351
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Liu XW, Li WW, Yu HQ. Cathodic catalysts in bioelectrochemical systems for energy recovery from wastewater. Chem Soc Rev 2014; 43:7718-45. [DOI: 10.1039/c3cs60130g] [Citation(s) in RCA: 183] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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352
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Enhanced start-up of anaerobic facultatively autotrophic biocathodes in bioelectrochemical systems. J Biotechnol 2013; 168:478-85. [DOI: 10.1016/j.jbiotec.2013.10.001] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 08/24/2013] [Accepted: 10/02/2013] [Indexed: 11/22/2022]
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353
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Nakata K, Ozaki T, Terashima C, Fujishima A, Einaga Y. High-Yield Electrochemical Production of Formaldehyde from CO2and Seawater. Angew Chem Int Ed Engl 2013; 53:871-4. [DOI: 10.1002/anie.201308657] [Citation(s) in RCA: 276] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 10/23/2013] [Indexed: 11/11/2022]
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354
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Nakata K, Ozaki T, Terashima C, Fujishima A, Einaga Y. High-Yield Electrochemical Production of Formaldehyde from CO2and Seawater. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201308657] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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355
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Bi C, Su P, Müller J, Yeh YC, Chhabra SR, Beller HR, Singer SW, Hillson NJ. Development of a broad-host synthetic biology toolbox for Ralstonia eutropha and its application to engineering hydrocarbon biofuel production. Microb Cell Fact 2013; 12:107. [PMID: 24219429 PMCID: PMC3831590 DOI: 10.1186/1475-2859-12-107] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 11/11/2013] [Indexed: 01/20/2023] Open
Abstract
Background The chemoautotrophic bacterium Ralstonia eutropha can utilize H2/CO2 for growth under aerobic conditions. While this microbial host has great potential to be engineered to produce desired compounds (beyond polyhydroxybutyrate) directly from CO2, little work has been done to develop genetic part libraries to enable such endeavors. Results We report the development of a toolbox for the metabolic engineering of Ralstonia eutropha H16. We have constructed a set of broad-host-range plasmids bearing a variety of origins of replication, promoters, 5’ mRNA stem-loop structures, and ribosomal binding sites. Specifically, we analyzed the origins of replication pCM62 (IncP), pBBR1, pKT (IncQ), and their variants. We tested the promoters PBAD, T7, Pxyls/PM, PlacUV5, and variants thereof for inducible expression. We also evaluated a T7 mRNA stem-loop structure sequence and compared a set of ribosomal binding site (RBS) sequences derived from Escherichia coli, R. eutropha, and a computational RBS design tool. Finally, we employed the toolbox to optimize hydrocarbon production in R. eutropha and demonstrated a 6-fold titer improvement using the appropriate combination of parts. Conclusion We constructed and evaluated a versatile synthetic biology toolbox for Ralstonia eutropha metabolic engineering that could apply to other microbial hosts as well.
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Affiliation(s)
| | | | | | | | - Swapnil R Chhabra
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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356
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Liu D, Lei L, Yang B, Yu Q, Li Z. Direct electron transfer from electrode to electrochemically active bacteria in a bioelectrochemical dechlorination system. BIORESOURCE TECHNOLOGY 2013; 148:9-14. [PMID: 24035815 DOI: 10.1016/j.biortech.2013.08.108] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 08/15/2013] [Accepted: 08/19/2013] [Indexed: 06/02/2023]
Abstract
Pentachlorophenol (PCP) was dechlorinated by electrochemically active bacteria using an electrode as the direct electron donor. Dechlorination efficiency and coulombic efficiency (CE) were investigated. When hydrogen evolution reaction was eliminated by controlling the potential, both dechlorination efficiency and CE increase as the potential decreases, which implied the dechlorination was stimulated by electric current rather than hydrogen gas. Further investigation of the cyclic voltammetry characterization of the medium revealed nearly no redox mediator secreted by the bacteria. Moreover, the comparison of dechlorination experiments carried out with filtered and unfiltered medium provided convincible evidence that the dominating electron transfer mechanism for the dechlorination is direct electron transfer. Additionally, 454 pyrosequencing technique was employed to gain a comprehensive understanding of the biocathodic microbial community. The results showed Proteobacteria, Bacteroidetes and Firmicutes were the three predominant groups. This paper demonstrated the direct electron transfer mechanism could be involved in PCP dechlorination with a biocathode.
