1
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Plummer SM, Plummer MA, Merkel PA, Waidner LA. Using directed evolution to improve hydrogen production in chimeric hydrogenases from algal species. Enzyme Microb Technol 2024; 173:110349. [PMID: 37984199 DOI: 10.1016/j.enzmictec.2023.110349] [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: 09/22/2023] [Revised: 10/22/2023] [Accepted: 10/23/2023] [Indexed: 11/22/2023]
Abstract
Algae generate hydrogen from sunlight and water utilizing high-energy electrons generated during photosynthesis. The amount of hydrogen produced in heterologous expression of the wild-type hydrogenase is currently insufficient for industrial applications. One approach to improve hydrogen yields is through directed evolution of the DNA of the native hydrogenase. Here, we created 113 chimeric algal hydrogenase gene variants derived from combining segments of three parent hydrogenases, two from Chlamydomonas reinhardtii (CrHydA1 and CrHydA2) and one from Scenedesmus obliquus (HydA1). To generate chimeras, there were seven segments into which each of the parent hydrogenase genes was divided and recombined in a variety of combinations. The chimeric and parental hydrogenase sequences were cloned for heterologous expression in Escherichia coli, and 40 of the resultant enzymes expressed were assayed for H2 production. Chimeric clones that resulted in equal or greater production obtained with the cloned CrHydA1 parent hydrogenase were those comprised of CrHydA1 sequence in segments #1, 2, 3, and/or 4. These best-performing chimeras all contained one common region, segment #2, the part of the sequence known to contain important amino acids involved in proton transfer or hydrogen cluster coordination. The amino acid sequence distances among all chimeric clones to that of the CrHydA1 parent were determined, and the relationship between sequence distances and experimentally-derived H2 production was evaluated. An additional model determined the correlation between electrostatic potential energy surface area ratios and H2 production. The model yielded several algal mutants with predicted hydrogen productions in a range of two to three times that of the wild-type hydrogenase. The mutant data and the model can now be used to predict which specific mutant sequences may result in even higher hydrogen yields. Overall, results provide more precise details in planning future directed evolution to functionally improve algal hydrogenases.
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Affiliation(s)
| | | | - Patricia A Merkel
- H2OPE Biofuels LLC, Greenwood Village, CO, USA; Children's Hospital, 3123 East 16th Avenue, B518, Aurora, CO, USA
| | - Lisa A Waidner
- H2OPE Biofuels LLC, Greenwood Village, CO, USA; University of West Florida, Pensacola, FL USA.
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2
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Stripp ST, Duffus BR, Fourmond V, Léger C, Leimkühler S, Hirota S, Hu Y, Jasniewski A, Ogata H, Ribbe MW. Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase. Chem Rev 2022; 122:11900-11973. [PMID: 35849738 PMCID: PMC9549741 DOI: 10.1021/acs.chemrev.1c00914] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Gases like H2, N2, CO2, and CO are increasingly recognized as critical feedstock in "green" energy conversion and as sources of nitrogen and carbon for the agricultural and chemical sectors. However, the industrial transformation of N2, CO2, and CO and the production of H2 require significant energy input, which renders processes like steam reforming and the Haber-Bosch reaction economically and environmentally unviable. Nature, on the other hand, performs similar tasks efficiently at ambient temperature and pressure, exploiting gas-processing metalloenzymes (GPMs) that bind low-valent metal cofactors based on iron, nickel, molybdenum, tungsten, and sulfur. Such systems are studied to understand the biocatalytic principles of gas conversion including N2 fixation by nitrogenase and H2 production by hydrogenase as well as CO2 and CO conversion by formate dehydrogenase, carbon monoxide dehydrogenase, and nitrogenase. In this review, we emphasize the importance of the cofactor/protein interface, discussing how second and outer coordination sphere effects determine, modulate, and optimize the catalytic activity of GPMs. These may comprise ionic interactions in the second coordination sphere that shape the electron density distribution across the cofactor, hydrogen bonding changes, and allosteric effects. In the outer coordination sphere, proton transfer and electron transfer are discussed, alongside the role of hydrophobic substrate channels and protein structural changes. Combining the information gained from structural biology, enzyme kinetics, and various spectroscopic techniques, we aim toward a comprehensive understanding of catalysis beyond the first coordination sphere.
