251
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Pal P, Nayak J. Acetic Acid Production and Purification: Critical Review Towards Process Intensification. SEPARATION AND PURIFICATION REVIEWS 2016. [DOI: 10.1080/15422119.2016.1185017] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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252
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Islam MA, Zengler K, Edwards EA, Mahadevan R, Stephanopoulos G. Investigating Moorella thermoacetica metabolism with a genome-scale constraint-based metabolic model. Integr Biol (Camb) 2016; 7:869-82. [PMID: 25994252 DOI: 10.1039/c5ib00095e] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Moorella thermoacetica is a strictly anaerobic, endospore-forming, and metabolically versatile acetogenic bacterium capable of conserving energy by both autotrophic (acetogenesis) and heterotrophic (homoacetogenesis) modes of metabolism. Its metabolic diversity and the ability to efficiently convert a wide range of compounds, including syngas (CO + H2) into acetyl-CoA have made this thermophilic bacterium a promising host for industrial biotechnology applications. However, lack of detailed information on M. thermoacetica's metabolism is a major impediment to its use as a microbial cell factory. In order to overcome this issue, a genome-scale constraint-based metabolic model of Moorella thermoacetica, iAI558, has been developed using its genome sequence and physiological data from published literature. The reconstructed metabolic network of M. thermoacetica comprises 558 metabolic genes, 705 biochemical reactions, and 698 metabolites. Of the total 705 model reactions, 680 are gene-associated while the rest are non-gene associated reactions. The model, in addition to simulating both autotrophic and heterotrophic growth of M. thermoacetica, revealed degeneracy in its TCA-cycle, a common characteristic of anaerobic metabolism. Furthermore, the model helped elucidate the poorly understood energy conservation mechanism of M. thermoacetica during autotrophy. Thus, in addition to generating experimentally testable hypotheses regarding its physiology, such a detailed model will facilitate rapid strain designing and metabolic engineering of M. thermoacetica for industrial applications.
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Affiliation(s)
- M Ahsanul Islam
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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253
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Groher A, Weuster-Botz D. Comparative reaction engineering analysis of different acetogenic bacteria for gas fermentation. J Biotechnol 2016; 228:82-94. [PMID: 27107467 DOI: 10.1016/j.jbiotec.2016.04.032] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 04/08/2016] [Accepted: 04/19/2016] [Indexed: 01/05/2023]
Abstract
The production of chemicals by syngas fermentation is a promising alternative to heterotrophic fermentation processes. The autotrophic process performances of the so far not well studied acetogens Acetobacterium fimetarium, Acetobacterium wieringae, Blautia hydrogenotrophica, Clostridium magnum, Eubacterium aggregans, Sporomusa acidovorans, Sporomusa ovata and Terrisporobacter mayombei were characterized. Acetobacterium woodii was used as reference strain. Standardized batch experiments with continuous supply of the gaseous substrates CO2 and H2 were performed in fully controlled stirred-tank bioreactors. A. wieringae and S. ovata showed by far the highest growth rates and maximum biomass concentrations among the acetogens under study. Aside from the reference strain A. woodii, highest volumetric (17.96gL(-1)d(-1)) as well as cell specific acetate formation rates (21.03gg(-1)d(-1)) were observed with S. ovata resulting in a final acetate concentration of 32.2gL(-1). Accumulation of formate with up to 4.8gL(-1) was observed with all acetogens. Ethanol was produced autotrophically with up to 0.42gL(-1) by four of the acetogenic bacteria under study (A. wieringae, C. magnum, S. acidovorans and S. ovata) and also by A. woodii. Butyrate was formed with up to 0.14gL(-1) by three of the acetogenic bacteria under study (C. magnum, B. hydrogenotrophica and E. aggregans). Due to its superior process performances S. ovata may be a promising host for redirecting carbon fluxes by applying metabolic engineering and tools of synthetic biology to produce non-natural chemicals from syngas.
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Affiliation(s)
- Anna Groher
- Institute of Biochemical Engineering, Technische Universität München, Boltzmannstr. 15, D 85748 Garching, Germany
| | - Dirk Weuster-Botz
- Institute of Biochemical Engineering, Technische Universität München, Boltzmannstr. 15, D 85748 Garching, Germany.
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254
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Marreiros BC, Calisto F, Castro PJ, Duarte AM, Sena FV, Silva AF, Sousa FM, Teixeira M, Refojo PN, Pereira MM. Exploring membrane respiratory chains. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1039-1067. [PMID: 27044012 DOI: 10.1016/j.bbabio.2016.03.028] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/16/2016] [Accepted: 03/18/2016] [Indexed: 01/20/2023]
Abstract
Acquisition of energy is central to life. In addition to the synthesis of ATP, organisms need energy for the establishment and maintenance of a transmembrane difference in electrochemical potential, in order to import and export metabolites or to their motility. The membrane potential is established by a variety of membrane bound respiratory complexes. In this work we explored the diversity of membrane respiratory chains and the presence of the different enzyme complexes in the several phyla of life. We performed taxonomic profiles of the several membrane bound respiratory proteins and complexes evaluating the presence of their respective coding genes in all species deposited in KEGG database. We evaluated 26 quinone reductases, 5 quinol:electron carriers oxidoreductases and 18 terminal electron acceptor reductases. We further included in the analyses enzymes performing redox or decarboxylation driven ion translocation, ATP synthase and transhydrogenase and we also investigated the electron carriers that perform functional connection between the membrane complexes, quinones or soluble proteins. Our results bring a novel, broad and integrated perspective of membrane bound respiratory complexes and thus of the several energetic metabolisms of living systems. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.
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Affiliation(s)
- Bruno C Marreiros
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Filipa Calisto
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Paulo J Castro
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Afonso M Duarte
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Filipa V Sena
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Andreia F Silva
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Filipe M Sousa
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Patrícia N Refojo
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal.
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255
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Wang L, Bradstock P, Li C, McInerney MJ, Krumholz LR. The role of Rnf in ion gradient formation in Desulfovibrio alaskensis. PeerJ 2016; 4:e1919. [PMID: 27114876 PMCID: PMC4841214 DOI: 10.7717/peerj.1919] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 03/19/2016] [Indexed: 02/05/2023] Open
Abstract
Rnf is a membrane protein complex that has been shown to be important in energy conservation. Here, Desulfovibrio alaskensis G20 and Rnf mutants of G20 were grown with different electron donor and acceptor combinations to determine the importance of Rnf in energy conservation and the type of ion gradient generated. The addition of the protonophore TCS strongly inhibited lactate-sulfate dependent growth whereas the sodium ionophore ETH2120 had no effect, indicating a role for the proton gradient during growth. Mutants in rnfA and rnfD were more sensitive to the protonophore at 5 µM than the parental strain, suggesting the importance of Rnf in the generation of a proton gradient. The electrical potential (ΔΨ), ΔpH and proton motive force were lower in the rnfA mutant than in the parental strain of D.alaskensis G20. These results provide evidence that the Rnf complex in D. alaskensis functions as a primary proton pump whose activity is important for growth.
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Affiliation(s)
- Luyao Wang
- Department of Microbiology and Plant Biology, University of Oklahoma , Norman, Oklahoma , USA
| | - Peter Bradstock
- Department of Microbiology and Plant Biology, University of Oklahoma , Norman, Oklahoma , USA
| | - Chuang Li
- Department of Microbiology and Plant Biology, University of Oklahoma , Norman, Oklahoma , USA
| | - Michael J McInerney
- Department of Microbiology and Plant Biology, University of Oklahoma , Norman, Oklahoma , USA
| | - Lee R Krumholz
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA; Institute for Energy and the Environment, University of Oklahoma, Norman, Oklahoma, USA
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256
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CO Metabolism in the Thermophilic Acetogen Thermoanaerobacter kivui. Appl Environ Microbiol 2016; 82:2312-2319. [PMID: 26850300 DOI: 10.1128/aem.00122-16] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 01/31/2016] [Indexed: 12/14/2022] Open
Abstract
The thermophilic acetogenic bacterium Thermoanaerobacter kivui, previously described not to use carbon monoxide as a carbon and energy source, was adapted to grow on CO. This was achieved by using a preculture grown on H2 plus CO2 and by increasing the CO concentration in small, 10% increments.T. kivui was finally able to grow within a 100% CO atmosphere. Growth on CO was found in complex and mineral media, and vitamins were not required. Carbon monoxide consumption was accompanied by acetate and hydrogen production. Cells also grew on synthesis gas (syngas) with the simultaneous use of CO and H2 coupled to acetate production. CO oxidation in resting cells was coupled to hydrogen and acetate production and accompanied by the synthesis of ATP. A protonophore abolished ATP synthesis but stimulated H2 production, which is consistent with a chemiosmotic mechanism of ATP synthesis. Hydrogenase activity was highest in crude extracts of CO-grown cells, and carbon monoxide dehydrogenase (CODH) activity was highest in H2-plus-CO2- or CO-grown cells. The genome of T. kivui harbors two CODH gene clusters, and both CODH proteins were present in crude extracts, but one CODH was more prevalent in crude extracts from CO-grown cells.