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Affiliation(s)
- Ding Liu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, Department of Chemical and Biological Engineering, Yuquan Campus, Zhejiang University, Hangzhou, Zhejiang 310027, China
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357
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Synthetic non-oxidative glycolysis enables complete carbon conservation. Nature 2013; 502:693-7. [PMID: 24077099 DOI: 10.1038/nature12575] [Citation(s) in RCA: 261] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 08/15/2013] [Indexed: 01/19/2023]
Abstract
Glycolysis, or its variations, is a fundamental metabolic pathway in life that functions in almost all organisms to decompose external or intracellular sugars. The pathway involves the partial oxidation and splitting of sugars to pyruvate, which in turn is decarboxylated to produce acetyl-coenzyme A (CoA) for various biosynthetic purposes. The decarboxylation of pyruvate loses a carbon equivalent, and limits the theoretical carbon yield to only two moles of two-carbon (C2) metabolites per mole of hexose. This native route is a major source of carbon loss in biorefining and microbial carbon metabolism. Here we design and construct a non-oxidative, cyclic pathway that allows the production of stoichiometric amounts of C2 metabolites from hexose, pentose and triose phosphates without carbon loss. We tested this pathway, termed non-oxidative glycolysis (NOG), in vitro and in vivo in Escherichia coli. NOG enables complete carbon conservation in sugar catabolism to acetyl-CoA, and can be used in conjunction with CO2 fixation and other one-carbon (C1) assimilation pathways to achieve a 100% carbon yield to desirable fuels and chemicals.
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358
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Joya KS, Joya YF, Ocakoglu K, van de Krol R. Water-Splitting Catalysis and Solar Fuel Devices: Artificial Leaves on the Move. Angew Chem Int Ed Engl 2013; 52:10426-37. [DOI: 10.1002/anie.201300136] [Citation(s) in RCA: 395] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Indexed: 11/10/2022]
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359
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Joya KS, Joya YF, Ocakoglu K, van de Krol R. Katalytische Wasserspaltung und Solarbrennstoffzellen: künstliche Blätter auf dem Vormarsch. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201300136] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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360
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Morimoto Y, Honda K, Ye X, Okano K, Ohtake H. Directed evolution of thermotolerant malic enzyme for improved malate production. J Biosci Bioeng 2013; 117:147-152. [PMID: 23932397 DOI: 10.1016/j.jbiosc.2013.07.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 07/10/2013] [Accepted: 07/11/2013] [Indexed: 10/26/2022]
Abstract
The directed evolution of the thermotolerant NADP(H)-dependent malic enzyme from Thermococcus kodakarensis was conducted to alter the cofactor preference of the enzyme from NADP(H) to NAD(H). The construction and screening of two generations of mutant libraries led to the isolation of a triple mutant that exhibited 6-fold higher kcat/Km with NAD(+) than the wild type. We serendipitously found that, in addition to the change in the cofactor preference, the reaction specificity of the mutant enzyme was altered. The reductive carboxylation of pyruvate to malate catalyzed by the wild type enzyme is accompanied by HCO(3)(-)-independent reduction of pyruvate and gives lactate as a byproduct. The reaction specificity of the triple mutant was significantly shifted to malate production and the mutant gave a less amount of the byproduct than the wild type. When the triple mutant enzyme was used as a catalyst for pyruvate carboxylation with NADH, the enzyme gave 1.2 times higher concentration of malate than the wild type with NADPH. Single-point mutation analysis revealed that the substitution of Arg221 with Gly is responsible for the shift in reaction specificity. This finding may shed light on the catalytic mechanisms of malic enzymes and other related CO2- and/or HCO(3)(-)-fixing enzymes.
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Affiliation(s)
- Yumi Morimoto
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kohsuke Honda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
| | - Xiaoting Ye
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kenji Okano
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hisao Ohtake
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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361
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Xiao Y, Ruan Z, Liu Z, Wu SG, Varman AM, Liu Y, Tang YJ. Engineering Escherichia coli to convert acetic acid to free fatty acids. Biochem Eng J 2013. [DOI: 10.1016/j.bej.2013.04.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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362
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Glasgow JE, Tullman-Ercek D. Synthetic biologists spring into action at the 245th American Chemical Society National Meeting. ACS Synth Biol 2013; 2:293-5. [PMID: 24884108 DOI: 10.1021/sb400046t] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As the field of synthetic biology continues to define itself, it has merged concepts from many related areas of research: molecular biology, genetics, bioengineering, and chemistry. At the 2013 Spring American Chemical Society National Meeting in New Orleans, LA, this mixture was manifested in a wealth of sessions emphasizing the use of modern synthetic biological approaches to solve many of today's biggest chemical problems. As a result of the field's diverse yet pervasive nature, synthetic biology concepts were present in several of the conferences many divisions, including Biological Chemistry, Biochemical Technology, Cellulose and Renewable Materials, and several others. Here we offer a snapshot of some of the exciting research discussed in the dedicated synthetic biology sessions throughout the week.
