-sea HTVs. Presently, no cultivable isolates of Campylobacteria are accessible in shallow water vent systems (<200 m), which exhibit markedly distinct environmental conditions from their deep-sea counterparts. In this study, we enriched a novel isolate (genus Sulfurospirillum, Campylobacteria) from shallow-water HTVs of Kueishan Island. Genomic and physiological analysis revealed that this novel Campylobacteria species grows on a variety of substrate and carbon/energy sources. The pan-genome and phenotypic comparisons with 12 previously isolated Sulfurospirillum species from different environments supported the identification of functional features in Sulfurospirillum genomes crucial for adaptation to vent environments, such as sulfur oxidation, carbon fixation, biofilm formation, and benzoate/toluene degradation, as well as diverse genes related with signal transportation. To conclude, the metabolic characteristics of this novel Campylobacteria augment our understanding of Campylobacteria spanning from deep-sea to shallow-water vent systems.IMPORTANCECampylobacteria emerge as the dominant and ubiquitous taxa within vent systems, playing important roles in the vent ecosystems. However, isolated representatives of Campylobacteria have been mainly from the deep-sea hydrothermal fields, leaving a significant knowledge gap regarding the functions, activities, and adaptation strategies of the vent microorganisms in shallow-water hydrothermal vents (HTVs). This study bridges this gap by providing insights into the phenomics and genomic diversity of genus Sulfurospirillum (order Campylobacterales, class Campylobacteria) based on data derived from a novel isolate obtained from shallow-water HTVs. Our mesophilic isolate of Sulfurospirillum not only augments the genus diversity of Campylobacteria pure cultures derived from vent systems but also serves as the inaugural reference isolate for Campylobacteria in shallow-water environments.
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Affiliation(s)
- Li Wang
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, China
| | - Xinyi Cheng
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, China
| | - Yizhe Guo
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, China
| | - Junwei Cao
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, China
| | - Mingye Sun
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, China
| | - Jiang-Shiou Hwang
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, Taiwan
| | - Rulong Liu
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, China
| | - Jiasong Fang
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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2
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Mota VT, Delforno TP, Ribeiro JC, Zaiat M, Oliveira VMD. Understanding microbiome dynamics and functional responses during acidogenic fermentation of sucrose and sugarcane vinasse through metatranscriptomic analysis. ENVIRONMENTAL RESEARCH 2024; 246:118150. [PMID: 38218518 DOI: 10.1016/j.envres.2024.118150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/20/2023] [Accepted: 01/05/2024] [Indexed: 01/15/2024]
Abstract
Improving anaerobic digestion of sugarcane vinasse - a high-strength wastewater from ethanol distillation - is a subject of great interest, in view of the reduction of the pollutants and recovery of methane and valuable metabolites as byproducts. Through metatranscriptomic analysis, this study evaluated the active microbiome and metabolic pathways in a continuous acidogenic reactor: Stage 1S (control): 100% sucrose-based substrate (SBS); Stage 2SV (acclimation): 50% SBS and 50% vinasse; Stage 3V: 100% vinasse. Metatranscriptome obtained from each Stage was subjected to taxonomic and functional annotations. Under SBS feeding, pH dropped to pH 2.7 and biohydrogen production was observed. As vinasse was added, pH increased to 4.1-4.5, resulting in community structure and metabolite changes. In Stage 3V, biohydrogen production ceased, and propionate and acetate prevailed among the volatile fatty acids. Release of homoacetogenesis enzymes by Clostridium ljungdahlii and of uptake hydrogenase (EC 1.12.99.6) by Pectinatus frisingensis were linked to hydrogen consumption in Stages 2SV and 3V. Metabolic pathways of vinasse compounds, such as carbohydrates, malate, oxalate, glycerol, sulfate and phenol, were investigated in detail. In pyruvate metabolism, gene transcripts of oadA (oxaloacetate decarboxylase) and mdh (malate dehydrogenase), were upregulated in Stage 3V, being mostly attributed to P. frisingensis. Acetate formation from vinasse degradation was mainly attributed to Megasphaera and Clostridium, and propionate formation to P. frisingensis. Glycerol removal from vinasse exceeded 99%, and gene transcripts encoding for glpF (glycerol uptake facilitator protein), glpK (glycerol kinase) and glpABC (glycerol-3-phosphate dehydrogenase) were expressed mostly by Pectinatus and Prevotella. mRNA profiling showed that active bacteria and gene expression greatly changed when vinasse replaced sucrose, and Pectinatus was the main active bacterium degrading the searched compounds from vinasse. The identification of the main metabolic routes and the associated microorganisms achieved in this work contributes with valuable information to support further optimization of fermentation towards the desired metabolites.
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Affiliation(s)
- Vera T Mota
- Research Center for Chemistry, Biology and Agriculture Research, University of Campinas (CPQBA/Unicamp), Paulínia, SP, Brazil.
| | - Tiago P Delforno
- SENAI Innovation Institute for Biotechnology, São Paulo, SP, Brazil
| | - Jaqueline C Ribeiro
- Biological Processes Laboratory, São Carlos School of Engineering, University of São Paulo (LPB/EESC/USP), São Carlos, SP, Brazil
| | - Marcelo Zaiat
- Biological Processes Laboratory, São Carlos School of Engineering, University of São Paulo (LPB/EESC/USP), São Carlos, SP, Brazil
| | - Valéria M de Oliveira
- Research Center for Chemistry, Biology and Agriculture Research, University of Campinas (CPQBA/Unicamp), Paulínia, SP, Brazil
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3
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Song Y, Finkelstein R, Rhoads W, Edwards MA, Pruden A. Shotgun Metagenomics Reveals Impacts of Copper and Water Heater Anodes on Pathogens and Microbiomes in Hot Water Plumbing Systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:13612-13624. [PMID: 37643149 PMCID: PMC10501123 DOI: 10.1021/acs.est.3c03568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/31/2023]
Abstract
Hot water building plumbing systems are vulnerable to the proliferation of opportunistic pathogens (OPs), including Legionella pneumophila and Mycobacterium avium. Implementation of copper as a disinfectant could help reduce OPs, but a mechanistic understanding of the effects on the microbial community under real-world plumbing conditions is lacking. Here, we carried out a controlled pilot-scale study of hot water systems and applied shotgun metagenomic sequencing to examine the effects of copper dose (0-2 mg/L), orthophosphate corrosion control agent, and water heater anode materials (aluminum vs magnesium vs powered anode) on the bulk water and biofilm microbiome composition. Metagenomic analysis revealed that, even though a copper dose of 1.2 mg/L was required to reduce Legionella and Mycobacterium numbers, lower doses (e.g., ≤0.6 mg/L) measurably impacted the broader microbial community, indicating that the OP strains colonizing these systems were highly copper tolerant. Orthophosphate addition reduced bioavailability of copper, both to OPs and to the broader microbiome. Functional gene analysis indicated that both membrane damage and interruption of nucleic acid replication are likely at play in copper inactivation mechanisms. This study identifies key factors (e.g., orthophosphate, copper resistance, and anode materials) that can confound the efficacy of copper for controlling OPs in hot water plumbing.