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257
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Diender M, Stams AJM, Sousa DZ. Production of medium-chain fatty acids and higher alcohols by a synthetic co-culture grown on carbon monoxide or syngas. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:82. [PMID: 27042211 PMCID: PMC4818930 DOI: 10.1186/s13068-016-0495-0] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 03/22/2016] [Indexed: 05/23/2023]
Abstract
BACKGROUND Synthesis gas, a mixture of CO, H2, and CO2, is a promising renewable feedstock for bio-based production of organic chemicals. Production of medium-chain fatty acids can be performed via chain elongation, utilizing acetate and ethanol as main substrates. Acetate and ethanol are main products of syngas fermentation by acetogens. Therefore, syngas can be indirectly used as a substrate for the chain elongation process. RESULTS Here, we report the establishment of a synthetic co-culture consisting of Clostridium autoethanogenum and Clostridium kluyveri. Together, these bacteria are capable of converting CO and syngas to a mixture of C4 and C6 fatty acids and their respective alcohols. The co-culture is able to grow using solely CO or syngas as a substrate, and presence of acetate significantly stimulated production rates. The co-culture produced butyrate and caproate at a rate of 8.5 ± 1.1 and 2.5 ± 0.63 mmol/l/day, respectively. Butanol and hexanol were produced at a rate of 3.5 ± 0.69 and 2.0 ± 0.46 mmol/l/day, respectively. The pH was found to be a major factor during cultivation, influencing the growth performance of the separate strains and caproate toxicity. CONCLUSION This co-culture poses an alternative way to produce medium-chain fatty acids and higher alcohols from carbon monoxide or syngas and the process can be regarded as an integration of syngas fermentation and chain elongation in one growth vessel.
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Affiliation(s)
- Martijn Diender
- />Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Alfons J. M. Stams
- />Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- />Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Diana Z. Sousa
- />Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
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258
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Lima DMF, Lazaro CZ, Rodrigues JAD, Ratusznei SM, Zaiat M. Optimization performance of an AnSBBR applied to biohydrogen production treating whey. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2016; 169:191-201. [PMID: 26751813 DOI: 10.1016/j.jenvman.2015.12.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 12/20/2015] [Accepted: 12/24/2015] [Indexed: 06/05/2023]
Abstract
The present study investigated the influence of the influent concentration of substrate, feeding time and temperature on the production of biohydrogen from cheese whey in an AnSBBR with liquid phase recirculation. The highest hydrogen yield (0.80 molH2.molLactose(-1)) and productivity (660 mLH2 L(-1) d(-1)) were achieved for influent concentrations of 5400 mgDQO L(-1). No significant difference was noted in the biological hydrogen production for the feeding time conditions analyzed. The lowest temperature tested (15 °C) promoted the highest hydrogen yield and productivity (1.12 molH2 molLactose(-1) and 1080 mLH2 L(-1) d(-1)), and for the highest temperature (45 °C), hydrogen production did not occur. The indicator values for the hydrogen production obtained with this configuration were higher than those obtained in other studies using traditional configurations such as UASBr and CSTR. A phylogenetic analysis showed that the majority of the analyzed clones were similar to Clostridium. In addition, clones phylogenetically similar to the Lactobacilaceae family, notably Lactobacillus rhamnosus, and clones with similar sequences to Acetobacter indonesiensis were observed in small proportion in the reactor.
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Affiliation(s)
- D M F Lima
- Escola de Engenharia de São Carlos (EESC), Universidade de São Paulo (USP), Av. Trabalhador São-Carlense 400, CEP 13.566-590, São Carlos, SP, Brazil
| | - C Z Lazaro
- Escola de Engenharia de São Carlos (EESC), Universidade de São Paulo (USP), Av. Trabalhador São-Carlense 400, CEP 13.566-590, São Carlos, SP, Brazil
| | - J A D Rodrigues
- Escola de Engenharia Mauá (EEM), Instituto Mauá de Tecnologia (IMT), Praça Mauá 1, CEP 09.580-900, São Caetano do Sul, SP, Brazil.
| | - S M Ratusznei
- Escola de Engenharia Mauá (EEM), Instituto Mauá de Tecnologia (IMT), Praça Mauá 1, CEP 09.580-900, São Caetano do Sul, SP, Brazil
| | - M Zaiat
- Escola de Engenharia de São Carlos (EESC), Universidade de São Paulo (USP), Av. Trabalhador São-Carlense 400, CEP 13.566-590, São Carlos, SP, Brazil
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259
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Glycerol acts as alternative electron sink during syngas fermentation by thermophilic anaerobe Moorella thermoacetica. J Biosci Bioeng 2016; 121:268-73. [DOI: 10.1016/j.jbiosc.2015.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 07/07/2015] [Accepted: 07/08/2015] [Indexed: 01/03/2023]
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260
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Lal S, Levin DB. Comparative Genomics of Core Metabolism Genes of Cellulolytic and Non-cellulolytic Clostridium Species. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 156:79-112. [PMID: 26907553 DOI: 10.1007/10_2015_5007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Microbial production of fuels such as ethanol, butanol, hydrogen (H2), and methane (CH4) from waste biomass has the potential to provide sustainable energy systems that can displace fossil fuel consumption. Screening for microbial diversity and genome sequencing of a wide-range of microorganisms can identify organisms with natural abilities to synthesize these alternative fuels and/or other biotechnological applications. Clostridium species are the most widely studied strict anaerobes capable of fermentative synthesis of ethanol, butanol, or hydrogen directly from waste biomass. Clostridium termitidis CT1112 is a mesophilic, cellulolytic species capable of direct cellulose fermentation to ethanol and organic acids, with concomitant synthesis of H2 and CO2. On the basis of 16S ribosomal RNA (rRNA) and chaperonin 60 (cpn60) gene sequence data, phylogenetic analyses revealed a close relationship between C. termitidis and C. cellobioparum. Comparative bioinformatic analyses of the C. termitidis genome with 18 cellulolytic and 10 non-cellulolytic Clostridium species confirmed this relationship, and further revealed that the majority of core metabolic pathway genes in C. termitidis and C. cellobioparum share more than 90% amino acid sequence identity. The gene loci and corresponding amino acid sequences of the encoded enzymes for each pathway were correlated by percentage identity, higher score (better alignment), and lowest e-value (most significant "hit"). In addition, the function of each enzyme was proposed by conserved domain analysis. In this chapter we discuss the comparative analysis of metabolic pathways involved in synthesis of various useful products by cellulolytic and non-cellulolytic biofuel and solvent producing Clostridium species. This study has generated valuable information concerning the core metabolism genes and pathways of C. termitidis CT1112, which is helpful in developing metabolic engineering strategies to enhance its natural capacity for better industrial applications.
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Affiliation(s)
- Sadhana Lal
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB, Canada, R3T 5V6
| | - David B Levin
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB, Canada, R3T 5V6.
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261
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Dürre P. Butanol formation from gaseous substrates. FEMS Microbiol Lett 2016; 363:fnw040. [PMID: 26903012 DOI: 10.1093/femsle/fnw040] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2016] [Indexed: 01/24/2023] Open
Abstract
Mostly, butanol is formed as a product by saccharolytic anaerobes, employing the so-called ABE fermentation (for acetone-butanol-ethanol). However, this alcohol can also be produced from gaseous substrates such as syn(thesis) gas (major components are carbon monoxide and hydrogen) by autotrophic acetogens. In view of economic considerations, a biotechnological process based on cheap and abundant gases such as CO and CO2 as a carbon source is preferable to more expensive sugar or starch fermentation. In addition, any conflict for use of substrates that can also serve as human nutrition is avoided. Natural formation of butanol has been found with, e.g. Clostridium carboxidivorans, while metabolic engineering for butanol production was successful using, e.g. C. ljungdahlii. Production of butanol from CO2 under photoautotrophic conditions was also possible by recombinant DNA construction of a respective cyanobacterial Synechococcus sp. PCC 7942 strain.
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Affiliation(s)
- Peter Dürre
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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262
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Lazar CS, Baker BJ, Seitz K, Hyde AS, Dick GJ, Hinrichs KU, Teske AP. Genomic evidence for distinct carbon substrate preferences and ecological niches of Bathyarchaeota in estuarine sediments. Environ Microbiol 2016; 18:1200-11. [PMID: 26626228 DOI: 10.1111/1462-2920.13142] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/19/2015] [Accepted: 11/19/2015] [Indexed: 11/28/2022]
Abstract
Investigations of the biogeochemical roles of benthic Archaea in marine sediments are hampered by the scarcity of cultured representatives. In order to determine their metabolic capacity, we reconstructed the genomic content of four widespread uncultured benthic Archaea recovered from estuary sediments at 48% to 95% completeness. Four genomic bins were found to belong to different subgroups of the former Miscellaneous Crenarcheota Group (MCG) now called Bathyarchaeota: MCG-6, MCG-1, MCG-7/17 and MCG-15. Metabolic predictions based on gene content of the different genome bins indicate that subgroup 6 has the ability to hydrolyse extracellular plant-derived carbohydrates, and that all four subgroups can degrade detrital proteins. Genes encoding enzymes involved in acetate production as well as in the reductive acetyl-CoA pathway were detected in all four genomes inferring that these Archaea are organo-heterotrophic and autotrophic acetogens. Genes involved in nitrite reduction were detected in all Bathyarchaeota subgroups and indicate a potential for dissimilatory nitrite reduction to ammonium. Comparing the genome content of the different Bathyarchaeota subgroups indicated preferences for distinct types of carbohydrate substrates and implicitly, for different niches within the sedimentary environment.