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Affiliation(s)
- Jeff E. Glasgow
- Department
of Chemistry and ‡Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720,
United States
| | - Danielle Tullman-Ercek
- Department
of Chemistry and ‡Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720,
United States
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363
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Habisreutinger SN, Schmidt-Mende L, Stolarczyk JK. Photocatalytic reduction of CO2 on TiO2 and other semiconductors. Angew Chem Int Ed Engl 2013; 52:7372-408. [PMID: 23765842 DOI: 10.1002/anie.201207199] [Citation(s) in RCA: 1248] [Impact Index Per Article: 113.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 12/21/2012] [Indexed: 02/06/2023]
Abstract
Rising atmospheric levels of carbon dioxide and the depletion of fossil fuel reserves raise serious concerns about the ensuing effects on the global climate and future energy supply. Utilizing the abundant solar energy to convert CO2 into fuels such as methane or methanol could address both problems simultaneously as well as provide a convenient means of energy storage. In this Review, current approaches for the heterogeneous photocatalytic reduction of CO2 on TiO2 and other metal oxide, oxynitride, sulfide, and phosphide semiconductors are presented. Research in this field is focused primarily on the development of novel nanostructured photocatalytic materials and on the investigation of the mechanism of the process, from light absorption through charge separation and transport to CO2 reduction pathways. The measures used to quantify the efficiency of the process are also discussed in detail.
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Affiliation(s)
- Severin N Habisreutinger
- Department für Physik und Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität (LMU) München, Amalienstrasse 54, 80799 München, Germany
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364
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Habisreutinger SN, Schmidt-Mende L, Stolarczyk JK. Photokatalytische Reduktion von CO2an TiO2und anderen Halbleitern. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201207199] [Citation(s) in RCA: 178] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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365
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Yeh YC, Müller J, Bi C, Hillson NJ, Beller HR, Chhabra SR, Singer SW. Functionalizing bacterial cell surfaces with a phage protein. Chem Commun (Camb) 2013; 49:910-2. [PMID: 23247551 DOI: 10.1039/c2cc37883c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Functionalization of bacterial cell surfaces has the potential to introduce new activities by chemical modification. Here we show that a bacteriophage-receptor complex can be used to functionalize the surface of two Gram-negative proteobacteria, Escherichia coli and Ralstonia eutropha with CdSe/ZnS nanoparticles. This work highlights the potential for using microbe-phage interactions to generate new functions on living cells.
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Affiliation(s)
- Yi-Chun Yeh
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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366
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Engineering of Ralstonia eutropha H16 for autotrophic and heterotrophic production of methyl ketones. Appl Environ Microbiol 2013; 79:4433-9. [PMID: 23686271 DOI: 10.1128/aem.00973-13] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ralstonia eutropha is a facultatively chemolithoautotrophic bacterium able to grow with organic substrates or H2 and CO2 under aerobic conditions. Under conditions of nutrient imbalance, R. eutropha produces copious amounts of poly[(R)-3-hydroxybutyrate] (PHB). Its ability to utilize CO2 as a sole carbon source renders it an interesting new candidate host for the production of renewable liquid transportation fuels. We engineered R. eutropha for the production of fatty acid-derived, diesel-range methyl ketones. Modifications engineered in R. eutropha included overexpression of a cytoplasmic version of the TesA thioesterase, which led to a substantial (>150-fold) increase in fatty acid titer under certain conditions. In addition, deletion of two putative β-oxidation operons and heterologous expression of three genes (the acyl coenzyme A oxidase gene from Micrococcus luteus and fadB and fadM from Escherichia coli) led to the production of 50 to 65 mg/liter of diesel-range methyl ketones under heterotrophic growth conditions and 50 to 180 mg/liter under chemolithoautotrophic growth conditions (with CO2 and H2 as the sole carbon source and electron donor, respectively). Induction of the methyl ketone pathway diverted substantial carbon flux away from PHB biosynthesis and appeared to enhance carbon flux through the pathway for biosynthesis of fatty acids, which are the precursors of methyl ketones.
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367
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Wen M, Bond-Watts BB, Chang MCY. Production of advanced biofuels in engineered E. coli. Curr Opin Chem Biol 2013; 17:472-9. [PMID: 23659832 DOI: 10.1016/j.cbpa.2013.03.034] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 03/01/2013] [Accepted: 03/28/2013] [Indexed: 12/21/2022]
Abstract
Commercial fermentation processes have long taken advantage of the synthetic power of living systems to rapidly and efficiently transform simple carbon sources into complex molecules. In this regard, the ability of yeasts to produce ethanol from glucose at exceptionally high yields has served as a key feature in its use as a fuel, but is also limited by the poor molecular properties of ethanol as a fuel such as high water miscibility and low energy density. Advances in metabolic engineering and synthetic biology allow us to begin constructing new high-flux pathways for production of next generation biofuels that are key to building a sustainable pipeline for liquid transportation fuels.