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Affiliation(s)
- Yang Song
- Civil
and Environmental Engineering, Virginia
Tech, 1145 Perry St., 418 Durham Hall, Blacksburg, Virginia 24061, United States
- Utilities
Department, Town of Cary, 316 N. Academy St., Cary, North Carolina 27512, United States
| | - Rachel Finkelstein
- Civil
and Environmental Engineering, Virginia
Tech, 1145 Perry St., 418 Durham Hall, Blacksburg, Virginia 24061, United States
- AECOM, 3101 Wilson Boulevard, Arlington, Virginia 22201, United States
| | - William Rhoads
- Civil
and Environmental Engineering, Virginia
Tech, 1145 Perry St., 418 Durham Hall, Blacksburg, Virginia 24061, United States
- Black
& Veatch, 8400 Ward
Pkwy, Kansas City, Missouri 64114, United States
| | - Marc A. Edwards
- Civil
and Environmental Engineering, Virginia
Tech, 1145 Perry St., 418 Durham Hall, Blacksburg, Virginia 24061, United States
| | - Amy Pruden
- Civil
and Environmental Engineering, Virginia
Tech, 1145 Perry St., 418 Durham Hall, Blacksburg, Virginia 24061, United States
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4
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Allan MG, Pichon T, McCune JA, Cavazza C, Le Goff A, Kühnel MF. Augmenting the Performance of Hydrogenase for Aerobic Photocatalytic Hydrogen Evolution via Solvent Tuning. Angew Chem Int Ed Engl 2023; 62:e202219176. [PMID: 36786366 PMCID: PMC10946759 DOI: 10.1002/anie.202219176] [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] [Received: 12/27/2022] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023]
Abstract
This work showcases the performance of [NiFeSe] hydrogenase from Desulfomicrobium baculatum for solar-driven hydrogen generation in a variety of organic-based deep eutectic solvents. Despite its well-known sensitivity towards air and organic solvents, the hydrogenase shows remarkable performance under an aerobic atmosphere in these solvents when paired with a TiO2 photocatalyst. Tuning the water content further increases hydrogen evolution activity to a TOF of 60±3 s-1 and quantum yield to 2.3±0.4 % under aerobic conditions, compared to a TOF of 4 s-1 in a purely aqueous solvent. Contrary to common belief, this work therefore demonstrates that placing natural hydrogenases into non-natural environments can enhance their intrinsic activity beyond their natural performance, paving the way for full water splitting using hydrogenases.
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Affiliation(s)
- Michael G. Allan
- Department of ChemistryFaculty of Science and EngineeringSwansea UniversitySingleton ParkSwanseaSA2 8PPWalesUK
| | - Thomas Pichon
- Univ. Grenoble AlpesCEACNRSIRIGCBM38000GrenobleFrance
| | - Jade A. McCune
- Melville Laboratory for Polymer SynthesisUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | | | - Alan Le Goff
- University Grenoble AlpesCNRSDCM UMR 5250F-38000GrenobleFrance
| | - Moritz F. Kühnel
- Department of ChemistryFaculty of Science and EngineeringSwansea UniversitySingleton ParkSwanseaSA2 8PPWalesUK
- Dept. Hydrogen Labs and Field TestsFraunhofer Institute for Wind Energy SystemsAm Haupttor, BC 431006237LeunaGermany
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5
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Wang KY, Zhang J, Hsu YC, Lin H, Han Z, Pang J, Yang Z, Liang RR, Shi W, Zhou HC. Bioinspired Framework Catalysts: From Enzyme Immobilization to Biomimetic Catalysis. Chem Rev 2023; 123:5347-5420. [PMID: 37043332 PMCID: PMC10853941 DOI: 10.1021/acs.chemrev.2c00879] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Indexed: 04/13/2023]
Abstract
Enzymatic catalysis has fueled considerable interest from chemists due to its high efficiency and selectivity. However, the structural complexity and vulnerability hamper the application potentials of enzymes. Driven by the practical demand for chemical conversion, there is a long-sought quest for bioinspired catalysts reproducing and even surpassing the functions of natural enzymes. As nanoporous materials with high surface areas and crystallinity, metal-organic frameworks (MOFs) represent an exquisite case of how natural enzymes and their active sites are integrated into porous solids, affording bioinspired heterogeneous catalysts with superior stability and customizable structures. In this review, we comprehensively summarize the advances of bioinspired MOFs for catalysis, discuss the design principle of various MOF-based catalysts, such as MOF-enzyme composites and MOFs embedded with active sites, and explore the utility of these catalysts in different reactions. The advantages of MOFs as enzyme mimetics are also highlighted, including confinement, templating effects, and functionality, in comparison with homogeneous supramolecular catalysts. A perspective is provided to discuss potential solutions addressing current challenges in MOF catalysis.