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Affiliation(s)
- Cassandre Sara Lazar
- University of North Carolina Chapel Hill, Marine Sciences, Chapel Hill, NC, USA.,Organic Geochemistry Group, MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany.,Institute of Ecology, Friedrich Schiller University Jena, Dornburger Straße 159, 07743, Jena, Germany
| | - Brett J Baker
- University of Texas Austin, Department of Marine Science, Marine Science Institute, Port Aransas, TX, 78383, USA
| | - Kiley Seitz
- University of Texas Austin, Department of Marine Science, Marine Science Institute, Port Aransas, TX, 78383, USA
| | - Andrew S Hyde
- University of North Carolina Chapel Hill, Marine Sciences, Chapel Hill, NC, USA
| | - Gregory J Dick
- University of Michigan, Earth and Environmental Sciences, Ann Arbor, MI, 48109, USA
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Andreas P Teske
- University of North Carolina Chapel Hill, Marine Sciences, Chapel Hill, NC, USA
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263
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Gaida SM, Liedtke A, Jentges AHW, Engels B, Jennewein S. Metabolic engineering of Clostridium cellulolyticum for the production of n-butanol from crystalline cellulose. Microb Cell Fact 2016. [PMID: 26758196 DOI: 10.1186/s12934-12015-10406-12932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023] Open
Abstract
BACKGROUND Sustainable alternatives for the production of fuels and chemicals are needed to reduce our dependency on fossil resources and to avoid the negative impact of their excessive use on the global climate. Lignocellulosic feedstock from agricultural residues, energy crops and municipal solid waste provides an abundant and carbon-neutral alternative, but it is recalcitrant towards microbial degradation and must therefore undergo extensive pretreatment to release the monomeric sugar units used by biofuel-producing microbes. These pretreatment steps can be reduced by using microbes such as Clostridium cellulolyticum that naturally digest lignocellulose, but this limits the range of biofuels that can be produced. We therefore developed a metabolic engineering approach in C. cellulolyticum to expand its natural product spectrum and to fine tune the engineered metabolic pathways. RESULTS Here we report the metabolic engineering of C. cellulolyticum to produce n-butanol, a next-generation biofuel and important chemical feedstock, directly from crystalline cellulose. We introduced the CoA-dependent pathway for n-butanol synthesis from C. acetobutylicum and measured the expression of functional enzymes (using targeted proteomics) and the abundance of metabolic intermediates (by LC-MS/MS) to identify potential bottlenecks in the n-butanol biosynthesis pathway. We achieved yields of 40 and 120 mg/L n-butanol from cellobiose and crystalline cellulose, respectively, after cultivating the bacteria for 6 and 20 days. CONCLUSION The analysis of enzyme activities and key intracellular metabolites provides a robust framework to determine the metabolic flux through heterologous pathways in C. cellulolyticum, allowing further improvements by fine tuning individual steps to improve the yields of n-butanol.
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Affiliation(s)
- Stefan Marcus Gaida
- Department of Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Forckenbeckstrasse 6, 52074, Aachen, Germany.
| | - Andrea Liedtke
- Department of Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Forckenbeckstrasse 6, 52074, Aachen, Germany.
| | - Andreas Heinz Wilhelm Jentges
- Department of Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Forckenbeckstrasse 6, 52074, Aachen, Germany.
| | - Benedikt Engels
- Department of Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Forckenbeckstrasse 6, 52074, Aachen, Germany.
| | - Stefan Jennewein
- Department of Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Forckenbeckstrasse 6, 52074, Aachen, Germany.
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264
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Gaida SM, Liedtke A, Jentges AHW, Engels B, Jennewein S. Metabolic engineering of Clostridium cellulolyticum for the production of n-butanol from crystalline cellulose. Microb Cell Fact 2016; 15:6. [PMID: 26758196 PMCID: PMC4711022 DOI: 10.1186/s12934-015-0406-2] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 12/19/2015] [Indexed: 01/13/2023] Open
Abstract
Background Sustainable alternatives for the production of fuels and chemicals are needed to reduce our dependency on fossil resources and to avoid the negative impact of their excessive use on the global climate. Lignocellulosic feedstock from agricultural residues, energy crops and municipal solid waste provides an abundant and carbon-neutral alternative, but it is recalcitrant towards microbial degradation and must therefore undergo extensive pretreatment to release the monomeric sugar units used by biofuel-producing microbes. These pretreatment steps can be reduced by using microbes such as Clostridium cellulolyticum that naturally digest lignocellulose, but this limits the range of biofuels that can be produced. We therefore developed a metabolic engineering approach in C. cellulolyticum to expand its natural product spectrum and to fine tune the engineered metabolic pathways. Results Here we report the metabolic engineering of C. cellulolyticum to produce n-butanol, a next-generation biofuel and important chemical feedstock, directly from crystalline cellulose. We introduced the CoA-dependent pathway for n-butanol synthesis from C. acetobutylicum and measured the expression of functional enzymes (using targeted proteomics) and the abundance of metabolic intermediates (by LC-MS/MS) to identify potential bottlenecks in the n-butanol biosynthesis pathway. We achieved yields of 40 and 120 mg/L n-butanol from cellobiose and crystalline cellulose, respectively, after cultivating the bacteria for 6 and 20 days. Conclusion The analysis of enzyme activities and key intracellular metabolites provides a robust framework to determine the metabolic flux through heterologous pathways in C. cellulolyticum, allowing further improvements by fine tuning individual steps to improve the yields of n-butanol. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0406-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stefan Marcus Gaida
- Department of Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Forckenbeckstrasse 6, 52074, Aachen, Germany.
| | - Andrea Liedtke
- Department of Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Forckenbeckstrasse 6, 52074, Aachen, Germany.
| | - Andreas Heinz Wilhelm Jentges
- Department of Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Forckenbeckstrasse 6, 52074, Aachen, Germany.
| | - Benedikt Engels
- Department of Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Forckenbeckstrasse 6, 52074, Aachen, Germany.
| | - Stefan Jennewein
- Department of Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Forckenbeckstrasse 6, 52074, Aachen, Germany.
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265
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Dash S, Ng CY, Maranas CD. Metabolic modeling of clostridia: current developments and applications. FEMS Microbiol Lett 2016; 363:fnw004. [PMID: 26755502 DOI: 10.1093/femsle/fnw004] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2016] [Indexed: 12/12/2022] Open
Abstract
Anaerobic Clostridium spp. is an important bioproduction microbial genus that can produce solvents and utilize a broad spectrum of substrates including cellulose and syngas. Genome-scale metabolic (GSM) models are increasingly being put forth for various clostridial strains to explore their respective metabolic capabilities and suitability for various bioconversions. In this study, we have selected representative GSM models for six different clostridia (Clostridium acetobutylicum, C. beijerinckii, C. butyricum, C. cellulolyticum, C. ljungdahlii and C. thermocellum) and performed a detailed model comparison contrasting their metabolic repertoire. We also discuss various applications of these GSM models to guide metabolic engineering interventions as well as assessing cellular physiology.
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Affiliation(s)
- Satyakam Dash
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802-1503, USA
| | - Chiam Yu Ng
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802-1503, USA
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802-1503, USA
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266
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Biobutanol—“A Renewable Green Alternative of Liquid Fuel” from Algae. GREEN FUELS TECHNOLOGY 2016. [DOI: 10.1007/978-3-319-30205-8_18] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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267
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268
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Kracke F, Virdis B, Bernhardt PV, Rabaey K, Krömer JO. Redox dependent metabolic shift in Clostridium autoethanogenum by extracellular electron supply. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:249. [PMID: 27882076 PMCID: PMC5112729 DOI: 10.1186/s13068-016-0663-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 11/04/2016] [Indexed: 05/22/2023]
Abstract
BACKGROUND Microbial electrosynthesis is a novel approach that aims at shifting the cellular metabolism towards electron-dense target products by extracellular electron supply. Many organisms including several acetogenic bacteria have been shown to be able to consume electrical current. However, suitable hosts for relevant industrial processes are yet to be discovered, and major knowledge gaps about the underlying fundamental processes still remain. RESULTS In this paper, we present the first report of electron uptake by the Gram-positive, ethanol-producing acetogen, Clostridium autoethanogenum. Under heterotrophic conditions, extracellular electron supply induced a significant metabolic shift away from acetate. In electrically enhanced fermentations on fructose, acetate production was cut by more than half, while production of lactate and 2,3-butanediol increased by 35-fold and threefold, respectively. The use of mediators with different redox potential revealed a direct dependency of the metabolic effect on the redox potential at which electrons are supplied. Only electrons delivered at a redox potential low enough to reduce ferredoxin caused the reported effect. CONCLUSIONS Production in acetogenic organisms is usually challenged by cellular energy limitations if the target product does not lead to a net energy gain as in the case of acetate. The presented results demonstrate a significant shift of carbon fluxes away from acetate towards the products, lactate and 2,3-butanediol, induced by small electricity input (~0.09 mol of electrons per mol of substrate). This presents a simple and attractive method to optimize acetogenic fermentations for production of chemicals and fuels using electrochemical techniques. The relationship between metabolic shift and redox potential of electron feed gives an indication of possible electron-transfer mechanisms and helps to prioritize further research efforts.