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Affiliation(s)
- Sven T Stripp
- Freie Universität Berlin, Experimental Molecular Biophysics, Berlin 14195, Germany
| | | | - Vincent Fourmond
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille 13402, France
| | - Christophe Léger
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille 13402, France
| | - Silke Leimkühler
- University of Potsdam, Molecular Enzymology, Potsdam 14476, Germany
| | - Shun Hirota
- Nara Institute of Science and Technology, Division of Materials Science, Graduate School of Science and Technology, Nara 630-0192, Japan
| | - Yilin Hu
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Andrew Jasniewski
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Hideaki Ogata
- Nara Institute of Science and Technology, Division of Materials Science, Graduate School of Science and Technology, Nara 630-0192, Japan
- Hokkaido University, Institute of Low Temperature Science, Sapporo 060-0819, Japan
- Graduate School of Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Markus W Ribbe
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
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3
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King SJ, Jerkovic A, Brown LJ, Petroll K, Willows RD. Synthetic biology for improved hydrogen production in Chlamydomonas reinhardtii. Microb Biotechnol 2022; 15:1946-1965. [PMID: 35338590 PMCID: PMC9249334 DOI: 10.1111/1751-7915.14024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/09/2022] [Accepted: 02/11/2022] [Indexed: 12/04/2022] Open
Abstract
Hydrogen is a clean alternative to fossil fuels. It has applications for electricity generation and transportation and is used for the manufacturing of ammonia and steel. However, today, H2 is almost exclusively produced from coal and natural gas. As such, methods to produce H2 that do not use fossil fuels need to be developed and adopted. The biological manufacturing of H2 may be one promising solution as this process is clean and renewable. Hydrogen is produced biologically via enzymes called hydrogenases. There are three classes of hydrogenases namely [FeFe], [NiFe] and [Fe] hydrogenases. The [FeFe] hydrogenase HydA1 from the model unicellular algae Chlamydomonas reinhardtii has been studied extensively and belongs to the A1 subclass of [FeFe] hydrogenases that have the highest turnover frequencies amongst hydrogenases (21,000 ± 12,000 H2 s−1 for CaHydA from Clostridium acetobutyliticum). Yet to date, limitations in C. reinhardtii H2 production pathways have hampered commercial scale implementation, in part due to O2 sensitivity of hydrogenases and competing metabolic pathways, resulting in low H2 production efficiency. Here, we describe key processes in the biogenesis of HydA1 and H2 production pathways in C. reinhardtii. We also summarize recent advancements of algal H2 production using synthetic biology and describe valuable tools such as high‐throughput screening (HTS) assays to accelerate the process of engineering algae for commercial biological H2 production.
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Affiliation(s)
- Samuel J King
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ante Jerkovic
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Louise J Brown
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Kerstin Petroll
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Robert D Willows
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
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4
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Yu Q, He J, Zhao Q, Wang X, Zhi Y, Li X, Li X, Li L, Ge B. Regulation of nitrogen source for enhanced photobiological H2 production by co-culture of Chlamydomonas reinhardtii and Mesorhizobium sangaii. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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5
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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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6
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Swartz J. Opportunities toward hydrogen production biotechnologies. Curr Opin Biotechnol 2020; 62:248-255. [PMID: 32278260 DOI: 10.1016/j.copbio.2020.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 03/09/2020] [Accepted: 03/10/2020] [Indexed: 01/08/2023]
Abstract
Hydrogen is already a major commodity and process intermediate for fertilizer production, petroleum processing, and chemical synthesis. It also offers unrealized potential for energy storage. While biological production offers an expandable and sustainable source, enthusiasm has been dampened by slow research progress. Also, the very low cost of natural gas (the major current hydrogen source) imposes severe economic challenges. This discussion describes process, metabolic, and protein engineering opportunities toward cost-effective biohydrogen production. Recent progress in hydrogenase engineering and photosynthetic bacterial research now suggests a favorable risk versus reward opportunity. Although the risks are still significant, successful technologies would provide important components in an integrated energy portfolio that enables global sustainability.
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Affiliation(s)
- James Swartz
- Dept. of Chemical Engineering, Dept. of Bioengineering Stanford University, United States.
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7
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Ge X, Xu J. Macromolecular crowding effects on transcription and translation are regulated by free magnesium ion. Biotechnol Appl Biochem 2020; 67:117-122. [PMID: 31576614 PMCID: PMC7263881 DOI: 10.1002/bab.1827] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/28/2019] [Indexed: 12/21/2022]
Abstract
Cell-free metabolic engineering is an emerging and promising alternative platform for the production of fuels and chemicals. In recent years, macromolecular crowding effect, which is an important function in living cells but ignored in cell-free systems, has been transferred to cell-free protein synthesis (CFPS). However, inhibitory effects of crowding agents on CFPS were frequently observed, and the mechanism is unclear. In this study, free Mg2+ was found to be a key factor that can regulate the macromolecular crowding effect on in vitro transcription, in vitro translation, and coupled transcript/translation. Addition of crowding agents (20% of Ficoll-70 or Ficoll-400) enhanced in vitro transcription at an index of free Mg2+ concentration (IFMC) below 2 mM but inhibited the transcription when the IFMC was higher than 2 mM. Similarly, Ficoll-400 enhanced in vitro translation and coupled transcription/translation at a lower IFMC (0.1-2 mM) and inhibited the reactions at higher IFMC (>2 mM). Based on the results, CFPS systems could be further optimized by adjusting the content of crowding agents and the IFMC. Besides, the results also indicate that macromolecular crowding effect is important for maintaining the efficiency of in vivo transcription and translation which occur at a low intracellular IFMC (<1 mM).