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Affiliation(s)
- Miao Wen
- Department of Chemistry, University of California, Berkeley, CA 94720-1460, USA
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368
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Lan EI, Liao JC. Microbial synthesis of n-butanol, isobutanol, and other higher alcohols from diverse resources. BIORESOURCE TECHNOLOGY 2013. [PMID: 23186690 DOI: 10.1016/j.biortech.2012.09.104] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Microbial production of fuel and chemical feedstock is a promising approach to solving energy and environmental problems. n-Butanol, isobutanol and other higher alcohols are of particular interest because they can serve as both fuel and chemical feedstock. Alternative resources such as CO2, syngas, waste protein, and lignocellulose are currently being investigated for their potential to produce these compounds. Except for lignocellulose, utilization of such alternative resource has not been examined extensively. This review aims to summarize the development of metabolic pathways for efficient synthesis of these higher alcohols and the current status of microbial strain development for the conversion of diverse resources into higher alcohols.
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Affiliation(s)
- Ethan I Lan
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
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369
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Next generation biofuel engineering in prokaryotes. Curr Opin Chem Biol 2013; 17:462-71. [PMID: 23623045 DOI: 10.1016/j.cbpa.2013.03.037] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 02/23/2013] [Accepted: 03/28/2013] [Indexed: 12/15/2022]
Abstract
Next-generation biofuels must be compatible with current transportation infrastructure and be derived from environmentally sustainable resources that do not compete with food crops. Many bacterial species have unique properties advantageous to the production of such next-generation fuels. However, no single species possesses all characteristics necessary to make high quantities of fuels from plant waste or CO2. Species containing a subset of the desired characteristics are used as starting points for engineering organisms with all desired attributes. Metabolic engineering of model organisms has yielded high titer production of advanced fuels, including alcohols, isoprenoids, and fatty acid derivatives. Technical developments now allow engineering of native fuel producers, as well as lignocellulolytic and autotrophic bacteria, for the production of biofuels. Continued research on multiple fronts is required to engineer organisms for truly sustainable and economical biofuel production.
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370
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Lee SJ, Lee SJ, Lee DW. Design and development of synthetic microbial platform cells for bioenergy. Front Microbiol 2013; 4:92. [PMID: 23626588 PMCID: PMC3630320 DOI: 10.3389/fmicb.2013.00092] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 04/03/2013] [Indexed: 12/26/2022] Open
Abstract
The finite reservation of fossil fuels accelerates the necessity of development of renewable energy sources. Recent advances in synthetic biology encompassing systems biology and metabolic engineering enable us to engineer and/or create tailor made microorganisms to produce alternative biofuels for the future bio-era. For the efficient transformation of biomass to bioenergy, microbial cells need to be designed and engineered to maximize the performance of cellular metabolisms for the production of biofuels during energy flow. Toward this end, two different conceptual approaches have been applied for the development of platform cell factories: forward minimization and reverse engineering. From the context of naturally minimized genomes,non-essential energy-consuming pathways and/or related gene clusters could be progressively deleted to optimize cellular energy status for bioenergy production. Alternatively, incorporation of non-indigenous parts and/or modules including biomass-degrading enzymes, carbon uptake transporters, photosynthesis, CO2 fixation, and etc. into chassis microorganisms allows the platform cells to gain novel metabolic functions for bioenergy. This review focuses on the current progress in synthetic biology-aided pathway engineering in microbial cells and discusses its impact on the production of sustainable bioenergy.
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Affiliation(s)
- Sang Jun Lee
- Systems and Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology Daejeon, South Korea
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371
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Lan EI, Dekishima Y, Chuang DS, Liao JC. Metabolic engineering of 2-pentanone synthesis inEscherichia coli. AIChE J 2013. [DOI: 10.1002/aic.14086] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | | | - Derrick S. Chuang
- Dept. of Chemical and Biomolecular Engineering; University of California; Los Angeles; CA; 90095
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372
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Hawkins AS, McTernan PM, Lian H, Kelly RM, Adams MWW. Biological conversion of carbon dioxide and hydrogen into liquid fuels and industrial chemicals. Curr Opin Biotechnol 2013; 24:376-84. [PMID: 23510698 DOI: 10.1016/j.copbio.2013.02.017] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 02/18/2013] [Accepted: 02/19/2013] [Indexed: 12/12/2022]
Abstract
Non-photosynthetic routes for biological fixation of carbon dioxide into valuable industrial chemical precursors and fuels are moving from concept to reality. The development of 'electrofuel'-producing microorganisms leverages techniques in synthetic biology, genetic and metabolic engineering, as well as systems-level multi-omic analysis, directed evolution, and in silico modeling. Electrofuel processes are being developed for a range of microorganisms and energy sources (e.g. hydrogen, formate, electricity) to produce a variety of target molecules (e.g. alcohols, terpenes, alkenes). This review examines the current landscape of electrofuel projects with a focus on hydrogen-utilizing organisms covering the biochemistry of hydrogenases and carbonic anhydrases, kinetic and energetic analyses of the known carbon fixation pathways, and the state of genetic systems for current and prospective electrofuel-producing microorganisms.