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Affiliation(s)
- Frauke Kracke
- Centre for Microbial Electrochemical Systems, The University of Queensland, Brisbane, QLD 4072 Australia
- Advanced Water Management Centre, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Bernardino Virdis
- Centre for Microbial Electrochemical Systems, The University of Queensland, Brisbane, QLD 4072 Australia
- Advanced Water Management Centre, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Paul V. Bernhardt
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072 Australia
| | - Korneel Rabaey
- Centre for Microbial Electrochemical Systems, The University of Queensland, Brisbane, QLD 4072 Australia
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Universiteit Ghent, Ghent, Belgium
| | - Jens O. Krömer
- Centre for Microbial Electrochemical Systems, The University of Queensland, Brisbane, QLD 4072 Australia
- Advanced Water Management Centre, The University of Queensland, Brisbane, QLD 4072 Australia
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269
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Humphreys CM, McLean S, Schatschneider S, Millat T, Henstra AM, Annan FJ, Breitkopf R, Pander B, Piatek P, Rowe P, Wichlacz AT, Woods C, Norman R, Blom J, Goesman A, Hodgman C, Barrett D, Thomas NR, Winzer K, Minton NP. Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium. BMC Genomics 2015; 16:1085. [PMID: 26692227 PMCID: PMC4687164 DOI: 10.1186/s12864-015-2287-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 12/10/2015] [Indexed: 11/30/2022] Open
Abstract
Background Clostridium autoethanogenum is an acetogenic bacterium capable of producing high value commodity chemicals and biofuels from the C1 gases present in synthesis gas. This common industrial waste gas can act as the sole energy and carbon source for the bacterium that converts the low value gaseous components into cellular building blocks and industrially relevant products via the action of the reductive acetyl-CoA (Wood-Ljungdahl) pathway. Current research efforts are focused on the enhancement and extension of product formation in this organism via synthetic biology approaches. However, crucial to metabolic modelling and directed pathway engineering is a reliable and comprehensively annotated genome sequence. Results We performed next generation sequencing using Illumina MiSeq technology on the DSM10061 strain of Clostridium autoethanogenum and observed 243 single nucleotide discrepancies when compared to the published finished sequence (NCBI: GCA_000484505.1), with 59.1 % present in coding regions. These variations were confirmed by Sanger sequencing and subsequent analysis suggested that the discrepancies were sequencing errors in the published genome not true single nucleotide polymorphisms. This was corroborated by the observation that over 90 % occurred within homopolymer regions of greater than 4 nucleotides in length. It was also observed that many genes containing these sequencing errors were annotated in the published closed genome as encoding proteins containing frameshift mutations (18 instances) or were annotated despite the coding frame containing stop codons, which if genuine, would severely hinder the organism’s ability to survive. Furthermore, we have completed a comprehensive manual curation to reduce errors in the annotation that occur through serial use of automated annotation pipelines in related species. As a result, different functions were assigned to gene products or previous functional annotations rejected because of missing evidence in various occasions. Conclusions We present a revised manually curated full genome sequence for Clostridium autoethanogenum DSM10061, which provides reliable information for genome-scale models that rely heavily on the accuracy of annotation, and represents an important step towards the manipulation and metabolic modelling of this industrially relevant acetogen. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2287-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christopher M Humphreys
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Samantha McLean
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | | | - Thomas Millat
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Anne M Henstra
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Florence J Annan
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Ronja Breitkopf
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Bart Pander
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Pawel Piatek
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Peter Rowe
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | | | - Craig Woods
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Rupert Norman
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, 35392, Giessen, Germany.
| | - Alexander Goesman
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, 35392, Giessen, Germany.
| | - Charlie Hodgman
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - David Barrett
- School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Neil R Thomas
- School of Chemistry, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Klaus Winzer
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Nigel P Minton
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
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270
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Wang Q, Wang CD, Li CH, Li JG, Chen Q, Li YZ. Clostridium luticellarii sp. nov., isolated from a mud cellar used for producing strong aromatic liquors. Int J Syst Evol Microbiol 2015; 65:4730-4733. [DOI: 10.1099/ijsem.0.000641] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strictly anaerobic, Gram-stain-positive bacterium, designated FW431T, was isolated from a mud cellar used for producing strong aromatic Chinese liquors. The strain was able to produce butanoic acid, an important component of the aroma style of Chinese liquors. Cells of strain FW431T were straight or slightly curved rods with a polar endospore and peritrichous flagella. The major cellular fatty acids (>10 % of the total) were C16 : 0, C18 : 1ω9c and C18 : 0. Biolog assays indicated that the strain preferably metabolizes palatinose, l-fucose, β-hydroxybutyric acid, l-rhamnose and α-ketobutyric acid among 95 carbon sources tested. FW431T was related most closely to Clostridium ljungdahlii DSM 13528T and Clostridium kluyveri DSM 555T based on 16S rRNA gene sequence similarities of 95.0 and 94.2 %, respectively. The DNA G+C content of the genomic DNA was 44.4 mol%. Based on the evidence presented here, FW431T ( = CGMCC 1.5201T = KCTC 15519T) is proposed as the type strain of a novel species, Clostridium luticellarii sp. nov.
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Affiliation(s)
- Qian Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Chuan-dong Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Cheng-hou Li
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Jun-gang Li
- School of Life Science and Biotechnology, Mianyang Normal University, Mianyang 621000, PR China
| | - Qi Chen
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Yue-zhong Li
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
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271
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Dürre P, Eikmanns BJ. C1-carbon sources for chemical and fuel production by microbial gas fermentation. Curr Opin Biotechnol 2015; 35:63-72. [DOI: 10.1016/j.copbio.2015.03.008] [Citation(s) in RCA: 164] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 03/06/2015] [Accepted: 03/12/2015] [Indexed: 12/25/2022]
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272
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Shen Y, Jarboe L, Brown R, Wen Z. A thermochemical–biochemical hybrid processing of lignocellulosic biomass for producing fuels and chemicals. Biotechnol Adv 2015; 33:1799-813. [DOI: 10.1016/j.biotechadv.2015.10.006] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 10/16/2015] [Accepted: 10/16/2015] [Indexed: 12/28/2022]
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273
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Affiliation(s)
- Yu-Sin Jang
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, KAIST, Daejeon, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, KAIST, Daejeon, Republic of Korea
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274
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Jabeen G, Farooq R. Microbial Fuel Cells and Their Applications for Cost Effective Water Pollution Remediation. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/s40011-015-0683-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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275
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Diender M, Stams AJM, Sousa DZ. Pathways and Bioenergetics of Anaerobic Carbon Monoxide Fermentation. Front Microbiol 2015; 6:1275. [PMID: 26635746 PMCID: PMC4652020 DOI: 10.3389/fmicb.2015.01275] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 10/31/2015] [Indexed: 11/29/2022] Open
Abstract
Carbon monoxide can act as a substrate for different modes of fermentative anaerobic metabolism. The trait of utilizing CO is spread among a diverse group of microorganisms, including members of bacteria as well as archaea. Over the last decade this metabolism has gained interest due to the potential of converting CO-rich gas, such as synthesis gas, into bio-based products. Three main types of fermentative CO metabolism can be distinguished: hydrogenogenesis, methanogenesis, and acetogenesis, generating hydrogen, methane and acetate, respectively. Here, we review the current knowledge on these three variants of microbial CO metabolism with an emphasis on the potential enzymatic routes and bio-energetics involved.