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Affiliation(s)
- Xumeng Ge
- Arkansas Biosciences Institute and College of Agriculture and Technology, Arkansas State University, Jonesboro, AR, USA
- Quasar Energy Group, Independence, OH, USA
| | - Jianfeng Xu
- Arkansas Biosciences Institute and College of Agriculture and Technology, Arkansas State University, Jonesboro, AR, USA
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8
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Evaluation of various sulfides for enhanced photobiological H2 production by a dual-species co-culture system of Chlamydomonas reinhardtii and Thiomonas intermedia. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.03.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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9
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Liu Y, Mohammadi M, Vashisth H. Diffusion network of CO in FeFe-Hydrogenase. J Chem Phys 2018; 149:204108. [PMID: 30501239 DOI: 10.1063/1.5054877] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
FeFe-hydrogenase is an efficient enzyme to produce H2 under optimal conditions. However, the activity of this enzyme is highly sensitive to the presence of inhibitory gases CO and O2 that cause irreversible damage to the active site. Therefore, a detailed knowledge of the diffusion pathways of these inhibitory gases is necessary to develop strategies for designing novel enzymes that are tolerant to these gases. In this work, we studied the diffusion pathways of CO in the CpI FeFe-hydrogenase from Clostridium pasteurianum. Specifically, we used several enhanced sampling and free-energy simulation methods to reconstruct a three-dimensional free-energy surface for CO diffusion which revealed 45 free-energy minima forming an interconnected network of pathways. We discovered multiple pathways of minimal free-energy as diffusion portals for CO and found that previously suggested hydrophobic pathways are not thermodynamically favorable for CO diffusion. We also observed that the global minimum in the free-energy surface is located in the vicinity of the active-site metal cluster, the H-cluster, which suggests a high-affinity for CO near the active site. Among 19 potential residues that we propose as candidates for future mutagenesis studies, 11 residues are shared with residues that have been previously proposed to increase the tolerance of this enzyme for O2. We hypothesize that these shared candidate residues are potentially useful for designing new variants of this enzyme that are tolerant to both inhibitory gases.
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Affiliation(s)
- Yong Liu
- Department of Chemical Engineering, University of New Hampshire, 33 Academic Way, Durham, New Hampshire 03824, USA
| | - Mohammadjavad Mohammadi
- Department of Chemical Engineering, University of New Hampshire, 33 Academic Way, Durham, New Hampshire 03824, USA
| | - Harish Vashisth
- Department of Chemical Engineering, University of New Hampshire, 33 Academic Way, Durham, New Hampshire 03824, USA
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10
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Mohammadi M, Vashisth H. Pathways and Thermodynamics of Oxygen Diffusion in [FeFe]-Hydrogenase. J Phys Chem B 2017; 121:10007-10017. [DOI: 10.1021/acs.jpcb.7b06489] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Mohammadjavad Mohammadi
- Department of Chemical Engineering, University of New Hampshire, Durham 03824, New Hampshire, United States
| | - Harish Vashisth
- Department of Chemical Engineering, University of New Hampshire, Durham 03824, New Hampshire, United States
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11
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Morra S, Valetti F, Gilardi G. [FeFe]-hydrogenases as biocatalysts in bio-hydrogen production. RENDICONTI LINCEI 2016. [DOI: 10.1007/s12210-016-0584-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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12
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Plummer SM, Plummer MA, Merkel PA, Hagen M, Biddle JF, Waidner LA. Using directed evolution to improve hydrogen production in chimeric hydrogenases from Clostridia species. Enzyme Microb Technol 2016; 93-94:132-141. [DOI: 10.1016/j.enzmictec.2016.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 07/17/2016] [Accepted: 07/19/2016] [Indexed: 01/28/2023]
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13
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Unification of [FeFe]-hydrogenases into three structural and functional groups. Biochim Biophys Acta Gen Subj 2016; 1860:1910-21. [DOI: 10.1016/j.bbagen.2016.05.034] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/20/2016] [Accepted: 05/26/2016] [Indexed: 11/22/2022]
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14
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Haplotype-Phased Synthetic Long Reads from Short-Read Sequencing. PLoS One 2016; 11:e0147229. [PMID: 26789840 PMCID: PMC4720449 DOI: 10.1371/journal.pone.0147229] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 12/30/2015] [Indexed: 12/26/2022] Open
Abstract
Next-generation DNA sequencing has revolutionized the study of biology. However, the short read lengths of the dominant instruments complicate assembly of complex genomes and haplotype phasing of mixtures of similar sequences. Here we demonstrate a method to reconstruct the sequences of individual nucleic acid molecules up to 11.6 kilobases in length from short (150-bp) reads. We show that our method can construct 99.97%-accurate synthetic reads from bacterial, plant, and animal genomic samples, full-length mRNA sequences from human cancer cell lines, and individual HIV env gene variants from a mixture. The preparation of multiple samples can be multiplexed into a single tube, further reducing effort and cost relative to competing approaches. Our approach generates sequencing libraries in three days from less than one microgram of DNA in a single-tube format without custom equipment or specialized expertise.