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Affiliation(s)
- Kun-Yu Wang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jiaqi Zhang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yu-Chuan Hsu
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Hengyu Lin
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Zongsu Han
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jiandong Pang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- School
of Materials Science and Engineering, Tianjin Key Laboratory of Metal
and Molecule-Based Material Chemistry, Nankai
University, Tianjin 300350, China
| | - Zhentao Yang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Rong-Ran Liang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Wei Shi
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Hong-Cai Zhou
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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6
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Maureira D, Romero O, Illanes A, Wilson L, Ottone C. Industrial bioelectrochemistry for waste valorization: State of the art and challenges. Biotechnol Adv 2023; 64:108123. [PMID: 36868391 DOI: 10.1016/j.biotechadv.2023.108123] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 02/24/2023] [Accepted: 02/26/2023] [Indexed: 03/05/2023]
Abstract
Bioelectrochemistry has gained importance in recent years for some of its applications on waste valorization, such as wastewater treatment and carbon dioxide conversion, among others. The aim of this review is to provide an updated overview of the applications of bioelectrochemical systems (BESs) for waste valorization in the industry, identifying current limitations and future perspectives of this technology. BESs are classified according to biorefinery concepts into three different categories: (i) waste to power, (ii) waste to fuel and (iii) waste to chemicals. The main issues related to the scalability of bioelectrochemical systems are discussed, such as electrode construction, the addition of redox mediators and the design parameters of the cells. Among the existing BESs, microbial fuel cells (MFCs) and microbial electrolysis cells (MECs) stand out as the more advanced technologies in terms of implementation and R&D investment. However, there has been little transfer of such achievements to enzymatic electrochemical systems. It is necessary that enzymatic systems learn from the knowledge reached with MFC and MEC to accelerate their development to achieve competitiveness in the short term.
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Affiliation(s)
- Diego Maureira
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085, Valparaíso, Chile
| | - Oscar Romero
- Bioprocess Engineering and Applied Biocatalysis Group, Departament of Chemical, Biological and Enviromental Engineering, Universitat Autònoma de Barcelona, 08193, Spain.
| | - Andrés Illanes
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085, Valparaíso, Chile
| | - Lorena Wilson
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085, Valparaíso, Chile
| | - Carminna Ottone
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085, Valparaíso, Chile.
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7
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Prakash O, Mostafa A, Im S, Song YC, Kang S, Kim DH. Enhanced anaerobic treatment of sulfate-rich wastewater by electrical voltage application. BIORESOURCE TECHNOLOGY 2023; 369:128430. [PMID: 36464001 DOI: 10.1016/j.biortech.2022.128430] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Treatment of sulfate-rich wastewater with high methane recovery is a major concern due to sulfide inhibition. Here, an electrical voltage (EV) aims to enhance methanogenesis and sulfidogenesis to treat sulfate-rich wastewater. Two (control and EV-applied) reactors were operated with a gradual decrease in chemical oxygen demand (COD)/SO42- ratios (CSR). EV-applied reactor (EVR) demonstrated an increase of ∼30 % in methane production and ∼40 % in sulfate removal, compared to the control till CSR of 2.0. At CSR 1.0, the control failed, while EVR still exhibited a stable performance of 50 % COD-methane recovery. Microbial community results showed that the relative abundance of sulfate-reducing bacteria in EVR was 1.5 times higher than the control. Furthermore, higher relative abundance of dissimilatory sulfate reductase (>50 %) and Ni/Fe hydrogenase (x15) genes demonstrated an improved tolerance against H2S toxicity. This study highlights the importance of EV application by minimizing the byproduct inhibition in sulfate-rich wastewater.
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Affiliation(s)
- Om Prakash
- Department of Smart-city Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Alsayed Mostafa
- Department of Smart-city Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Seongwon Im
- Department of Smart-city Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Young-Chae Song
- Department of Environmental Engineering, Korea Maritime and Ocean University, Busan 49112, Republic of Korea
| | - Seoktae Kang
- Department of Civil and Environmental Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Dong-Hoon Kim
- Department of Smart-city Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea.
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8
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Ruiz-Rodríguez MA, Cooper CD, Rocchia W, Casalegno M, López de los Santos Y, Raos G. Modeling of the Electrostatic Interaction and Catalytic Activity of [NiFe] Hydrogenases on a Planar Electrode. J Phys Chem B 2022; 126:8777-8790. [PMID: 36269122 PMCID: PMC9639099 DOI: 10.1021/acs.jpcb.2c05371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Hydrogenases are a group of enzymes that have caught the interest of researchers in renewable energies, due to their ability to catalyze the redox reaction of hydrogen. The exploitation of hydrogenases in electrochemical devices requires their immobilization on the surface of suitable electrodes, such as graphite. The orientation of the enzyme on the electrode is important to ensure a good flux of electrons to the catalytic center, through an array of iron-sulfur clusters. Here we present a computational approach to determine the possible orientations of a [NiFe] hydrogenase (PDB 1e3d) on a planar electrode, as a function of pH, salinity, and electrode potential. The calculations are based on the solution of the linearized Poisson-Boltzmann equation, using the PyGBe software. The results reveal that electrostatic interactions do not truly immobilize the enzyme on the surface of the electrode, but there is instead a dynamic equilibrium between different orientations. Nonetheless, after averaging over all thermally accessible orientations, we find significant differences related to the solution's salinity and pH, while the effect of the electrode potential is relatively weak. We also combine models for the protein adsoption-desorption equilibria and for the electron transfer between the proteins and the electrode to arrive at a prediction of the electrode's activity as a function of the enzyme concentration.