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Affiliation(s)
- Martijn Diender
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands ; Centre of Biological Engineering, University of Minho Braga, Portugal
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands
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276
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Adaptation of the autotrophic acetogen Sporomusa ovata to methanol accelerates the conversion of CO2 to organic products. Sci Rep 2015; 5:16168. [PMID: 26530351 PMCID: PMC4632017 DOI: 10.1038/srep16168] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 10/08/2015] [Indexed: 12/21/2022] Open
Abstract
Acetogens are efficient microbial catalysts for bioprocesses converting C1 compounds into organic products. Here, an adaptive laboratory evolution approach was implemented to adapt Sporomusa ovata for faster autotrophic metabolism and CO2 conversion to organic chemicals. S. ovata was first adapted to grow quicker autotrophically with methanol, a toxic C1 compound, as the sole substrate. Better growth on different concentrations of methanol and with H2-CO2 indicated the adapted strain had a more efficient autotrophic metabolism and a higher tolerance to solvent. The growth rate on methanol was increased 5-fold. Furthermore, acetate production rate from CO2 with an electrode serving as the electron donor was increased 6.5-fold confirming that the acceleration of the autotrophic metabolism of the adapted strain is independent of the electron donor provided. Whole-genome sequencing, transcriptomic, and biochemical studies revealed that the molecular mechanisms responsible for the novel characteristics of the adapted strain were associated with the methanol oxidation pathway and the Wood-Ljungdahl pathway of acetogens along with biosynthetic pathways, cell wall components, and protein chaperones. The results demonstrate that an efficient strategy to increase rates of CO2 conversion in bioprocesses like microbial electrosynthesis is to evolve the microbial catalyst by adaptive laboratory evolution to optimize its autotrophic metabolism.
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277
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Current status and prospects of industrial bio-production of n-butanol in China. Biotechnol Adv 2015; 33:1493-501. [DOI: 10.1016/j.biotechadv.2014.10.007] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 10/17/2014] [Accepted: 10/19/2014] [Indexed: 01/04/2023]
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278
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Geelhoed JS, Henstra AM, Stams AJM. Carboxydotrophic growth of Geobacter sulfurreducens. Appl Microbiol Biotechnol 2015; 100:997-1007. [PMID: 26481622 PMCID: PMC4703632 DOI: 10.1007/s00253-015-7033-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 09/14/2015] [Accepted: 09/21/2015] [Indexed: 12/16/2022]
Abstract
This study shows that Geobacter sulfurreducens grows on carbon monoxide (CO) as electron donor with fumarate as electron acceptor. Geobacter sulfurreducens was tolerant to high CO levels, with up to 150 kPa in the headspace tested. During growth, hydrogen was detected in very slight amounts (∼5 Pa). In assays with cell-free extract of cells grown with CO and fumarate, production of hydrogen from CO was not observed, and hydrogenase activity with benzyl viologen as electron acceptor was very low. Taken together, this suggested that CO is not utilized via hydrogen as intermediate. In the presence of CO, reduction of NADP+ was observed at a rate comparable to CO oxidation coupled to fumarate reduction in vivo. The G. sulfurreducens genome contains a single putative carbon monoxide dehydrogenase-encoding gene. The gene is part of a predicted operon also comprising a putative Fe–S cluster-binding subunit (CooF) and a FAD–NAD(P) oxidoreductase and is preceded by a putative CO-sensing transcription factor. This cluster may be involved in a novel pathway for CO oxidation, but further studies are necessary to ascertain this. Similar gene clusters are present in several other species belonging to the Deltaproteobacteria and Firmicutes, for which CO utilization is currently not known.
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Affiliation(s)
- Jeanine S Geelhoed
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands.
- NIOZ Royal Netherlands Institute for Sea Research, Korringaweg 7, 4401 NT, Yerseke, The Netherlands.
| | - Anne M Henstra
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
- Centre for Biomolecular Sciences, University of Nottingham, University Park, NG7 2EF, Nottingham, UK
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
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279
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Metabolic response of Clostridium ljungdahlii to oxygen exposure. Appl Environ Microbiol 2015; 81:8379-91. [PMID: 26431975 DOI: 10.1128/aem.02491-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 09/23/2015] [Indexed: 12/31/2022] Open
Abstract
Clostridium ljungdahlii is an important synthesis gas-fermenting bacterium used in the biofuels industry, and a preliminary investigation showed that it has some tolerance to oxygen when cultured in rich mixotrophic medium. Batch cultures not only continue to grow and consume H2, CO, and fructose after 8% O2 exposure, but fermentation product analysis revealed an increase in ethanol concentration and decreased acetate concentration compared to non-oxygen-exposed cultures. In this study, the mechanisms for higher ethanol production and oxygen/reactive oxygen species (ROS) detoxification were identified using a combination of fermentation, transcriptome sequencing (RNA-seq) differential expression, and enzyme activity analyses. The results indicate that the higher ethanol and lower acetate concentrations were due to the carboxylic acid reductase activity of a more highly expressed predicted aldehyde oxidoreductase (CLJU_c24130) and that C. ljungdahlii's primary defense upon oxygen exposure is a predicted rubrerythrin (CLJU_c39340). The metabolic responses of higher ethanol production and oxygen/ROS detoxification were found to be linked by cofactor management and substrate and energy metabolism. This study contributes new insights into the physiology and metabolism of C. ljungdahlii and provides new genetic targets to generate C. ljungdahlii strains that produce more ethanol and are more tolerant to syngas contaminants.
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280
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Zhou J, Zhou X, Li Y, Xing J. Bacterial communities in haloalkaliphilic sulfate-reducing bioreactors under different electron donors revealed by 16S rRNA MiSeq sequencing. JOURNAL OF HAZARDOUS MATERIALS 2015; 295:176-184. [PMID: 25897699 DOI: 10.1016/j.jhazmat.2015.04.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 03/17/2015] [Accepted: 04/04/2015] [Indexed: 06/04/2023]
Abstract
Biological technology used to treat flue gas is useful to replace conventional treatment, but there is sulfide inhibition. However, no sulfide toxicity effect was observed in haloalkaliphilic bioreactors. The performance of the ethanol-fed bioreactor was better than that of lactate-, glucose-, and formate-fed bioreactor, respectively. To support this result strongly, Illumina MiSeq paired-end sequencing of 16S rRNA gene was applied to investigate the bacterial communities. A total of 389,971 effective sequences were obtained and all of them were assigned to 10,220 operational taxonomic units (OTUs) at a 97% similarity. Bacterial communities in the glucose-fed bioreactor showed the greatest richness and evenness. The highest relative abundance of sulfate-reducing bacteria (SRB) was found in the ethanol-fed bioreactor, which can explain why the performance of the ethanol-fed bioreactor was the best. Different types of SRB, sulfur-oxidizing bacteria, and sulfur-reducing bacteria were detected, indicating that sulfur may be cycled among these microorganisms. Because high-throughput 16S rRNA gene paired-end sequencing has improved resolution of bacterial community analysis, many rare microorganisms were detected, such as Halanaerobium, Halothiobacillus, Desulfonatronum, Syntrophobacter, and Fusibacter. 16S rRNA gene sequencing of these bacteria would provide more functional and phylogenetic information about the bacterial communities.
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Affiliation(s)
- Jiemin Zhou
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, P.O. Box 353, Beijing 100190, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xuemei Zhou
- 101 Institute, Ministry of Civil Affairs, Beijing 100070, PR China
| | - Yuguang Li
- 101 Institute, Ministry of Civil Affairs, Beijing 100070, PR China
| | - Jianmin Xing
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, P.O. Box 353, Beijing 100190, PR China.
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281
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Martin ME, Richter H, Saha S, Angenent LT. Traits of selectedClostridiumstrains for syngas fermentation to ethanol. Biotechnol Bioeng 2015; 113:531-9. [DOI: 10.1002/bit.25827] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 08/05/2015] [Accepted: 08/23/2015] [Indexed: 12/24/2022]
Affiliation(s)
- Michael E. Martin
- Department of Biological and Environmental Engineering; Cornell University; Ithaca New York 14853
| | - Hanno Richter
- Department of Biological and Environmental Engineering; Cornell University; Ithaca New York 14853
| | - Surya Saha
- Boyce Thompson Institute for Plant Research; 533 Tower Road; Ithaca New York 14853
| | - Largus T. Angenent
- Department of Biological and Environmental Engineering; Cornell University; Ithaca New York 14853
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282
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The Complete Genome Sequence of Clostridium aceticum: a Missing Link between Rnf- and Cytochrome-Containing Autotrophic Acetogens. mBio 2015; 6:e01168-15. [PMID: 26350967 PMCID: PMC4600107 DOI: 10.1128/mbio.01168-15] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clostridium aceticum was the first isolated autotrophic acetogen, converting CO2 plus H2 or syngas to acetate. Its genome has now been completely sequenced and consists of a 4.2-Mbp chromosome and a small circular plasmid of 5.7 kbp. Sequence analysis revealed major differences from other autotrophic acetogens. C. aceticum contains an Rnf complex for energy conservation (via pumping protons or sodium ions). Such systems have also been found in C. ljungdahlii and Acetobacterium woodii. However, C. aceticum also contains a cytochrome, as does Moorella thermoacetica, which has been proposed to be involved in the generation of a proton gradient. Thus, C. aceticum seems to represent a link between Rnf- and cytochrome-containing autotrophic acetogens. In C. aceticum, however, the cytochrome is probably not involved in an electron transport chain that leads to proton translocation, as no genes for quinone biosynthesis are present in the genome. Autotrophic acetogenic bacteria are receiving more and more industrial focus, as CO2 plus H2 as well as syngas are interesting new substrates for biotechnological processes. They are both cheap and abundant, and their use, if it results in sustainable products, also leads to reduction of greenhouse gases. Clostridium aceticum can use both gas mixtures, is phylogenetically not closely related to the commonly used species, and may thus become an even more attractive workhorse. In addition, its energy metabolism, which is characterized here, and the ability to synthesize cytochromes might offer new targets for improving the ATP yield by metabolic engineering and thus allow use of C. aceticum for production of compounds by pathways that currently present challenges for energy-limited acetogens.