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15
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Morra S, Cordara A, Gilardi G, Valetti F. Atypical effect of temperature tuning on the insertion of the catalytic iron-sulfur center in a recombinant [FeFe]-hydrogenase. Protein Sci 2015; 24:2090-4. [PMID: 26362685 DOI: 10.1002/pro.2805] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/08/2015] [Accepted: 09/11/2015] [Indexed: 01/04/2023]
Abstract
The expression of recombinant [FeFe]-hydrogenases is an important step for the production of large amount of these enzymes for their exploitation in biotechnology and for the characterization of the protein-metal cofactor interactions. The correct assembly of the organometallic catalytic site, named H-cluster, requires a dedicated set of maturases that must be coexpressed in the microbial hosts or used for in vitro assembly of the active enzymes. In this work, the effect of the post-induction temperature on the recombinant expression of CaHydA [FeFe]-hydrogenase in E. coli is investigated. The results show a peculiar behavior: the enzyme expression is maximum at lower temperatures (20°C), while the specific activity of the purified CaHydA is higher at higher temperature (30°C), as a consequence of improved protein folding and active site incorporation.
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Affiliation(s)
- Simone Morra
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, Torino, 10123, Italy
| | - Alessandro Cordara
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, Torino, 10123, Italy
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, Torino, 10123, Italy
| | - Francesca Valetti
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, Torino, 10123, Italy
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16
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Ghirardi ML. Implementation of photobiological H2 production: the O 2 sensitivity of hydrogenases. PHOTOSYNTHESIS RESEARCH 2015; 125:383-93. [PMID: 26022106 DOI: 10.1007/s11120-015-0158-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/13/2015] [Indexed: 05/10/2023]
Abstract
The search for the ultimate carbon-free fuel has intensified in recent years, with a major focus on photoproduction of H2. Biological sources of H2 include oxygenic photosynthetic green algae and cyanobacteria, both of which contain hydrogenase enzymes. Although algal and cyanobacterial hydrogenases perform the same enzymatic reaction through metallo-clusters, their hydrogenases have evolved separately, are expressed differently (transcription of algal hydrogenases is anaerobically induced, while bacterial hydrogenases are constitutively expressed), and display different sensitivity to O2 inactivation. Among various physiological factors, the sensitivity of hydrogenases to O2 has been one of the major factors preventing implementation of biological systems for commercial production of renewable H2. This review addresses recent strategies aimed at engineering increased O2 tolerance into hydrogenases (as of now mainly unsuccessful), as well as towards the development of methods to bypass the O2 sensitivity of hydrogenases (successful but still yielding low solar conversion efficiencies). The author concludes with a description of current approaches from various laboratories to incorporate multiple genetic traits into either algae or cyanobacteria to jointly address limiting factors other than the hydrogenase O2 sensitivity and achieve more sustained H2 photoproduction activity.
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Affiliation(s)
- Maria L Ghirardi
- National Renewable Energy Laboratory, 15013 Denver West Pkway, Golden, CO, 80401, USA,
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17
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Structural Insight into the Complex of Ferredoxin and [FeFe] Hydrogenase fromChlamydomonas reinhardtii. Chembiochem 2015; 16:1663-9. [DOI: 10.1002/cbic.201500130] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Indexed: 01/01/2023]
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18
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Boyd ES, Hamilton TL, Swanson KD, Howells AE, Baxter BK, Meuser JE, Posewitz MC, Peters JW. [FeFe]-hydrogenase abundance and diversity along a vertical redox gradient in Great Salt Lake, USA. Int J Mol Sci 2014; 15:21947-66. [PMID: 25464382 PMCID: PMC4284687 DOI: 10.3390/ijms151221947] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 11/11/2014] [Accepted: 11/13/2014] [Indexed: 11/29/2022] Open
Abstract
The use of [FeFe]-hydrogenase enzymes for the biotechnological production of H2 or other reduced products has been limited by their sensitivity to oxygen (O2). Here, we apply a PCR-directed approach to determine the distribution, abundance, and diversity of hydA gene fragments along co-varying salinity and O2 gradients in a vertical water column of Great Salt Lake (GSL), UT. The distribution of hydA was constrained to water column transects that had high salt and relatively low O2 concentrations. Recovered HydA deduced amino acid sequences were enriched in hydrophilic amino acids relative to HydA from less saline environments. In addition, they harbored interesting variations in the amino acid environment of the complex H-cluster metalloenzyme active site and putative gas transfer channels that may be important for both H2 transfer and O2 susceptibility. A phylogenetic framework was created to infer the accessory cluster composition and quaternary structure of recovered HydA protein sequences based on phylogenetic relationships and the gene contexts of known complete HydA sequences. Numerous recovered HydA are predicted to harbor multiple N- and C-terminal accessory iron-sulfur cluster binding domains and are likely to exist as multisubunit complexes. This study indicates an important role for [FeFe]-hydrogenases in the functioning of the GSL ecosystem and provides new target genes and variants for use in identifying O2 tolerant enzymes for biotechnological applications.