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Affiliation(s)
| | - Christopher D. Cooper
- Department
of Mechanical Engineering and Centro Científico Tecnológico
de Valparaíso, Universidad Técnica
Federico Santa María, Valparaíso, 2340000, Chile
| | - Walter Rocchia
- CONCEPT
Lab, Istituto Italiano di Tecnologia, 16163Genova, Italy
| | - Mosè Casalegno
- Dipartimento
di Chimica, Materiali e Ingegneria Chimica “G. Natta”, Politecnico di Milano, 20133Milano, Italy
| | - Yossef López de los Santos
- Centre
Armand-Frappier Santé, Biotechnologie, Institut national de
la recherche scientifique (INRS), Université
du Québec, Laval, QuébecHV7 1B7, Canada
| | - Guido Raos
- Dipartimento
di Chimica, Materiali e Ingegneria Chimica “G. Natta”, Politecnico di Milano, 20133Milano, Italy,
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9
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Lin WY, Liaw SJ. Deacidification by FhlA-dependent hydrogenase is involved in urease activity and urinary stone formation in uropathogenic Proteus mirabilis. Sci Rep 2020; 10:19546. [PMID: 33177598 PMCID: PMC7658346 DOI: 10.1038/s41598-020-76561-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/26/2020] [Indexed: 11/09/2022] Open
Abstract
Proteus mirabilis is an important uropathogen, featured with urinary stone formation. Formate hydrogenlyase (FHL), consisting of formate dehydrogenase H and hydrogenase for converting proton to hydrogen, has been implicated in virulence. In this study, we investigated the role of P. mirabilis FHL hydrogenase and the FHL activator, FhlA. fhlA and hyfG (encoding hydrogenase large subunit) displayed a defect in acid resistance. fhlA and hyfG mutants displayed a delay in medium deacidification compared to wild-type and ureC mutant failed to deacidify the medium. In addition, loss of fhlA or hyfG decreased urease activity in the pH range of 5-8. The reduction of urease activities in fhlA and hyfG mutants subsided gradually over the pH range and disappeared at pH 9. Furthermore, mutation of fhlA or hyfG resulted in a decrease in urinary stone formation in synthetic urine. These indicate fhlA- and hyf-mediated deacidification affected urease activity and stone formation. Finally, fhlA and hyfG mutants exhibited attenuated colonization in mice. Altogether, we found expression of fhlA and hyf confers medium deacidification via facilitating urease activity, thereby urinary stone formation and mouse colonization. The link of acid resistance to urease activity provides a potential strategy for counteracting urinary tract infections by P. mirabilis.
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Affiliation(s)
- Wen-Yuan Lin
- Department and Graduate Institute of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, No. 1, Chang-Te Street, Taipei, 10016, Taiwan, ROC
| | - Shwu-Jen Liaw
- Department and Graduate Institute of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, No. 1, Chang-Te Street, Taipei, 10016, Taiwan, ROC. .,Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University, Taipei, Taiwan, Republic of China.
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10
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Fan Q, Neubauer P, Lenz O, Gimpel M. Heterologous Hydrogenase Overproduction Systems for Biotechnology-An Overview. Int J Mol Sci 2020; 21:E5890. [PMID: 32824336 PMCID: PMC7460606 DOI: 10.3390/ijms21165890] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/06/2020] [Accepted: 08/14/2020] [Indexed: 01/16/2023] Open
Abstract
Hydrogenases are complex metalloenzymes, showing tremendous potential as H2-converting redox catalysts for application in light-driven H2 production, enzymatic fuel cells and H2-driven cofactor regeneration. They catalyze the reversible oxidation of hydrogen into protons and electrons. The apo-enzymes are not active unless they are modified by a complicated post-translational maturation process that is responsible for the assembly and incorporation of the complex metal center. The catalytic center is usually easily inactivated by oxidation, and the separation and purification of the active protein is challenging. The understanding of the catalytic mechanisms progresses slowly, since the purification of the enzymes from their native hosts is often difficult, and in some case impossible. Over the past decades, only a limited number of studies report the homologous or heterologous production of high yields of hydrogenase. In this review, we emphasize recent discoveries that have greatly improved our understanding of microbial hydrogenases. We compare various heterologous hydrogenase production systems as well as in vitro hydrogenase maturation systems and discuss their perspectives for enhanced biohydrogen production. Additionally, activities of hydrogenases isolated from either recombinant organisms or in vivo/in vitro maturation approaches were systematically compared, and future perspectives for this research area are discussed.
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Affiliation(s)
- Qin Fan
- Institute of Biotechnology, Technical University of Berlin, Ackerstraße 76, 13355 Berlin, Germany; (Q.F.); (P.N.)
| | - Peter Neubauer
- Institute of Biotechnology, Technical University of Berlin, Ackerstraße 76, 13355 Berlin, Germany; (Q.F.); (P.N.)
| | - Oliver Lenz
- Department of Chemistry, Technical University of Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany;
| | - Matthias Gimpel
- Institute of Biotechnology, Technical University of Berlin, Ackerstraße 76, 13355 Berlin, Germany; (Q.F.); (P.N.)
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11
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Enhanced relative stability of heterobimetallic Fe(II), Zn(II), and Mg(II) clusters supported by a µ-phenoxo bridge. Inorganica Chim Acta 2020. [DOI: 10.1016/j.ica.2020.119547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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12
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New insights into Fe–H$$_{2}$$ and Fe–H$$^{-}$$ bonding of a [NiFe] hydrogenase mimic: a local vibrational mode study. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2463-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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13
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Teng Y, Xu Y, Wang X, Christie P. Function of Biohydrogen Metabolism and Related Microbial Communities in Environmental Bioremediation. Front Microbiol 2019; 10:106. [PMID: 30837956 PMCID: PMC6383490 DOI: 10.3389/fmicb.2019.00106] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/17/2019] [Indexed: 01/30/2023] Open
Abstract
Hydrogen (H2) metabolism has attracted considerable interest because the activities of H2-producing and consuming microbes shape the global H2 cycle and may have vital relationships with the global cycling of other elements. There are many pathways of microbial H2 emission and consumption which may affect the structure and function of microbial communities. A wide range of microbial groups employ H2 as an electron donor to catalyze the reduction of pollutants such as organohalides, azo compounds, and trace metals. Syntrophy coupled mutualistic interaction between H2-producing and H2-consuming microorganisms can transfer H2 and be accompanied by the removal of toxic compounds. Moreover, hydrogenases have been gradually recognized to have a key role in the progress of pollutant degradation. This paper reviews recent advances in elucidating role of H2 metabolism involved in syntrophy and hydrogenases in environmental bioremediation. Further investigations should focus on the application of bioenergy in bioremediation to make microbiological H2 metabolism a promising remediation strategy.