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283
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Cueto-Rojas HF, van Maris A, Wahl SA, Heijnen J. Thermodynamics-based design of microbial cell factories for anaerobic product formation. Trends Biotechnol 2015; 33:534-46. [DOI: 10.1016/j.tibtech.2015.06.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 05/20/2015] [Accepted: 06/23/2015] [Indexed: 11/29/2022]
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284
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Mock J, Zheng Y, Mueller AP, Ly S, Tran L, Segovia S, Nagaraju S, Köpke M, Dürre P, Thauer RK. Energy Conservation Associated with Ethanol Formation from H2 and CO2 in Clostridium autoethanogenum Involving Electron Bifurcation. J Bacteriol 2015; 197:2965-80. [PMID: 26148714 PMCID: PMC4542177 DOI: 10.1128/jb.00399-15] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 06/29/2015] [Indexed: 02/01/2023] Open
Abstract
UNLABELLED Most acetogens can reduce CO2 with H2 to acetic acid via the Wood-Ljungdahl pathway, in which the ATP required for formate activation is regenerated in the acetate kinase reaction. However, a few acetogens, such as Clostridium autoethanogenum, Clostridium ljungdahlii, and Clostridium ragsdalei, also form large amounts of ethanol from CO2 and H2. How these anaerobes with a growth pH optimum near 5 conserve energy has remained elusive. We investigated this question by determining the specific activities and cofactor specificities of all relevant oxidoreductases in cell extracts of H2/CO2-grown C. autoethanogenum. The activity studies were backed up by transcriptional and mutational analyses. Most notably, despite the presence of six hydrogenase systems of various types encoded in the genome, the cells appear to contain only one active hydrogenase. The active [FeFe]-hydrogenase is electron bifurcating, with ferredoxin and NADP as the two electron acceptors. Consistently, most of the other active oxidoreductases rely on either reduced ferredoxin and/or NADPH as the electron donor. An exception is ethanol dehydrogenase, which was found to be NAD specific. Methylenetetrahydrofolate reductase activity could only be demonstrated with artificial electron donors. Key to the understanding of this energy metabolism is the presence of membrane-associated reduced ferredoxin:NAD(+) oxidoreductase (Rnf), of electron-bifurcating and ferredoxin-dependent transhydrogenase (Nfn), and of acetaldehyde:ferredoxin oxidoreductase, which is present with very high specific activities in H2/CO2-grown cells. Based on these findings and on thermodynamic considerations, we propose metabolic schemes that allow, depending on the H2 partial pressure, the chemiosmotic synthesis of 0.14 to 1.5 mol ATP per mol ethanol synthesized from CO2 and H2. IMPORTANCE Ethanol formation from syngas (H2, CO, and CO2) and from H2 and CO2 that is catalyzed by bacteria is presently a much-discussed process for sustainable production of biofuels. Although the process is already in use, its biochemistry is only incompletely understood. The most pertinent question is how the bacteria conserve energy for growth during ethanol formation from H2 and CO2, considering that acetyl coenzyme A (acetyl-CoA), is an intermediate. Can reduction of the activated acetic acid to ethanol with H2 be coupled with the phosphorylation of ADP? Evidence is presented that this is indeed possible, via both substrate-level phosphorylation and electron transport phosphorylation. In the case of substrate-level phosphorylation, acetyl-CoA reduction to ethanol proceeds via free acetic acid involving acetaldehyde:ferredoxin oxidoreductase (carboxylate reductase).
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Affiliation(s)
- Johanna Mock
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Yanning Zheng
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | | | - San Ly
- LanzaTech Inc., Skokie, Illinois, USA
| | - Loan Tran
- LanzaTech Inc., Skokie, Illinois, USA
| | | | | | | | - Peter Dürre
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Rudolf K Thauer
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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285
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Ramió-Pujol S, Ganigué R, Bañeras L, Colprim J. Incubation at 25 °C prevents acid crash and enhances alcohol production in Clostridium carboxidivorans P7. BIORESOURCE TECHNOLOGY 2015; 192:296-303. [PMID: 26046429 DOI: 10.1016/j.biortech.2015.05.077] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 05/20/2015] [Accepted: 05/21/2015] [Indexed: 05/06/2023]
Abstract
Incubation of carboxydotrophs at 37 °C provides optimal conditions for their growth. However, a fast accumulation of organic acids, specifically acetate, during the exponential growth phase may result in low alcohol production and substrate consumption due to a phenomenon known as "acid crash". The present work investigates growth and productivity of Clostridium carboxidivorans P7 at two incubation temperatures. At 37 °C the culture was not able to override the "acid crash", resulting in low ethanol titers (1.56 mM). On the other hand, lower metabolic rates at 25 °C enhanced ethanol and butanol production (32.1 and 14.5 mM, respectively). Moreover, at low temperatures, hexanol and caproic acid were also produced at significant concentrations, 8.21 and 9.02 mM respectively, among the highest values reported for P7. Our results demonstrate that production of biofuels with longer carbon chains molecules may be enhanced incubating syngas-fermenting acetogenic bacteria at sub-optimal temperatures.
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Affiliation(s)
- Sara Ramió-Pujol
- LEQUIA, Institute of the Environment, University of Girona, Campus Montilivi, E-17071 Girona, Catalonia, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology (IEA), University of Girona, Campus Montilivi, E-17071 Girona, Catalonia, Spain
| | - Ramon Ganigué
- LEQUIA, Institute of the Environment, University of Girona, Campus Montilivi, E-17071 Girona, Catalonia, Spain.
| | - Lluís Bañeras
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology (IEA), University of Girona, Campus Montilivi, E-17071 Girona, Catalonia, Spain
| | - Jesús Colprim
- LEQUIA, Institute of the Environment, University of Girona, Campus Montilivi, E-17071 Girona, Catalonia, Spain
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286
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Abstract
Formation of heat-resistant endospores is a specific property of the members of the phylum Firmicutes (low-G+C Gram-positive bacteria). It is found in representatives of four different classes of Firmicutes, Bacilli, Clostridia, Erysipelotrichia, and Negativicutes, which all encode similar sets of core sporulation proteins. Each of these classes also includes non-spore-forming organisms that sometimes belong to the same genus or even species as their spore-forming relatives. This chapter reviews the diversity of the members of phylum Firmicutes, its current taxonomy, and the status of genome-sequencing projects for various subgroups within the phylum. It also discusses the evolution of the Firmicutes from their apparently spore-forming common ancestor and the independent loss of sporulation genes in several different lineages (staphylococci, streptococci, listeria, lactobacilli, ruminococci) in the course of their adaptation to the saprophytic lifestyle in a nutrient-rich environment. It argues that the systematics of Firmicutes is a rapidly developing area of research that benefits from the evolutionary approaches to the ever-increasing amount of genomic and phenotypic data and allows arranging these data into a common framework.
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287
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Complete Genome Sequence of Rnf- and Cytochrome-Containing Autotrophic Acetogen Clostridium aceticum DSM 1496. GENOME ANNOUNCEMENTS 2015; 3:3/4/e00786-15. [PMID: 26184942 PMCID: PMC4505130 DOI: 10.1128/genomea.00786-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Here, we report the closed genome sequence of Clostridium aceticum, an Rnf- and cytochrome-containing autotrophic acetogen that is able to convert CO2 and H2 to acetate using the Wood-Ljungdahl pathway. The genome consists of a circular chromosome (4.2 Mbp) and a small circular plasmid (5.7 kbp).