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Affiliation(s)
- Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA.
| | - Trinity L Hamilton
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Kevin D Swanson
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Alta E Howells
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Bonnie K Baxter
- Department of Biology and the Great Salt Lake Institute, Westminster College, Salt Lake City, UT 84105, USA.
| | - Jonathan E Meuser
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO 80401, USA.
| | - Matthew C Posewitz
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO 80401, USA.
| | - John W Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA.
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19
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Wecker MSA, Ghirardi ML. High-throughput biosensor discriminates between different algal H2 -photoproducing strains. Biotechnol Bioeng 2014; 111:1332-40. [PMID: 24578287 DOI: 10.1002/bit.25206] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 01/15/2014] [Accepted: 01/28/2014] [Indexed: 12/24/2022]
Abstract
A number of species of microalgae and cyanobacteria photosynthetically produce H2 gas by coupling water oxidation with the reduction of protons to molecular hydrogen, generating renewable energy from sunlight and water. Photosynthetic H2 production, however, is transitory, and there is considerable interest in increasing and extending it for commercial applications. Here we report a Petri-plate version of our previous, microplate-based assay that detects photosynthetic H2 production by algae. The assay consists of an agar overlay of H2 -sensing Rhodobacter capsulatus bacteria carrying a green fluorescent protein that responds to H2 produced by single algal colonies in the bottom agar layer. The assay distinguishes between algal strains that photoproduce H2 at different levels under high light intensities, and it does so in a simple, inexpensive, and high-throughput manner. The assay will be useful for screening both natural populations and mutant libraries for strains having increased H2 production, and useful for identifying various genetic factors that physiologically or genetically alter algal hydrogen production.
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20
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Alternative fermentation conditions for improved Escherichia coli-based cell-free protein synthesis for proteins requiring supplemental components for proper synthesis. Process Biochem 2014. [DOI: 10.1016/j.procbio.2013.10.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Faiella M, Roy A, Sommer D, Ghirlanda G. De novo design of functional proteins: Toward artificial hydrogenases. Biopolymers 2013; 100:558-71. [DOI: 10.1002/bip.22420] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 07/08/2013] [Accepted: 09/18/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Marina Faiella
- Department of Chemistry and Biochemistry; Arizona State University; Tempe AZ
| | - Anindya Roy
- Department of Chemistry and Biochemistry; Arizona State University; Tempe AZ
| | - Dayn Sommer
- Department of Chemistry and Biochemistry; Arizona State University; Tempe AZ
| | - Giovanna Ghirlanda
- Department of Chemistry and Biochemistry; Arizona State University; Tempe AZ
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Catherine C, Lee KH, Oh SJ, Kim DM. Cell-free platforms for flexible expression and screening of enzymes. Biotechnol Adv 2013; 31:797-803. [DOI: 10.1016/j.biotechadv.2013.04.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 04/06/2013] [Accepted: 04/26/2013] [Indexed: 12/20/2022]
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Improvement of biocatalysts for industrial and environmental purposes by saturation mutagenesis. Biomolecules 2013; 3:778-811. [PMID: 24970191 PMCID: PMC4030971 DOI: 10.3390/biom3040778] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 09/22/2013] [Accepted: 09/23/2013] [Indexed: 11/16/2022] Open
Abstract
Laboratory evolution techniques are becoming increasingly widespread among protein engineers for the development of novel and designed biocatalysts. The palette of different approaches ranges from complete randomized strategies to rational and structure-guided mutagenesis, with a wide variety of costs, impacts, drawbacks and relevance to biotechnology. A technique that convincingly compromises the extremes of fully randomized vs. rational mutagenesis, with a high benefit/cost ratio, is saturation mutagenesis. Here we will present and discuss this approach in its many facets, also tackling the issue of randomization, statistical evaluation of library completeness and throughput efficiency of screening methods. Successful recent applications covering different classes of enzymes will be presented referring to the literature and to research lines pursued in our group. The focus is put on saturation mutagenesis as a tool for designing novel biocatalysts specifically relevant to production of fine chemicals for improving bulk enzymes for industry and engineering technical enzymes involved in treatment of waste, detoxification and production of clean energy from renewable sources.