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Affiliation(s)
- Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yongfeng Xu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaomi Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Peter Christie
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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14
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Breglia R, Greco C, Fantucci P, De Gioia L, Bruschi M. Reactivation of the Ready and Unready Oxidized States of [NiFe]-Hydrogenases: Mechanistic Insights from DFT Calculations. Inorg Chem 2018; 58:279-293. [PMID: 30576127 DOI: 10.1021/acs.inorgchem.8b02348] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The apparently simple dihydrogen formation from protons and electrons (2H+ + 2e- ⇄ H2) is one of the most challenging reactions in nature. It is catalyzed by metalloenzymes of amazing complexity, called hydrogenases. A better understanding of the chemistry of these enzymes, especially that of the [NiFe]-hydrogenases subgroup, has important implications for production of H2 as alternative sustainable fuel. In this work, reactivation mechanism of the oxidized and inactive Ni-B and Ni-A states of the [NiFe]-hydrogenases active site has been investigated using density functional theory. Results obtained from this study show that one-electron reduction and protonation of the active site promote the removal of the bridging hydroxide ligand contained in Ni-B and Ni-A. However, this process is sufficient to activate only the Ni-B state. H2 binding to the active site is required to convert Ni-A to the active Ni-SIa state. Here, we also propose a reasonable structure for the spectroscopically well-characterized Ni-SIr and Ni-SU species, formed respectively from the one-electron reduction of Ni-B and Ni-A. Ni-SIr, depending on the pH at which the reaction occurs, features a bridging hydroxide ligand or a water molecule terminally coordinated to the Ni atom, whereas in Ni-SU a water molecule is terminally coordinated to the Fe atom, and the Cys64 residue is oxidized to sulfenate. The sulfenate oxygen atom in the Ni-A state affects the stereoelectronic properties of the binuclear cluster by modifying the coordination geometry of Ni, and consequently, by switching the regiochemistry of H2O and H2 binding from the Ni to the Fe atom. This effect is predicted to be at the origin of the different reactivation kinetics of the oxidized and inactive Ni-B and Ni-A states.
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15
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The effect of the counteranion on the loss of hydrogen from cationic ruthenium dihydrogen complexes in the solid state. Polyhedron 2018. [DOI: 10.1016/j.poly.2018.09.056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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16
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Song Y, Liu M, Xie L, You C, Sun J, Zhang YHPJ. A Recombinant 12-His Tagged Pyrococcus furiosus Soluble [NiFe]-Hydrogenase I Overexpressed in Thermococcus kodakarensis KOD1 Facilitates Hydrogen-Powered in vitro NADH Regeneration. Biotechnol J 2018; 14:e1800301. [PMID: 30307115 DOI: 10.1002/biot.201800301] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/27/2018] [Indexed: 01/11/2023]
Abstract
Soluble hydrogenase I (SHI) from the hyperthermophilic archaeon Pyrococcus furiosus is a heterotetrameric [NiFe] hydrogenase that catalyzes the reversible reduction of protons by NADPH into hydrogen gas (H2 ). Here, the authors expressed the four αβγδ subunits of SHI encoded by one gene cluster in another hyperthermophilic archaeon, Thermococcus kodakarensis KOD1, which uses its hydrogenase maturation apparatus without the coexpression of native P. furiosus hydrogenase endopeptidases (maturation proteases). The SHI overexpression of T. kodakarensis resulted in more than 1200-fold enhancement in the hydrogenase activity of the cell lysate compared to that of the host strain with an empty vector. An active, purified 12-His tagged recombinant SHI (rSHI) is obtained by one-step affinity adsorption on nickel-charged resin. Size-exclusion chromatography show that purified rSHI is heterotetrameric and has a molecular mass of 150 kDa. The purified rSHI has a half-life of 70 h at 80 °C. This rSHI is used to design a novel in vitro synthetic enzymatic biosystem to convert pyruvate and H2 gas into lactate in a theoretical yield, whereas rSHI is used for NADPH regeneration; an FMN-containing diaphorase (DI) is used to match NADP-preferred SHI and NAD-preferred lactate dehydrogenase (LDH). This study provides a cost-efficient method to obtain hyperthermostable hydrogenases, which can be used in in vitro synthetic enzymatic biosystems for cofactor regeneration and hydrogen production.
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Affiliation(s)
- Yunhong Song
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Meixia Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Leipeng Xie
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.,College of Life Sciences, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, China
| | - Chun You
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Junsong Sun
- Biorefinery Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Haike Road 99, Shanghai, 201210, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, 201210, China
| | - Yi-Heng P Job Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
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17
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Isegawa M, Sharma AK, Ogo S, Morokuma K. DFT Study on Fe(IV)-Peroxo Formation and H Atom Transfer Triggered O2 Activation by NiFe Complex. Organometallics 2018. [DOI: 10.1021/acs.organomet.8b00098] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Miho Isegawa
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University 744 Moto-oka, Nishi-ku, Fukuoka 819-0385, Japan
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - Akhilesh K. Sharma
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - Seiji Ogo
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University 744 Moto-oka, Nishi-ku, Fukuoka 819-0385, Japan
| | - Keiji Morokuma
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
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18
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Jugder BE, Ertan H, Wong YK, Braidy N, Manefield M, Marquis CP, Lee M. Genomic, transcriptomic and proteomic analyses of Dehalobacter UNSWDHB in response to chloroform. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:814-824. [PMID: 27452500 DOI: 10.1111/1758-2229.12444] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/25/2016] [Indexed: 06/06/2023]
Abstract
Organohalide respiring bacteria (ORB) are capable of utilising organohalides as electron acceptors for the generation of cellular energy and consequently play an important role in the turnover of natural and anthropogenically-derived organohalides. In this study, the response of a Dehalobacter sp. strain UNSWDHB to the addition of trichloromethane (TCM) after a 50 h period of its absence (suffocation) was evaluated from a transcriptomic and proteomic perspective. The up-regulation of TCM reductive dehalogenase genes (tmrABC) and their gene products (TmrABC) was confirmed at both transcriptional and proteomic levels. Other findings include the upregulation of various hydrogenases (membrane-associated Ni-Fe hydrogenase complexes and soluble Fe-Fe hydrogenases), formate dehydrogenases, complex I and a pyrophosphate-energized proton pump. The elevated expression of enzymes associated with carbon metabolism, including complete Wood Ljungdahl pathway, during TCM respiration raises interesting questions on possible fates of intracellular formate and its potential role in the physiology of this bacterium. Overall, the findings presented here provide a broader view on the bioenergetics and general physiology of Dehalobacter UNSWDHB cells actively respiring with TCM.