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288
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Ramió-Pujol S, Ganigué R, Bañeras L, Colprim J. How can alcohol production be improved in carboxydotrophic clostridia? Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.03.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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289
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CO Metabolism in the Acetogen Acetobacterium woodii. Appl Environ Microbiol 2015; 81:5949-56. [PMID: 26092462 DOI: 10.1128/aem.01772-15] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 06/17/2015] [Indexed: 01/07/2023] Open
Abstract
The Wood-Ljungdahl pathway allows acetogenic bacteria to grow on a number of one-carbon substrates, such as carbon dioxide, formate, methyl groups, or even carbon monoxide. Since carbon monoxide alone or in combination with hydrogen and carbon dioxide (synthesis gas) is an increasingly important feedstock for third-generation biotechnology, we studied CO metabolism in the model acetogen Acetobacterium woodii. When cells grew on H2-CO2, addition of 5 to 15% CO led to higher final optical densities, indicating the utilization of CO as a cosubstrate. However, the growth rate was decreased by the presence of small amounts of CO, which correlated with an inhibition of H2 consumption. Experiments with resting cells revealed that the degree of inhibition of H2 consumption was a function of the CO concentration. Since the hydrogen-dependent CO2 reductase (HDCR) of A. woodii is known to be very sensitive to CO, we speculated that cells may be more tolerant toward CO when growing on formate, the product of the HDCR reaction. Indeed, addition of up to 25% CO did not influence growth rates on formate, while the final optical densities and the production of acetate increased. Higher concentrations (75 and 100%) led to a slight inhibition of growth and to decreasing rates of formate and CO consumption. Experiments with resting cells revealed that the HDCR is a site of CO inhibition. In contrast, A. woodii was not able to grow on CO as a sole carbon and energy source, and growth on fructose-CO or methanol-CO was not observed.
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290
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Kracke F, Vassilev I, Krömer JO. Microbial electron transport and energy conservation - the foundation for optimizing bioelectrochemical systems. Front Microbiol 2015; 6:575. [PMID: 26124754 PMCID: PMC4463002 DOI: 10.3389/fmicb.2015.00575] [Citation(s) in RCA: 307] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 05/25/2015] [Indexed: 12/23/2022] Open
Abstract
Microbial electrochemical techniques describe a variety of emerging technologies that use electrode–bacteria interactions for biotechnology applications including the production of electricity, waste and wastewater treatment, bioremediation and the production of valuable products. Central in each application is the ability of the microbial catalyst to interact with external electron acceptors and/or donors and its metabolic properties that enable the combination of electron transport and carbon metabolism. And here also lies the key challenge. A wide range of microbes has been discovered to be able to exchange electrons with solid surfaces or mediators but only a few have been studied in depth. Especially electron transfer mechanisms from cathodes towards the microbial organism are poorly understood but are essential for many applications such as microbial electrosynthesis. We analyze the different electron transport chains that nature offers for organisms such as metal respiring bacteria and acetogens, but also standard biotechnological organisms currently used in bio-production. Special focus lies on the essential connection of redox and energy metabolism, which is often ignored when studying bioelectrochemical systems. The possibility of extracellular electron exchange at different points in each organism is discussed regarding required redox potentials and effect on cellular redox and energy levels. Key compounds such as electron carriers (e.g., cytochromes, ferredoxin, quinones, flavins) are identified and analyzed regarding their possible role in electrode–microbe interactions. This work summarizes our current knowledge on electron transport processes and uses a theoretical approach to predict the impact of different modes of transfer on the energy metabolism. As such it adds an important piece of fundamental understanding of microbial electron transport possibilities to the research community and will help to optimize and advance bioelectrochemical techniques.
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Affiliation(s)
- Frauke Kracke
- Centre for Microbial Electrochemical Systems, The University of Queensland, Brisbane QLD, Australia ; Advanced Water Management Centre, The University of Queensland, Brisbane QLD, Australia
| | - Igor Vassilev
- Centre for Microbial Electrochemical Systems, The University of Queensland, Brisbane QLD, Australia ; Advanced Water Management Centre, The University of Queensland, Brisbane QLD, Australia
| | - Jens O Krömer
- Centre for Microbial Electrochemical Systems, The University of Queensland, Brisbane QLD, Australia ; Advanced Water Management Centre, The University of Queensland, Brisbane QLD, Australia
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291
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Lima DMF, Inoue RK, Rodrigues JAD, Ratusznei SM, Zaiat M. BIOHYDROGEN FROM CHEESE WHEY TREATMENT IN AN AnSBBR: ACHIEVING PROCESS STABILITY. BRAZILIAN JOURNAL OF CHEMICAL ENGINEERING 2015. [DOI: 10.1590/0104-6632.20150322s00003342] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
| | | | | | | | - M. Zaiat
- Universidade de São Paulo, Brasil
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292
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Maddock DJ, Patrick WM, Gerth ML. Substitutions at the cofactor phosphate-binding site of a clostridial alcohol dehydrogenase lead to unexpected changes in substrate specificity. Protein Eng Des Sel 2015; 28:251-8. [PMID: 26034298 PMCID: PMC4498498 DOI: 10.1093/protein/gzv028] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 05/05/2015] [Indexed: 12/22/2022] Open
Abstract
Changing the cofactor specificity of an enzyme from nicotinamide adenine dinucleotide 2′-phosphate (NADPH) to the more abundant NADH is a common strategy for increasing overall enzyme efficiency in microbial metabolic engineering. The aim of this study was to switch the cofactor specificity of the primary–secondary alcohol dehydrogenase from Clostridium autoethanogenum, a bacterium with considerable promise for the bio-manufacturing of fuels and other petrochemicals, from strictly NADPH-dependent to NADH-dependent. We used insights from a homology model to build a site-saturation library focussed on residue S199, the position deemed most likely to disrupt binding of the 2′-phosphate of NADPH. Although the CaADH(S199X) library did not yield any NADH-dependent enzymes, it did reveal that substitutions at the cofactor phosphate-binding site can cause unanticipated changes in the substrate specificity of the enzyme. Using consensus-guided site-directed mutagenesis, we were able to create an enzyme that was stringently NADH-dependent, albeit with a concomitant reduction in activity. This study highlights the role that distal residues play in substrate specificity and the complexity of enzyme–cofactor interactions.
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Affiliation(s)
- Danielle J Maddock
- Department of Biochemistry, University of Otago, Dunedin 9010, New Zealand
| | - Wayne M Patrick
- Department of Biochemistry, University of Otago, Dunedin 9010, New Zealand
| | - Monica L Gerth
- Department of Biochemistry, University of Otago, Dunedin 9010, New Zealand
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293
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Energy Conservation Model Based on Genomic and Experimental Analyses of a Carbon Monoxide-Utilizing, Butyrate-Forming Acetogen, Eubacterium limosum KIST612. Appl Environ Microbiol 2015; 81:4782-90. [PMID: 25956767 DOI: 10.1128/aem.00675-15] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 05/01/2015] [Indexed: 12/19/2022] Open
Abstract
Eubacterium limosum KIST612 is one of the few acetogens that can produce butyrate from carbon monoxide. We have used a genome-guided analysis to delineate the path of butyrate formation, the enzymes involved, and the potential coupling to ATP synthesis. Oxidation of CO is catalyzed by the acetyl-coenzyme A (CoA) synthase/CO dehydrogenase and coupled to the reduction of ferredoxin. Oxidation of reduced ferredoxin is catalyzed by the Rnf complex and Na(+) dependent. Consistent with the finding of a Na(+)-dependent Rnf complex is the presence of a conserved Na(+)-binding motif in the c subunit of the ATP synthase. Butyrate formation is from acetyl-CoA via acetoacetyl-CoA, hydroxybutyryl-CoA, crotonyl-CoA, and butyryl-CoA and is consistent with the finding of a gene cluster that encodes the enzymes for this pathway. The activity of the butyryl-CoA dehydrogenase was demonstrated. Reduction of crotonyl-CoA to butyryl-CoA with NADH as the reductant was coupled to reduction of ferredoxin. We postulate that the butyryl-CoA dehydrogenase uses flavin-based electron bifurcation to reduce ferredoxin, which is consistent with the finding of etfA and etfB genes next to it. The overall ATP yield was calculated and is significantly higher than the one obtained with H2 + CO2. The energetic benefit may be one reason that butyrate is formed only from CO but not from H2 + CO2.
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294
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Nybo SE, Khan NE, Woolston BM, Curtis WR. Metabolic engineering in chemolithoautotrophic hosts for the production of fuels and chemicals. Metab Eng 2015; 30:105-120. [PMID: 25959019 DOI: 10.1016/j.ymben.2015.04.008] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 04/06/2015] [Accepted: 04/29/2015] [Indexed: 12/19/2022]
Abstract
The ability of autotrophic organisms to fix CO2 presents an opportunity to utilize this 'greenhouse gas' as an inexpensive substrate for biochemical production. Unlike conventional heterotrophic microorganisms that consume carbohydrates and amino acids, prokaryotic chemolithoautotrophs have evolved the capacity to utilize reduced chemical compounds to fix CO2 and drive metabolic processes. The use of chemolithoautotrophic hosts as production platforms has been renewed by the prospect of metabolically engineered commodity chemicals and fuels. Efforts such as the ARPA-E electrofuels program highlight both the potential and obstacles that chemolithoautotrophic biosynthetic platforms provide. This review surveys the numerous advances that have been made in chemolithoautotrophic metabolic engineering with a focus on hydrogen oxidizing bacteria such as the model chemolithoautotrophic organism (Ralstonia), the purple photosynthetic bacteria (Rhodobacter), and anaerobic acetogens. Two alternative strategies of microbial chassis development are considered: (1) introducing or enhancing autotrophic capabilities (carbon fixation, hydrogen utilization) in model heterotrophic organisms, or (2) improving tools for pathway engineering (transformation methods, promoters, vectors etc.) in native autotrophic organisms. Unique characteristics of autotrophic growth as they relate to bioreactor design and process development are also discussed in the context of challenges and opportunities for genetic manipulation of organisms as production platforms.