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Affiliation(s)
- Aaron S Hawkins
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, United States
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373
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Rabinovitch-Deere CA, Oliver JWK, Rodriguez GM, Atsumi S. Synthetic biology and metabolic engineering approaches to produce biofuels. Chem Rev 2013; 113:4611-32. [PMID: 23488968 DOI: 10.1021/cr300361t] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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374
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Lovley DR, Nevin KP. Electrobiocommodities: powering microbial production of fuels and commodity chemicals from carbon dioxide with electricity. Curr Opin Biotechnol 2013; 24:385-90. [PMID: 23465755 DOI: 10.1016/j.copbio.2013.02.012] [Citation(s) in RCA: 226] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 02/04/2013] [Accepted: 02/08/2013] [Indexed: 01/07/2023]
Abstract
Electricity can be an energy source for microbially catalyzed production of fuels and other organic commodities from carbon dioxide. These electrobiocommodities (E-BCs) can be produced directly via electrode-to-microbe electron transfer or indirectly with electrochemically generated electron donors such as H2 or formate. Producing E-BCs may be a more efficient and environmentally sustainable strategy for converting solar energy to biocommodities than approaches that rely on biological photosynthesis. A diversity of microbial physiologies could potentially be adapted for E-BC production, but to date acetogenic microorganisms are the only organisms shown to covert electrically generated low potential electrons and carbon dioxide into multi-carbon organic products with high recovery of electrons in product. Substantial research and development will be required for E-BC commercialization.
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Affiliation(s)
- Derek R Lovley
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA.
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375
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Li H, Liao JC. Engineering a cyanobacterium as the catalyst for the photosynthetic conversion of CO2 to 1,2-propanediol. Microb Cell Fact 2013; 12:4. [PMID: 23339487 PMCID: PMC3556108 DOI: 10.1186/1475-2859-12-4] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 01/07/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The modern society primarily relies on petroleum and natural gas for the production of fuels and chemicals. One of the major commodity chemicals 1,2-propanediol (1,2-PDO), which has an annual production of more than 0.5 million tons in the United States, is currently produced by chemical processes from petroleum derived propylene oxide, which is energy intensive and not sustainable. In this study, we sought to achieve photosynthetic production of 1,2-PDO from CO2 using a genetically engineered cyanobacterium Synechococcus elongatus PCC 7942. Compared to the previously reported biological 1,2-PDO production processes which used sugar or glycerol as the substrates, direct chemical production from CO2 in photosynthetic organisms recycles the atmospheric CO2 and will not compete with food crops for arable land. RESULTS In this study, we reported photosynthetic production of 1,2-PDO from CO2 using a genetically engineered cyanobacterium Synechococcus elongatus PCC 7942. Introduction of the genes encoding methylglyoxal synthase (mgsA), glycerol dehydrogenase (gldA), and aldehyde reductase (yqhD) resulted in the production of ~22 mg/L 1,2-PDO from CO2. However, a comparable amount of the pathway intermediate acetol was also produced, especially during the stationary phase. The production of 1,2-PDO requires a robust input of reducing equivalents from cellular metabolism. To take advantage of cyanobacteria's NADPH pool, the synthetic pathway of 1,2-PDO was engineered to be NADPH-dependent by exploiting the NADPH-specific secondary alcohol dehydrogenases which have not been reported for 1,2-PDO production previously. This optimization strategy resulted in the production of ~150 mg/L 1,2-PDO and minimized the accumulation of the incomplete reduction product, acetol. CONCLUSION This work demonstrated that cyanobacteria can be engineered as a catalyst for the photosynthetic conversion of CO2 to 1,2-PDO. This work also characterized two NADPH-dependent sADHs for their catalytic capacity in 1,2-PDO formation, and suggested that they may be useful tools for renewable production of reduced chemicals in photosynthetic organisms.