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Affiliation(s)
- Bat-Erdene Jugder
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Haluk Ertan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
- Department of Molecular Biology and Genetics, Istanbul University, Turkey
| | - Yie Kuan Wong
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Nady Braidy
- Faculty of Medicine, School of Psychiatry, Centre for Healthy Brain Ageing, University of New South Wales, Sydney, Australia
| | - Michael Manefield
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Christopher P Marquis
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Matthew Lee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
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19
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Jugder BE, Welch J, Braidy N, Marquis CP. Construction and use of a Cupriavidus necator H16 soluble hydrogenase promoter (PSH) fusion to gfp (green fluorescent protein). PeerJ 2016; 4:e2269. [PMID: 27547572 PMCID: PMC4974937 DOI: 10.7717/peerj.2269] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 06/28/2016] [Indexed: 12/30/2022] Open
Abstract
Hydrogenases are metalloenzymes that reversibly catalyse the oxidation or production of molecular hydrogen (H2). Amongst a number of promising candidates for application in the oxidation of H2 is a soluble [Ni–Fe] uptake hydrogenase (SH) produced by Cupriavidus necator H16. In the present study, molecular characterisation of the SH operon, responsible for functional SH synthesis, was investigated by developing a green fluorescent protein (GFP) reporter system to characterise PSH promoter activity using several gene cloning approaches. A PSH promoter-gfp fusion was successfully constructed and inducible GFP expression driven by the PSH promoter under de-repressing conditions in heterotrophic growth media was demonstrated in the recombinant C. necator H16 cells. Here we report the first successful fluorescent reporter system to study PSH promoter activity in C. necator H16. The fusion construct allowed for the design of a simple screening assay to evaluate PSH activity. Furthermore, the constructed reporter system can serve as a model to develop a rapid fluorescent based reporter for subsequent small-scale process optimisation experiments for SH expression.
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Affiliation(s)
- Bat-Erdene Jugder
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Jeffrey Welch
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Nady Braidy
- Centre for Health Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
| | - Christopher P Marquis
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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20
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Production and purification of a soluble hydrogenase from Ralstonia eutropha H16 for potential hydrogen fuel cell applications. MethodsX 2016; 3:242-50. [PMID: 27077052 PMCID: PMC4816682 DOI: 10.1016/j.mex.2016.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 03/07/2016] [Indexed: 11/22/2022] Open
Abstract
The soluble hydrogenase (SH) from Ralstonia eutropha H16 is a promising candidate enzyme for H2-based biofuel application as it favours H2 oxidation and is relatively oxygen-tolerant. In this report, bioprocess development studies undertaken to produce and purify an active SH are described, based on the methods previously reported [1], [2], [3], [4]. Our modifications are: Upstream method optimizations were undertaken on heterotrophic growth media and cell lysis involving ultrasonication. Two anion exchangers (Q Sepharose and RESOURCE Q) and size exclusion chromatographic (Superdex 200) matrices were successfully employed for purification of a hexameric SH from R. eutropha. The H2 oxidizing activity of the SH was demonstrated spectrophotometrically in solution and also immobilized on an EPG electrode using cyclic voltammetry.
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21
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Jugder BE, Ertan H, Bohl S, Lee M, Marquis CP, Manefield M. Organohalide Respiring Bacteria and Reductive Dehalogenases: Key Tools in Organohalide Bioremediation. Front Microbiol 2016; 7:249. [PMID: 26973626 PMCID: PMC4771760 DOI: 10.3389/fmicb.2016.00249] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/15/2016] [Indexed: 01/31/2023] Open
Abstract
Organohalides are recalcitrant pollutants that have been responsible for substantial contamination of soils and groundwater. Organohalide-respiring bacteria (ORB) provide a potential solution to remediate contaminated sites, through their ability to use organohalides as terminal electron acceptors to yield energy for growth (i.e., organohalide respiration). Ideally, this process results in non- or lesser-halogenated compounds that are mostly less toxic to the environment or more easily degraded. At the heart of these processes are reductive dehalogenases (RDases), which are membrane bound enzymes coupled with other components that facilitate dehalogenation of organohalides to generate cellular energy. This review focuses on RDases, concentrating on those which have been purified (partially or wholly) and functionally characterized. Further, the paper reviews the major bacteria involved in organohalide breakdown and the evidence for microbial evolution of RDases. Finally, the capacity for using ORB in a bioremediation and bioaugmentation capacity are discussed.