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Winkler M, Esselborn J, Happe T. Molecular basis of [FeFe]-hydrogenase function: an insight into the complex interplay between protein and catalytic cofactor. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:974-85. [PMID: 23507618 DOI: 10.1016/j.bbabio.2013.03.004] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 02/21/2013] [Accepted: 03/08/2013] [Indexed: 12/20/2022]
Abstract
The precise electrochemical features of metal cofactors that convey the functions of redox enzymes are essentially determined by the specific interaction pattern between cofactor and enclosing protein environment. However, while biophysical techniques allow a detailed understanding of the features characterizing the cofactor itself, knowledge about the contribution of the protein part is much harder to obtain. [FeFe]-hydrogenases are an interesting class of enzymes that catalyze both, H2 oxidation and the reduction of protons to molecular hydrogen with significant efficiency. The active site of these proteins consists of an unusual prosthetic group (H-cluster) with six iron and six sulfur atoms. While H-cluster architecture and catalytic states during the different steps of H2 turnover have been thoroughly investigated during the last 20 years, possible functional contributions from the polypeptide framework were only assumed according to the level of conservancy and X-ray structure analyses. Due to the recent development of simpler and more efficient expression systems the role of single amino acids can now be experimentally investigated. This article summarizes, compares and categorizes the results of recent investigations based on site directed and random mutagenesis according to their informative value about structure function relationships in [FeFe]-hydrogenases. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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Affiliation(s)
- Martin Winkler
- Ruhr-Universität Bochum, Fakultät für Biologie und Biotechnologie, Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie, Bochum, Germany
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25
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Li S, Yang X, Yang S, Zhu M, Wang X. Technology prospecting on enzymes: application, marketing and engineering. Comput Struct Biotechnol J 2012; 2:e201209017. [PMID: 24688658 PMCID: PMC3962110 DOI: 10.5936/csbj.201209017] [Citation(s) in RCA: 180] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 10/25/2012] [Accepted: 10/29/2012] [Indexed: 01/10/2023] Open
Abstract
Enzymes are protein molecules functioning as specialized catalysts for chemical reactions. They have contributed greatly to the traditional and modern chemical industry by improving existing processes. In this article, we first give a survey of representative industrial applications of enzymes, focusing on the technical applications, feed industry, food processing and cosmetic products. The recent important developments and applications of enzymes in industry are reviewed. Then large efforts are dedicated to the worldwide enzyme market from the demand and production perspectives. Special attention is laid on the Chinese enzyme market. Although enzyme applications are being developed in full swing, breakthroughs are needed to overcome their weaknesses in maintaining activities during the catalytic processes. Strategies of metagomic analysis, cell surface display technology and cell-free system might give valuable solutions in novel enzyme exploiting and enzyme engineering.
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Affiliation(s)
- Shuang Li
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China
| | - Xiaofeng Yang
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China
| | - Shuai Yang
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China
| | - Muzi Zhu
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China
| | - Xiaoning Wang
- School of Life Science, General Hospital of PLA, Beijing 100853, China
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Site saturation mutagenesis demonstrates a central role for cysteine 298 as proton donor to the catalytic site in CaHydA [FeFe]-hydrogenase. PLoS One 2012; 7:e48400. [PMID: 23133586 PMCID: PMC3485046 DOI: 10.1371/journal.pone.0048400] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 09/25/2012] [Indexed: 01/24/2023] Open
Abstract
[FeFe]-hydrogenases reversibly catalyse molecular hydrogen evolution by reduction of two protons. Proton supply to the catalytic site (H-cluster) is essential for enzymatic activity. Cysteine 298 is a highly conserved residue in all [FeFe]-hydrogenases; moreover C298 is structurally very close to the H-cluster and it is important for hydrogenase activity. Here, the function of C298 in catalysis was investigated in detail by means of site saturation mutagenesis, simultaneously studying the effect of C298 replacement with all other 19 amino acids and selecting for mutants with high retained activity. We demonstrated that efficient enzymatic turnover was maintained only when C298 was replaced by aspartic acid, despite the structural diversity between the two residues. Purified CaHydA C298D does not show any significant structural difference in terms of secondary structure and iron incorporation, demonstrating that the mutation does not affect the overall protein fold. C298D retains the hydrogen evolution activity with a decrease of kcat only by 2-fold at pH 8.0 and it caused a shift of the optimum pH from 8.0 to 7.0. Moreover, the oxygen inactivation rate was not affected demonstrating that the mutation does not influence O2 diffusion to the active site or its reactivity with the H-cluster. Our results clearly demonstrate that, in order to maintain the catalytic efficiency and the high turnover number typical of [FeFe] hydrogenases, the highly conserved C298 can be replaced only by another ionisable residue with similar steric hindrance, giving evidence of its involvement in the catalytic function of [FeFe]-hydrogenases in agreement with an essential role in proton transfer to the active site.
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27
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Wang M, Si T, Zhao H. Biocatalyst development by directed evolution. BIORESOURCE TECHNOLOGY 2012; 115:117-25. [PMID: 22310212 PMCID: PMC3351540 DOI: 10.1016/j.biortech.2012.01.054] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 01/11/2012] [Accepted: 01/13/2012] [Indexed: 05/13/2023]
Abstract
Biocatalysis has emerged as a great addition to traditional chemical processes for production of bulk chemicals and pharmaceuticals. To overcome the limitations of naturally occurring enzymes, directed evolution has become the most important tool for improving critical traits of biocatalysts such as thermostability, activity, selectivity, and tolerance towards organic solvents for industrial applications. Recent advances in mutant library creation and high-throughput screening have greatly facilitated the engineering of novel and improved biocatalysts. This review provides an update of the recent developments in the use of directed evolution to engineer biocatalysts for practical applications.