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Affiliation(s)
- Han Li
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
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376
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Wernick DG, Liao JC. Protein-based biorefining: metabolic engineering for production of chemicals and fuel with regeneration of nitrogen fertilizers. Appl Microbiol Biotechnol 2013; 97:1397-406. [DOI: 10.1007/s00253-012-4605-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 11/17/2012] [Accepted: 11/20/2012] [Indexed: 11/24/2022]
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377
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Kang P, Meyer TJ, Brookhart M. Selective electrocatalytic reduction of carbon dioxide to formate by a water-soluble iridium pincer catalyst. Chem Sci 2013. [DOI: 10.1039/c3sc51339d] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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378
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Zhao LL, Wang SY, Xu XP, Ji SJ. Dual 1,3-dipolar cycloaddition of carbon dioxide: two CO bonds of CO2 react in one reaction. Chem Commun (Camb) 2013; 49:2569-71. [DOI: 10.1039/c3cc38526d] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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379
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Ye X, Honda K, Morimoto Y, Okano K, Ohtake H. Direct conversion of glucose to malate by synthetic metabolic engineering. J Biotechnol 2012; 164:34-40. [PMID: 23246984 DOI: 10.1016/j.jbiotec.2012.11.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 11/22/2012] [Accepted: 11/27/2012] [Indexed: 11/28/2022]
Abstract
Synthetic metabolic engineering enables us to construct an in vitro artificial synthetic pathways specialized for chemical manufacturing through the simple heat-treatment of the recombinant mesophiles having thermophilic enzymes, followed by rational combination of those biocatalytic modules. In this work, we constructed a synthetic pathway capable of direct conversion of glucose to malate. The reversible carboxylation of pyruvate catalyzed by a malic enzyme derived from Thermococcus kodakarensis (TkME) (ΔG°'=+7.3kJmol(-1)) was coupled with a thermodynamically favorable non-ATP-forming Embden-Meyerhof pathway to balance the consumption and regeneration of redox cofactors and to shift the overall equilibrium toward malate production (glucose+2HCO3(-)+2H→2 malate+2H2O; ΔG°'=-121.4kJmol(-1)). TkME exhibited both pyruvate carboxylation (malate-forming) and pyruvate reduction (lactate-forming) activities. By increasing HCO3(-) concentration, the reaction specificity could be redirected to malate production. As a result, the direct conversion of glucose to malate was achieved with a molar yield of 60%.
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Affiliation(s)
- Xiaoting Ye
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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380
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Xiao Y, Feng X, Varman AM, He L, Yu H, Tang YJ. Kinetic Modeling and Isotopic Investigation of Isobutanol Fermentation by Two Engineered Escherichia coli Strains. Ind Eng Chem Res 2012. [DOI: 10.1021/ie202936t] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yi Xiao
- Department
of Energy, Environmental and Chemical Engineering, Washington University, One Brookings Drive, St. Louis,
Missouri 63130, United States
| | - Xueyang Feng
- Department
of Energy, Environmental and Chemical Engineering, Washington University, One Brookings Drive, St. Louis,
Missouri 63130, United States
| | - Arul M. Varman
- Department
of Energy, Environmental and Chemical Engineering, Washington University, One Brookings Drive, St. Louis,
Missouri 63130, United States
| | - Lian He
- Department
of Energy, Environmental and Chemical Engineering, Washington University, One Brookings Drive, St. Louis,
Missouri 63130, United States
| | - Huifeng Yu
- Department
of Energy, Environmental and Chemical Engineering, Washington University, One Brookings Drive, St. Louis,
Missouri 63130, United States
| | - Yinjie J. Tang
- Department
of Energy, Environmental and Chemical Engineering, Washington University, One Brookings Drive, St. Louis,
Missouri 63130, United States
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381
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Fast AG, Papoutsakis ET. Stoichiometric and energetic analyses of non-photosynthetic CO2-fixation pathways to support synthetic biology strategies for production of fuels and chemicals. Curr Opin Chem Eng 2012. [DOI: 10.1016/j.coche.2012.07.005] [Citation(s) in RCA: 171] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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382
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383
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Bar-Even A, Noor E, Flamholz A, Milo R. Design and analysis of metabolic pathways supporting formatotrophic growth for electricity-dependent cultivation of microbes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:1039-47. [PMID: 23123556 DOI: 10.1016/j.bbabio.2012.10.013] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 10/05/2012] [Accepted: 10/25/2012] [Indexed: 11/29/2022]
Abstract
Electrosynthesis is a promising approach that enables the biological production of commodities, like fuels and fine chemicals, using renewably produced electricity. Several techniques have been proposed to mediate the transfer of electrons from the cathode to living cells. Of these, the electroproduction of formate as a mediator seems especially promising: formate is readily soluble, of low toxicity and can be produced at relatively high efficiency and at reasonable current density. While organisms that are capable of formatotrophic growth, i.e. growth on formate, exist naturally, they are generally less suitable for bulk cultivation and industrial needs. Hence, it may be helpful to engineer a model organism of industrial relevance, such as E. coli, for growth on formate. There are numerous metabolic pathways that can potentially support formatotrophic growth. Here we analyze these diverse pathways according to various criteria including biomass yield, thermodynamic favorability, chemical motive force, kinetics and the practical challenges posed by their expression. We find that the reductive glycine pathway, composed of the tetrahydrofolate system, the glycine cleavage system, serine hydroxymethyltransferase and serine deaminase, is a promising candidate to support electrosynthesis in E. coli. The approach presented here exemplifies how combining different computational approaches into a systematic analysis methodology provides assistance in redesigning metabolism. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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Affiliation(s)
- Arren Bar-Even
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot, Israel.