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Affiliation(s)
- Bat-Erdene Jugder
- School of Biotechnology and Biomolecular Sciences, University of New South Wales Sydney, NSW, Australia
| | - Haluk Ertan
- School of Biotechnology and Biomolecular Sciences, University of New South WalesSydney, NSW, Australia; Department of Molecular Biology and Genetics, Istanbul UniversityIstanbul, Turkey
| | - Susanne Bohl
- School of Biotechnology and Biomolecular Sciences, University of New South WalesSydney, NSW, Australia; Department of Biotechnology, Mannheim University of Applied SciencesMannheim, Germany
| | - Matthew Lee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales Sydney, NSW, Australia
| | - Christopher P Marquis
- School of Biotechnology and Biomolecular Sciences, University of New South Wales Sydney, NSW, Australia
| | - Michael Manefield
- School of Biotechnology and Biomolecular Sciences, University of New South Wales Sydney, NSW, Australia
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22
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Wang H, Yoda Y, Ogata H, Tanaka Y, Lubitz W. A strenuous experimental journey searching for spectroscopic evidence of a bridging nickel-iron-hydride in [NiFe] hydrogenase. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:1334-44. [PMID: 26524296 PMCID: PMC4629863 DOI: 10.1107/s1600577515017816] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 09/23/2015] [Indexed: 05/24/2023]
Abstract
Direct spectroscopic evidence for a hydride bridge in the Ni-R form of [NiFe] hydrogenase has been obtained using iron-specific nuclear resonance vibrational spectroscopy (NRVS). The Ni-H-Fe wag mode at 675 cm(-1) is the first spectroscopic evidence for a bridging hydride in Ni-R as well as the first iron-hydride-related NRVS feature observed for a biological system. Although density function theory (DFT) calculation assisted the determination of the Ni-R structure, it did not predict the Ni-H-Fe wag mode at ∼ 675 cm(-1) before NRVS. Instead, the observed Ni-H-Fe mode provided a critical reference for the DFT calculations. While the overall science about Ni-R is presented and discussed elsewhere, this article focuses on the long and strenuous experimental journey to search for and experimentally identify the Ni-H-Fe wag mode in a Ni-R sample. As a methodology, the results presented here will go beyond Ni-R and hydrogenase research and will also be of interest to other scientists who use synchrotron radiation for measuring dilute samples or weak spectroscopic features.
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Affiliation(s)
- Hongxin Wang
- Department of Chemistry, University of California, 1 Cyclotron Road, Davis, CA 95616, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yoshitaka Yoda
- Research and Utilization Division, SPring-8/JASRI, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion, D-45470 Mülheim an der Ruhr, Germany
| | - Yoshihito Tanaka
- Research and Utilization Division, SPring-8/JASRI, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
- Graduate School of Material Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, D-45470 Mülheim an der Ruhr, Germany
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23
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Jugder BE, Ertan H, Lee M, Manefield M, Marquis CP. Reductive Dehalogenases Come of Age in Biological Destruction of Organohalides. Trends Biotechnol 2015; 33:595-610. [DOI: 10.1016/j.tibtech.2015.07.004] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/27/2015] [Accepted: 07/30/2015] [Indexed: 11/28/2022]
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Hydride bridge in [NiFe]-hydrogenase observed by nuclear resonance vibrational spectroscopy. Nat Commun 2015; 6:7890. [PMID: 26259066 PMCID: PMC4531378 DOI: 10.1038/ncomms8890] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 06/18/2015] [Indexed: 11/28/2022] Open
Abstract
The metabolism of many anaerobes relies on [NiFe]-hydrogenases, whose characterization when bound to substrates has proven non-trivial. Presented here is direct evidence for a hydride bridge in the active site of the 57Fe-labelled fully reduced Ni-R form of Desulfovibrio vulgaris Miyazaki F [NiFe]-hydrogenase. A unique ‘wagging' mode involving H− motion perpendicular to the Ni(μ-H)57Fe plane was studied using 57Fe-specific nuclear resonance vibrational spectroscopy and density functional theory (DFT) calculations. On Ni(μ-D)57Fe deuteride substitution, this wagging causes a characteristic perturbation of Fe–CO/CN bands. Spectra have been interpreted by comparison with Ni(μ-H/D)57Fe enzyme mimics [(dppe)Ni(μ-pdt)(μ-H/D)57Fe(CO)3]+ and DFT calculations, which collectively indicate a low-spin Ni(II)(μ-H)Fe(II) core for Ni-R, with H− binding Ni more tightly than Fe. The present methodology is also relevant to characterizing Fe–H moieties in other important natural and synthetic catalysts. Understanding the catalytic mechanism of redox-active hydrogenases is a key to efficient hydrogen production and consumption. Here, the authors use nuclear resonance vibrational spectroscopy to study [NiFe]-hydrogenase, and observe a bridging hydride structure in an EPR silent intermediate.
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25
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Liu J, Zorin NA, Chen M, Qian DJ. Pd(II)-Directed Encapsulation of Hydrogenase within the Layer-by-Layer Multilayers of Carbon Nanotube Polyelectrolyte Used as a Heterogeneous Catalyst for Oxidation of Hydrogen. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:6546-6553. [PMID: 26010012 DOI: 10.1021/acs.langmuir.5b01376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A metal-directed assembling approach has been developed to encapsulate hydrogenase (H2ase) within a layer-by-layer (LBL) multilayer of carbon nanotube polyelectrolyte (MWNT-PVPMe), which showed efficient biocatalytic oxidation of H2 gas. The MWNT-PVPMe was prepared via a diazonium process and addition reactions with poly(4-vinylpyridine) (PVP) and methyl iodide (MeI). The covalently attached polymers and organic substituents in the polyelectrolyte comprised 60-70% of the total weight. The polyelectrolyte was then used as a substrate for H2ase binding to produce MWNT-PVPMe@H2ase bionanocomposites. X-ray photoelectron spectra revealed that the bionanocomposites included the elements of Br, S, C, N, O, I, Fe, and Ni, which confirmed that they were composed of MWNT-PVPMe and H2ase. Field emission transmission electron microscope images revealed that the H2ase was adsorbed on the surface of MWNT-PVPMe with the domains ranging from 20 to 40 nm. Further, with the use of the bionanocomposites as nanolinkers and Na2PdCl4 as connectors, the (Pd/MWNT-PVPMe@H2ase)n multilayers were constructed on the quartz and gold substrate surfaces by the Pd(II)-directed LBL assembling technique. Finally, the as-prepared LBL multilayers were used as heterogeneous catalysts for hydrogen oxidation with methyl viologen (MV(2+)) as an electron carrier. The dynamic processes for the reversible color change between blue-colored MV(+) and colorless MV(2+) (catalyzed by the LBL multilayers) were video recorded, which confirmed that the H2ase encapsulated within the present LBL multilayers was of much stronger stability and higher biocatalytic activity of H2 oxidation resulting in potential applications for the development of H2 biosensors and fuel cells.
