Low carbon fuels and commodity chemicals from waste gases – systematic approach to understand energy metabolism in a model acetogen

Marcellin, Esteban; Behrendorff, James B. Y. H.; Nagaraju, Shilpa; DeTissera, Sashini; Segovia, Simón; Palfreyman, Robin W.; Daniell, James; Licona-Cassani, Cuauhtémoc; Quek, Lake‐Ee; Speight, Robert; Hodson, Mark P.; Simpson, Séan D.; Mitchell, Wayne; Köpke, Michael; Nielsen, Lars K.

doi:10.1039/c5gc02708j

Cited by 147 publications

(185 citation statements)

References 59 publications

(91 reference statements)

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“…The genome-scale metabolic model (GEM) was reconstructed previously by Marcellin et al, 2016 and refined here. The core metabolic pathways were reconstructed based on the SEED model annotation pipeline (Henry et al, 2010).…”

Section: Metabolic Reconstruction Processmentioning

confidence: 99%

“…During the balanced growth phase and uptake of all 4AAs (based on exo- Gene expression patterns on 4AA medium were compared against RNA-seq data of the same C. autoethanogenum strain (DSM 10061) grown heterotrophically on standard PETC-MES (including YE) and published previously (Marcellin et al, 2016). Sequencing reads of both heterotrophic conditions were trimmed to avoid reading errors and then aligned/realigned to the genome using TopHat2 (Kim et al, 2013) with two mismatches allowed per read alignment.…”

Section: Transcriptome Analysismentioning

confidence: 99%

“…From the many acetogens, Clostridium autoethanogenum is a promising gas-fermenting biocatalyst used at industrial scale (Liew et al, 2016b). C. autoethanogenum natively produces acetate, ethanol, 2,3-butanediol and lactate as by-products of growth (Abrini et al, 1994;Köpke et al, 2011;Marcellin et al, 2016). In most cases, the majority of carbon (both during heteroand autotrophic growth) is excreted as acetate to restore ATP balance in the WLP, which is an unwanted carbon loss in a bioprocess.…”

Section: Introductionmentioning

confidence: 99%

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Arginine deiminase pathway provides ATP and boosts growth of the gas-fermenting acetogen Clostridium autoethanogenum

Valgepea

Loi

Behrendorff

et al. 2017

Metabolic Engineering

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Arginine deiminase pathway provides ATP and boosts growth of the gas-fermenting acetogen Clostridium autoethanogenum Metabolic Engineering, http://dx.doi.org/10.1016Engineering, http://dx.doi.org/10. /j.ymben.2017 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting galley proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. AbstractAcetogens are attractive organisms for the production of chemicals and fuels from inexpensive and non-food feedstocks such as syngas (CO, CO 2 and H 2 ). Expanding their product spectrum beyond native compounds is dictated by energetics, particularly ATP availability. Acetogens have evolved sophisticated strategies to conserve energy from reduction potential differences between major redox couples, however, this coupling is sensitive to small changes in thermodynamic equilibria. To accelerate the development of strains for energy-intensive products from gases, we used a genome-scale metabolic model (GEM) to explore alternative ATP-generating pathways in the gas-fermenting acetogen 1 Present address: Department of Plant and Environmental Science, University of Copenhagen, Copenhagen, Denmark Clostridium autoethanogenum. Shadow price analysis revealed a preference of C.autoethanogenum for nine amino acids. This prediction was experimentally confirmed under heterotrophic conditions. Subsequent in silico simulations identified arginine (ARG) as a key enhancer for growth. Predictions were experimentally validated, and faster growth was measured in media containing ARG (t D~4 h) compared to growth on yeast extract (t D~9 h). The growth-boosting effect of ARG was confirmed during autotrophic growth.Metabolic modelling and experiments showed that acetate production is nearly abolished and fast growth is realised by a three-fold increase in ATP production through the arginine deiminase (ADI) pathway. The involvement of the ADI pathway was confirmed by metabolomics and RNA-sequencing which revealed a ~500-fold up-regulation of the ADI pathway with an unexpected down-regulation of the Wood-Ljungdahl pathway. The data presented here offer a potential route for supplying cells with ATP, while demonstrating the usefulness of metabolic modelling for the discovery of native pathways for stimulating growth or enhancing energy availability.