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384
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Abstract
Advanced biofuels produced by microorganisms have similar properties to petroleum-based fuels, and can 'drop in' to the existing transportation infrastructure. However, producing these biofuels in yields high enough to be useful requires the engineering of the microorganism's metabolism. Such engineering is not based on just one specific feedstock or host organism. Data-driven and synthetic-biology approaches can be used to optimize both the host and pathways to maximize fuel production. Despite some success, challenges still need to be met to move advanced biofuels towards commercialization, and to compete with more conventional fuels.
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385
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Electrosynthesis of commodity chemicals by an autotrophic microbial community. Appl Environ Microbiol 2012; 78:8412-20. [PMID: 23001672 DOI: 10.1128/aem.02401-12] [Citation(s) in RCA: 224] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
A microbial community originating from brewery waste produced methane, acetate, and hydrogen when selected on a granular graphite cathode poised at -590 mV versus the standard hydrogen electrode (SHE) with CO(2) as the only carbon source. This is the first report on the simultaneous electrosynthesis of these commodity chemicals and the first description of electroacetogenesis by a microbial community. Deep sequencing of the active community 16S rRNA revealed a dynamic microbial community composed of an invariant Archaea population of Methanobacterium spp. and a shifting Bacteria population. Acetobacterium spp. were the most abundant Bacteria on the cathode when acetogenesis dominated. Methane was generally the dominant product with rates increasing from <1 to 7 mM day(-1) (per cathode liquid volume) and was concomitantly produced with acetate and hydrogen. Acetogenesis increased to >4 mM day(-1) (accumulated to 28.5 mM over 12 days), and methanogenesis ceased following the addition of 2-bromoethanesulfonic acid. Traces of hydrogen accumulated during initial selection and subsequently accelerated to >11 mM day(-1) (versus 0.045 mM day(-1) abiotic production). The hypothesis of electrosynthetic biocatalysis occurring at the microbe-electrode interface was supported by a catalytic wave (midpoint potential of -460 mV versus SHE) in cyclic voltammetry scans of the biocathode, the lack of redox active components in the medium, and the generation of comparatively high amounts of products (even after medium exchange). In addition, the volumetric production rates of these three commodity chemicals are marked improvements for electrosynthesis, advancing the process toward economic feasibility.
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386
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Khunjar WO, Sahin A, West AC, Chandran K, Banta S. Biomass production from electricity using ammonia as an electron carrier in a reverse microbial fuel cell. PLoS One 2012; 7:e44846. [PMID: 23028643 PMCID: PMC3446996 DOI: 10.1371/journal.pone.0044846] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 08/08/2012] [Indexed: 01/23/2023] Open
Abstract
The storage of renewable electrical energy within chemical bonds of biofuels and other chemicals is a route to decreasing petroleum usage. A critical challenge is the efficient transfer of electrons into a biological host that can covert this energy into high energy organic compounds. In this paper, we describe an approach whereby biomass is grown using energy obtained from a soluble mediator that is regenerated electrochemically. The net result is a separate-stage reverse microbial fuel cell (rMFC) that fixes CO₂ into biomass using electrical energy. We selected ammonia as a low cost, abundant, safe, and soluble redox mediator that facilitated energy transfer to biomass. Nitrosomonas europaea, a chemolithoautotroph, was used as the biocatalyst due to its inherent capability to utilize ammonia as its sole energy source for growth. An electrochemical reactor was designed for the regeneration of ammonia from nitrite, and current efficiencies of 100% were achieved. Calculations indicated that overall bioproduction efficiency could approach 2.7±0.2% under optimal electrolysis conditions. The application of chemolithoautotrophy for industrial bioproduction has been largely unexplored, and results suggest that this and related rMFC platforms may enable biofuel and related biochemical production.