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Affiliation(s)
- Jiang Liu
- †Department of Chemistry, Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Nikolay A Zorin
- ‡Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Meng Chen
- †Department of Chemistry, Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Dong-Jin Qian
- †Department of Chemistry, Fudan University, 220 Handan Road, Shanghai 200433, China
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26
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Jugder BE, Chen Z, Ping DTT, Lebhar H, Welch J, Marquis CP. An analysis of the changes in soluble hydrogenase and global gene expression in Cupriavidus necator (Ralstonia eutropha) H16 grown in heterotrophic diauxic batch culture. Microb Cell Fact 2015; 14:42. [PMID: 25880663 PMCID: PMC4377017 DOI: 10.1186/s12934-015-0226-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 03/12/2015] [Indexed: 12/20/2022] Open
Abstract
Background Soluble hydrogenases (SH) are enzymes that catalyse the oxidation of molecular hydrogen. The SH enzyme from Cupriavidus necator H16 is relatively oxygen tolerant and makes an attractive target for potential application in biochemical hydrogen fuel cells. Expression of the enzyme can be mediated by derepression of the hox promoter system under heterotrophic conditions. However, the overall impact of hox derepression, from a transcriptomic perspective, has never been previously reported. Results Derepression of hydrogenase gene expression upon fructose depletion was confirmed in replicate experiments. Using qRT-PCR, hoxF was 4.6-fold up-regulated, hypF2 was up-regulated in the cells grown 2.2-fold and the regulatory gene hoxA was up-regulated by a mean factor of 4.5. A full transcriptomic evaluation revealed a substantial shift in the global pattern of gene expression. In addition to up-regulation of genes associated with hydrogenase expression, significant changes were observed in genes associated with energy transduction, amino acid metabolism, transcription and translation (and regulation thereof), genes associated with cell stress, lipid and cell wall biogenesis and other functions, including cell motility. Conclusions We report the first full transcriptome analysis of C. necator H16 grown heterotrophically on fructose and glycerol in diauxic batch culture, which permits expression of soluble hydrogenase under heterotrophic conditions. The data presented deepens our understanding of the changes in global gene expression patterns that occur during the switch to growth on glycerol and suggests that energy deficit is a key driver for induction of hydrogenase expression in this organism. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0226-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bat-Erdene Jugder
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia.
| | - Zhiliang Chen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia. .,Systems Biology Initiative, University of New South Wales, Sydney, 2052, Australia.
| | - Darren Tan Tek Ping
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia.
| | - Helene Lebhar
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia.
| | - Jeffrey Welch
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia.
| | - Christopher P Marquis
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia.
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27
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Zhou C, Liu Z, Pataranutaporn P, Vannela R, Hayes KF, Rittmann BE. Biogenic nano-particulate iron-sulfide produced through sulfate and Fe(iii)-(hydr)oxide reductions was enhanced by pyruvate as the electron donor. RSC Adv 2015. [DOI: 10.1039/c5ra20556e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In nature, the formation of iron sulfide solids is mainly attributed to reductions of sulfate and ferric minerals by microorganisms such asDesulfovibrio vulgaris.
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Affiliation(s)
- Chen Zhou
- Swette Center for Environmental Biotechnology
- Biodesign Institute
- Arizona State University
- Tempe
- USA
| | - Zhuolin Liu
- Swette Center for Environmental Biotechnology
- Biodesign Institute
- Arizona State University
- Tempe
- USA
| | - Pat Pataranutaporn
- Swette Center for Environmental Biotechnology
- Biodesign Institute
- Arizona State University
- Tempe
- USA
| | - Raveender Vannela
- Swette Center for Environmental Biotechnology
- Biodesign Institute
- Arizona State University
- Tempe
- USA
| | - Kim F. Hayes
- Department of Civil and Environmental Engineering
- University of Michigan
- USA
| | - Bruce E. Rittmann
- Swette Center for Environmental Biotechnology
- Biodesign Institute
- Arizona State University
- Tempe
- USA
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28
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Wang Y, Zhang T, Li B, Jiang S, Sheng L. Synthesis, characterization, electrochemical properties and catalytic reactivity of N-heterocyclic carbene-containing diiron complexes. RSC Adv 2015. [DOI: 10.1039/c4ra15150j] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Four new [Fe–Fe]–NHC complexes were synthesized and used as highly selective homogeneous catalysts for the direct hydroxylation of benzene to phenol.
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Affiliation(s)
- Yanhong Wang
- School of Chemical Engineering and Technology
- Tianjin Key Laboratory of Applied Catalysis Science and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Tianyong Zhang
- School of Chemical Engineering and Technology
- Tianjin Key Laboratory of Applied Catalysis Science and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Bin Li
- School of Chemical Engineering and Technology
- Tianjin Key Laboratory of Applied Catalysis Science and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Shuang Jiang
- School of Chemical Engineering and Technology
- Tianjin Key Laboratory of Applied Catalysis Science and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Liao Sheng
- School of Chemical Engineering and Technology
- Tianjin Key Laboratory of Applied Catalysis Science and Technology
- Tianjin University
- Tianjin 300072
- China
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29
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Adamska-Venkatesh A, Krawietz D, Siebel J, Weber K, Happe T, Reijerse E, Lubitz W. New Redox States Observed in [FeFe] Hydrogenases Reveal Redox Coupling Within the H-Cluster. J Am Chem Soc 2014; 136:11339-46. [DOI: 10.1021/ja503390c] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | - Danuta Krawietz
- Fakultät
für Biologie und Biotechnologie, Lehrstuhl für Biochemie
der Pflanzen, AG Photobiotechnologie, Ruhr Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Judith Siebel
- Max-Planck-Institut
für Chemische Energiekonversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Katharina Weber
- 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
| | - 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
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