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Affiliation(s)
- Meng Wang
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Tong Si
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Departments of Chemistry, Biochemistry, and Bioengineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- To whom correspondence should be addressed. Phone: (217) 333-2631. Fax: (217) 333-5052.
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Ge X, Luo D, Xu J. Cell-free protein expression under macromolecular crowding conditions. PLoS One 2011; 6:e28707. [PMID: 22174874 PMCID: PMC3234285 DOI: 10.1371/journal.pone.0028707] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 11/14/2011] [Indexed: 01/29/2023] Open
Abstract
Background Cell-free protein expression (CFPE) comprised of in vitro transcription and translation is currently manipulated in relatively dilute solutions, in which the macromolecular crowding effects present in living cells are largely ignored. This may not only affect the efficiency of protein synthesis in vitro, but also limit our understanding of the functions and interactions of biomolecules involved in this fundamental biological process. Methodology/Principal Findings Using cell-free synthesis of Renilla luciferase in wheat germ extract as a model system, we investigated the CFPE under macromolecular crowding environments emulated with three different crowding agents: PEG-8000, Ficoll-70 and Ficoll-400, which vary in chemical properties and molecular size. We found that transcription was substantially enhanced in the macromolecular crowding solutions; up to 4-fold increase in the mRNA production was detected in the presence of 20% (w/v) of Ficoll-70. In contrast, translation was generally inhibited by the addition of each of the three crowding agents. This might be due to PEG-induced protein precipitation and non-specific binding of translation factors to Ficoll molecules. We further explored a two-stage CFPE in which transcription and translation was carried out under high then low macromolecular crowding conditions, respectively. It produced 2.2-fold higher protein yield than the coupled CFPE control. The macromolecular crowding effects on CFPE were subsequently confirmed by cell-free synthesis of an approximately two-fold larger protein, Firefly luciferase, under macromolecular crowding environments. Conclusions/Significance Three macromolecular crowding agents used in this research had opposite effects on transcription and translation. The results of this study should aid researchers in their choice of macromolecular crowding agents and shows that two-stage CFPE is more efficient than coupled CFPE.
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Affiliation(s)
- Xumeng Ge
- Arkansas Biosciences Institute and College of Agriculture and Technology, Arkansas State University, Jonesboro, Arkansas, United States of America
| | - Dan Luo
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York, United States of America
| | - Jianfeng Xu
- Arkansas Biosciences Institute and College of Agriculture and Technology, Arkansas State University, Jonesboro, Arkansas, United States of America
- * E-mail:
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Abstract
The production of hydrogen via microbial biotechnology is an active field of research. Given its ease of manipulation, the best‐studied bacterium Escherichia coli has become a workhorse for enhanced hydrogen production through metabolic engineering, heterologous gene expression, adaptive evolution, and protein engineering. Herein, the utility of E. coli strains to produce hydrogen, via native hydrogenases or heterologous ones, is reviewed. In addition, potential strategies for increasing hydrogen production are outlined and whole‐cell systems and cell‐free systems are compared.
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Affiliation(s)
- Toshinari Maeda
- Department of Chemical Engineering, Texas A & M University, 220 Jack E. Brown Building, College Station, TX 77843-3122, USA.
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A synthetic system links FeFe-hydrogenases to essential E. coli sulfur metabolism. J Biol Eng 2011; 5:7. [PMID: 21615937 PMCID: PMC3130634 DOI: 10.1186/1754-1611-5-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 05/26/2011] [Indexed: 01/11/2023] Open
Abstract
Background FeFe-hydrogenases are the most active class of H2-producing enzymes known in nature and may have important applications in clean H2 energy production. Many potential uses are currently complicated by a crucial weakness: the active sites of all known FeFe-hydrogenases are irreversibly inactivated by O2. Results We have developed a synthetic metabolic pathway in E. coli that links FeFe-hydrogenase activity to the production of the essential amino acid cysteine. Our design includes a complementary host strain whose endogenous redox pool is insulated from the synthetic metabolic pathway. Host viability on a selective medium requires hydrogenase expression, and moderate O2 levels eliminate growth. This pathway forms the basis for a genetic selection for O2 tolerance. Genetically selected hydrogenases did not show improved stability in O2 and in many cases had lost H2 production activity. The isolated mutations cluster significantly on charged surface residues, suggesting the evolution of binding surfaces that may accelerate hydrogenase electron transfer. Conclusions Rational design can optimize a fully heterologous three-component pathway to provide an essential metabolic flux while remaining insulated from the endogenous redox pool. We have developed a number of convenient in vivo assays to aid in the engineering of synthetic H2 metabolism. Our results also indicate a H2-independent redox activity in three different FeFe-hydrogenases, with implications for the future directed evolution of H2-activating catalysts.