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Affiliation(s)
- Wendell O. Khunjar
- Department of Earth and Environmental Engineering, Department of Chemical Engineering, Columbia University, New York, New York, New York, United States of America
| | - Asli Sahin
- Department of Chemical Engineering, Columbia University, New York, New York, New York, United States of America
| | - Alan C. West
- Department of Chemical Engineering, Columbia University, New York, New York, New York, United States of America
- * E-mail: (ACW); (KC); (SB)
| | - Kartik Chandran
- Department of Earth and Environmental Engineering, Department of Chemical Engineering, Columbia University, New York, New York, New York, United States of America
- * E-mail: (ACW); (KC); (SB)
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, New York, New York, New York, United States of America
- * E-mail: (ACW); (KC); (SB)
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387
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Improved 2-methyl-1-propanol production in an engineered Bacillus subtilis by constructing inducible pathways. Biotechnol Lett 2012; 34:2253-8. [PMID: 22941373 DOI: 10.1007/s10529-012-1041-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2012] [Accepted: 07/16/2012] [Indexed: 12/15/2022]
Abstract
High-level constitutive gene expression can result in cellular metabolic imbalance and limit production. To circumvent these problems, a P(alsSD)-controlled auto-inducible 2-ketoisovalerate biosynthetic pathway and a P(spac)-controlled IPTG-inducible Ehrlich pathway were constructed in Bacillus subtilis to modulate gene expression. Based on the precise gene expression characteristics of the two inducible pathways, the optimal IPTG induction time point and dose for 2-methyl-1-propanol biosynthesis were determined as 9.5 h and 300 μM, respectively. Under the optimized conditions, strain BSUΔL-03 with inducible pathways produced up to 3.83 ± 0.46 g 2-methyl-1-propanol/l, which was about 60 % higher than BSUL04 with constitutive pathways.
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388
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Lu J, Brigham CJ, Gai CS, Sinskey AJ. Studies on the production of branched-chain alcohols in engineered Ralstonia eutropha. Appl Microbiol Biotechnol 2012; 96:283-97. [DOI: 10.1007/s00253-012-4320-9] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 07/16/2012] [Accepted: 07/17/2012] [Indexed: 11/25/2022]
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389
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Machado HB, Dekishima Y, Luo H, Lan EI, Liao JC. A selection platform for carbon chain elongation using the CoA-dependent pathway to produce linear higher alcohols. Metab Eng 2012; 14:504-11. [PMID: 22819734 DOI: 10.1016/j.ymben.2012.07.002] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 06/01/2012] [Accepted: 07/09/2012] [Indexed: 01/16/2023]
Abstract
Production of green chemicals and fuels using metabolically engineered organisms has been a promising alternative to petroleum-based production. Higher chain alcohols (C4-C8) are of interest because they can be used as chemical feedstock as well as fuels. Recently, the feasibility of n-hexanol synthesis using Escherichia coli has been demonstrated by extending the modified Clostridium CoA-dependent n-butanol synthesis pathway, thereby elongating carbon chain length via reactions in reversed β-oxidation, (or β-reduction). Here, we developed an anaerobic growth selection platform that allows selection or enrichment of enzymes for increased synthesis of C6 and C8 linear alcohols. Using this selection, we were able to improve the carbon flux towards the synthesis of C6 and C8 acyl-CoA intermediates. Replacement of the original enzyme Clostridium acetobutylicum Hbd with Ralstonia eutropha homologue PaaH1 increased production of n-hexanol by 10-fold. Further directed evolution by random mutagenesis of PaaH1 improved n-hexanol and n-octanol production. This anaerobic growth selection platform may be useful for selecting enzymes for production of long-chain alcohols and acids using this CoA-dependent pathway.
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Affiliation(s)
- Hidevaldo B Machado
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, 5531 Boelter Hall, Los Angeles, California 90095-1570, USA
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390
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Brigham CJ, Zhila N, Shishatskaya E, Volova TG, Sinskey AJ. Manipulation of Ralstonia eutropha carbon storage pathways to produce useful bio-based products. Subcell Biochem 2012; 64:343-366. [PMID: 23080259 DOI: 10.1007/978-94-007-5055-5_17] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Ralstonia eutrophais a Gram-negative betaproteobacterium found natively in soils that can utilize a wide array of carbon sources for growth, and can store carbon intracellularly in the form of polyhydroxyalkanoate. Many aspects of R. eutrophamake it a good candidate for use in biotechnological production of polyhydroxyalkanoate and other bio-based, value added compounds. Manipulation of the organism's carbon flux is a cornerstone to success in developing it as a biotechnologically relevant organism. Here, we examine the methods of controlling and adapting the flow of carbon in R. eutrophametabolism and the wide range of compounds that can be synthesized as a result. The presence of many different carbon utilization pathways and the custom genetic toolkit for manipulation of those pathways gives R. eutrophaa versatility that allows it to be a biotechnologically important organism.
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Affiliation(s)
- Christopher J Brigham
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
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