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Section: Metabolic Reconstruction Processmentioning

confidence: 99%

Section: Transcriptome Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Arginine deiminase pathway provides ATP and boosts growth of the gas-fermenting acetogen Clostridium autoethanogenum

Valgepea

Loi

Behrendorff

et al. 2017

Metabolic Engineering

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100

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“…A study on technical risk for sugar platforms in a kraft mill biorefinery focused on the challenges of generating added waste water and contamination issues in fermentation (Mariano 2014). Carbon monoxide from synthesis gas (syngas), methane, and carbon dioxide are also potential carbon sources for the fermentation processes that can be obtained from kraft mill waste streams (Shen et al 2015;Drzyzga et al 2015;Bomgardner 2016;Marcellin et al 2016). A large market potential for biobased platform chemicals from sugars exists in fermentation intermediates generated for manufacturing polymers such as bio-PET, bio-PE, and bio-nylon (Collias et al 2014;Becker et al 2015b).…”

Section: Bio-advantaged Platform Chemicals From Woodmentioning

confidence: 99%

Integrating a Biorefinery into an Operating Kraft Mill

Johnson¹,

Hart²

2016

BioResources

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Kraft pulp and paper mills have several advantages for serving the emerging biorefinery industry as a source of raw materials. This review examines technologies for producing liquid biofuels, chemicals, and advanced materials from woody feedstocks to generate new sources of revenue. Market pull comes in part from government policies that drive substitution of petroleum-based products with biobased equivalents. Kraft mills have ample networks to supply feedstocks, whether these are forest residues or byproduct side streams. Pulp mills are well suited to expand sufficiently to accommodate production of value added platform chemicals that are in demand because of brand owner sustainability commitments.

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“…289 The biotech company LANZATECH is commercialising gas fermentations processes with C. autoethanogenum for the production of biofuels and constantly advances available tools for metabolic and genetic engineering as well as fundamental understanding of the acetogenic metabolism. 295,296 Within this chapter we investigate the effect of extracellular electron supply at different potentials on the production of C. autoethanogenum in heterotrophic fermentations.…”

Section: Acetogenic Organisms As Host For Mesmentioning

confidence: 99%

Understanding extracellular electron transport of industrial microorganisms and optimization for production application

Kracke¹

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Microbial electrosynthesis (MES) and electro-fermentation are novel approaches to increase microbial production by stimulating the metabolism of the cells electrically. The technique is still in its infancy and while already hyped as promising method to convert CO 2 or cheap carbon sources and electrical energy into valuable chemicals and fuels, little is known about its true potential. This project uses a combination of in silico and in vivo approaches to gather novel information about the benefits and limitations of microbial electrosynthesis as well as its fundamental mechanisms.Understanding microbial electron transport mechanisms is the key to optimization of any bioelectrochemical technology. Therefore, this work analyses 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 bioproduction.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, ferredoxins, quinones, flavins) are identified and analysed regarding their possible role in electrode-microbe-interactions.Based on these findings a stoichiometric network analysis is performed analysing the effect of electrical stimulation on the microbial metabolism theoretically. Escherichia coli is used as model organism for production with the aim to identify target processes for MES.For the first time, 20 different valuable products were screened for their potential to show increased yields during anaerobic electrically enhanced fermentation. Surprisingly it was found that an increase in product formation by electrical enhancement is not necessarily dependent on the degree of reduction of the product but rather the metabolic pathway it is derived from. Contrary to the usual assumption a reduced product would always require electron supply by a cathode this study shows that a complex metabolic analysis is needed to identify the overall redox state of each process. A variety of beneficial processes is presented with product yield increases of maximal +36% in reductive and +84% in oxidative fermentations and final theoretical product yields up to 100%. This includes compounds that are already produced at industrial scale such as succinic acid, ii lysine and diaminopentane as well as potential novel bio-commodities such as isoprene, para-hydroxybenzoic acid and para-aminobenzoic acid. Furthermore, it is shown that the way of electron transport has major impact on achievable biomass and product yields. The coupling of electron transport to energy conservation could be identified as crucial for most processes.The in vivo approach of this project introduces the development of a standardised reactor platfor...

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Low carbon fuels and commodity chemicals from waste gases – systematic approach to understand energy metabolism in a model acetogen

Abstract: Insight into energy metabolism of gas-fermenting acetogens using a systems level approach for sustainable production of fuels and chemicals.

Cited by 147 publications

References 59 publications

Arginine deiminase pathway provides ATP and boosts growth of the gas-fermenting acetogen Clostridium autoethanogenum

Arginine deiminase pathway provides ATP and boosts growth of the gas-fermenting acetogen Clostridium autoethanogenum

Integrating a Biorefinery into an Operating Kraft Mill

Understanding extracellular electron transport of industrial microorganisms and optimization for production application

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