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Affiliation(s)
- S Eric Nybo
- Department of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, MI, United States
| | - Nymul E Khan
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, United States
| | - Benjamin M Woolston
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Wayne R Curtis
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, United States.
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295
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Gutiérrez-Preciado A, Torres AG, Merino E, Bonomi HR, Goldbaum FA, García-Angulo VA. Extensive Identification of Bacterial Riboflavin Transporters and Their Distribution across Bacterial Species. PLoS One 2015; 10:e0126124. [PMID: 25938806 PMCID: PMC4418817 DOI: 10.1371/journal.pone.0126124] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 03/29/2015] [Indexed: 11/18/2022] Open
Abstract
Riboflavin, the precursor for the cofactors flavin mononucleotide (FMN) and flavin adenine dinucleotide, is an essential metabolite in all organisms. While the functions for de novo riboflavin biosynthesis and riboflavin import may coexist in bacteria, the extent of this co-occurrence is undetermined. The RibM, RibN, RfuABCD and the energy-coupling factor-RibU bacterial riboflavin transporters have been experimentally characterized. In addition, ImpX, RfnT and RibXY are proposed as riboflavin transporters based on positional clustering with riboflavin biosynthetic pathway (RBP) genes or conservation of the FMN riboswitch regulatory element. Here, we searched for the FMN riboswitch in bacterial genomes to identify genes encoding riboflavin transporters and assessed their distribution among bacteria. Two new putative riboflavin transporters were identified: RibZ in Clostridium and RibV in Mesoplasma florum. Trans-complementation of an Escherichia coli riboflavin auxotroph strain confirmed the riboflavin transport activity of RibZ from Clostridium difficile, RibXY from Chloroflexus aurantiacus, ImpX from Fusobacterium nucleatum and RfnT from Ochrobactrum anthropi. The analysis of the genomic distribution of all known bacterial riboflavin transporters revealed that most occur in species possessing the RBP and that some bacteria may even encode functional riboflavin transporters from two different families. Our results indicate that some species possess ancestral riboflavin transporters, while others possess transporters that appear to have evolved recently. Moreover, our data suggest that unidentified riboflavin transporters also exist. The present study doubles the number of experimentally characterized riboflavin transporters and suggests a specific, non-accessory role for these proteins in riboflavin-prototrophic bacteria.
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Affiliation(s)
- Ana Gutiérrez-Preciado
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Alfredo Gabriel Torres
- Department of Microbiology and Immunology, Sealy Center for Vaccine Development, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Pathology, Sealy Center for Vaccine Development, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Enrique Merino
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | | | | | - Víctor Antonio García-Angulo
- Department of Microbiology and Immunology, Sealy Center for Vaccine Development, University of Texas Medical Branch, Galveston, Texas, United States of America
- Centro de Genómica y Bioinformática, Universidad Mayor, Campus Huechuraba, Santiago, Chile
- * E-mail:
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296
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Draft Genome Sequence of Clostridium sp. Ne2, Clostridia from an Enrichment Culture Obtained from Australian Subterranean Termite, Nasutitermes exitiosus. GENOME ANNOUNCEMENTS 2015; 3:3/2/e00304-15. [PMID: 25908129 PMCID: PMC4408330 DOI: 10.1128/genomea.00304-15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The draft genome sequence of Clostridium sp. Ne2 was reconstructed from a metagenome of a hydrogenogenic microbial consortium. The organism is most closely related to Clostridium magnum and is a strict anaerobe that is predicted to ferment a range of simple sugars.
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297
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Utturkar SM, Klingeman DM, Bruno-Barcena JM, Chinn MS, Grunden AM, Köpke M, Brown SD. Sequence data for Clostridium autoethanogenum using three generations of sequencing technologies. Sci Data 2015; 2:150014. [PMID: 25977818 PMCID: PMC4409012 DOI: 10.1038/sdata.2015.14] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 03/12/2015] [Indexed: 01/07/2023] Open
Abstract
During the past decade, DNA sequencing output has been mostly dominated by the second generation sequencing platforms which are characterized by low cost, high throughput and shorter read lengths for example, Illumina. The emergence and development of so called third generation sequencing platforms such as PacBio has permitted exceptionally long reads (over 20 kb) to be generated. Due to read length increases, algorithm improvements and hybrid assembly approaches, the concept of one chromosome, one contig and automated finishing of microbial genomes is now a realistic and achievable task for many microbial laboratories. In this paper, we describe high quality sequence datasets which span three generations of sequencing technologies, containing six types of data from four NGS platforms and originating from a single microorganism, Clostridium autoethanogenum. The dataset reported here will be useful for the scientific community to evaluate upcoming NGS platforms, enabling comparison of existing and novel bioinformatics approaches and will encourage interest in the development of innovative experimental and computational methods for NGS data.
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Affiliation(s)
- Sagar M Utturkar
- Graduate School of Genome Science and Technology, University of Tennessee , Knoxville, Tennessee 37919, USA
| | - Dawn M Klingeman
- Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, USA
| | - José M Bruno-Barcena
- Department of Plant and Microbial Biology, North Carolina State University , Raleigh, North Carolina 27695, USA
| | - Mari S Chinn
- Department of Biological and Agricultural Engineering, North Carolina State University , Raleigh, North Carolina 27695, USA
| | - Amy M Grunden
- Department of Plant and Microbial Biology, North Carolina State University , Raleigh, North Carolina 27695, USA
| | | | - Steven D Brown
- Graduate School of Genome Science and Technology, University of Tennessee , Knoxville, Tennessee 37919, USA ; Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, USA
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298
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Zhou J, Xing J. Effect of electron donors on the performance of haloalkaliphilic sulfate-reducing bioreactors for flue gas treatment and microbial degradation patterns related to sulfate reduction of different electron donors. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2014.12.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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299
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Tremblay PL, Zhang T. Electrifying microbes for the production of chemicals. Front Microbiol 2015; 6:201. [PMID: 25814988 PMCID: PMC4356085 DOI: 10.3389/fmicb.2015.00201] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 02/24/2015] [Indexed: 01/06/2023] Open
Abstract
Powering microbes with electrical energy to produce valuable chemicals such as biofuels has recently gained traction as a biosustainable strategy to reduce our dependence on oil. Microbial electrosynthesis (MES) is one of the bioelectrochemical approaches developed in the last decade that could have critical impact on the current methods of chemical synthesis. MES is a process in which electroautotrophic microbes use electrical current as electron source to reduce CO2 to multicarbon organics. Electricity necessary for MES can be harvested from renewable resources such as solar energy, wind turbine, or wastewater treatment processes. The net outcome is that renewable energy is stored in the covalent bonds of organic compounds synthesized from greenhouse gas. This review will discuss the future of MES and the challenges that lie ahead for its development into a mature technology.
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Affiliation(s)
- Pier-Luc Tremblay
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm Denmark
| | - Tian Zhang
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm Denmark
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Olson DG, Sparling R, Lynd LR. Ethanol production by engineered thermophiles. Curr Opin Biotechnol 2015; 33:130-41. [PMID: 25745810 DOI: 10.1016/j.copbio.2015.02.006] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 02/11/2015] [Accepted: 02/13/2015] [Indexed: 12/17/2022]
Abstract
We compare a number of different strategies that have been pursued to engineer thermophilic microorganisms for increased ethanol production. Ethanol production from pyruvate can proceed via one of four pathways, which are named by the key pyruvate dissimilating enzyme: pyruvate decarboxylase (PDC), pyruvate dehydrogenase (PDH), pyruvate formate lyase (PFL), and pyruvate ferredoxin oxidoreductase (PFOR). For each of these pathways except PFL, we see examples where ethanol production has been engineered with a yield of >90% of the theoretical maximum. In each of these cases, this engineering was achieved mainly by modulating expression of native genes. We have not found an example where a thermophilic ethanol production pathway has been transferred to a non-ethanol-producing organism to produce ethanol at high yield. A key reason for the lack of transferability of ethanol production pathways is the current lack of understanding of the enzymes involved.
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Affiliation(s)
- Daniel G Olson
- Thayer School of Engineering at Dartmouth College, Hanover, NH 03755, United States; BioEnergy Science Center, Oak Ridge, TN 37830, United States
| | - Richard Sparling
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada R3T 5V6
| | - Lee R Lynd
- Thayer School of Engineering at Dartmouth College, Hanover, NH 03755, United States; BioEnergy Science Center, Oak Ridge, TN 37830, United States.
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