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Burgess SJ, Tamburic B, Zemichael F, Hellgardt K, Nixon PJ. Solar-driven hydrogen production in green algae. ADVANCES IN APPLIED MICROBIOLOGY 2011; 75:71-110. [PMID: 21807246 DOI: 10.1016/b978-0-12-387046-9.00004-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The twin problems of energy security and global warming make hydrogen an attractive alternative to traditional fossil fuels with its combustion resulting only in the release of water vapor. Biological hydrogen production represents a renewable source of the gas and can be performed by a diverse range of microorganisms from strict anaerobic bacteria to eukaryotic green algae. Compared to conventional methods for generating H(2), biological systems can operate at ambient temperatures and pressures without the need for rare metals and could potentially be coupled to a variety of biotechnological processes ranging from desalination and waste water treatment to pharmaceutical production. Photobiological hydrogen production by microalgae is particularly attractive as the main inputs for the process (water and solar energy) are plentiful. This chapter focuses on recent developments in solar-driven H(2) production in green algae with emphasis on the model organism Chlamydomonas reinhardtii. We review the current methods used to achieve sustained H(2) evolution and discuss possible approaches to improve H(2) yields, including the optimization of culturing conditions, reducing light-harvesting antennae and targeting auxiliary electron transport and fermentative pathways that compete with the hydrogenase for reductant. Finally, industrial scale-up is discussed in the context of photobioreactor design and the future prospects of the field are considered within the broader context of a biorefinery concept.
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Affiliation(s)
- Steven J Burgess
- Department of Life Sciences, Imperial College London, London, United Kingdom.
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Park CG, Kwon MA, Song JK, Kim DM. Cell-free synthesis and multifold screening of Candida antarctica lipase B (CalB) variants after combinatorial mutagenesis of hot spots. Biotechnol Prog 2010; 27:47-53. [PMID: 21312354 DOI: 10.1002/btpr.532] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Revised: 09/09/2010] [Indexed: 01/27/2023]
Abstract
We have developed a strategy for rapid and combinatorial optimization of the hot spot residues of enzymes. After combinatorial randomization of target locations in the Candida antarctica lipase B (CalB) gene, the individual variant genes isolated in the E.coli cells were expressed in the cell-free protein synthesis system to analyze different parameters of the resulting CalB variants. The enzymatic assays for the hydrolysis of para-nitrophenyl-ester (pNP-ester) and triglyceride, synthesis of wax ester, and thermal stability of the variant enzymes were carried out simultaneously in 96-well microtiter plates. From the 1,000 variant genes tested in each assay, we were able to identify a series of the variant enzymes having markedly improved hydrolytic, synthetic activity, or thermal stability. The improved traits of the cell-free selected CalB variants were well reproduced when the corresponding genes were expressed in Pichia pastoris. Therefore, we expect that the proposed strategy of cell-free expression screening can serve as a viable option for rapid and precise tuning of enzyme molecules, not only for analytical purposes but also for industrial applications through large scale production using microbial cells transformed with variant genes selected from the cell-free expression screening.
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Affiliation(s)
- Chang-Gil Park
- Dept. of Fine Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon 305-764, Korea
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Stapleton JA, Swartz JR. Development of an in vitro compartmentalization screen for high-throughput directed evolution of [FeFe] hydrogenases. PLoS One 2010; 5:e15275. [PMID: 21151915 PMCID: PMC2997796 DOI: 10.1371/journal.pone.0015275] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Accepted: 11/03/2010] [Indexed: 01/10/2023] Open
Abstract
Background [FeFe] hydrogenase enzymes catalyze the formation and dissociation of molecular hydrogen with the help of a complex prosthetic group composed of common elements. The development of energy conversion technologies based on these renewable catalysts has been hindered by their extreme oxygen sensitivity. Attempts to improve the enzymes by directed evolution have failed for want of a screening platform capable of throughputs high enough to adequately sample heavily mutated DNA libraries. In vitro compartmentalization (IVC) is a powerful method capable of screening for multiple-turnover enzymatic activity at very high throughputs. Recent advances have allowed [FeFe] hydrogenases to be expressed and activated in the cell-free protein synthesis reactions on which IVC is based; however, IVC is a demanding technique with which many enzymes have proven incompatible. Methodology/Principal Findings Here we describe an extremely high-throughput IVC screen for oxygen-tolerant [FeFe] hydrogenases. We demonstrate that the [FeFe] hydrogenase CpI can be expressed and activated within emulsion droplets, and identify a fluorogenic substrate that links activity after oxygen exposure to the generation of a fluorescent signal. We present a screening protocol in which attachment of mutant genes and the proteins they encode to the surfaces of microbeads is followed by three separate emulsion steps for amplification, expression, and evaluation of hydrogenase mutants. We show that beads displaying active hydrogenase can be isolated by fluorescence-activated cell-sorting, and we use the method to enrich such beads from a mock library. Conclusions/Significance [FeFe] hydrogenases are the most complex enzymes to be produced by cell-free protein synthesis, and the most challenging targets to which IVC has yet been applied. The technique described here is an enabling step towards the development of biocatalysts for a biological hydrogen economy.
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Affiliation(s)
- James A. Stapleton
- Department of Chemical Engineering, Stanford University, Stanford, California, United States of America
| | - James R. Swartz
- Department of Chemical Engineering, Stanford University, Stanford, California, United States of America
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
- * E-mail:
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