Aerosol Sources, Transport Pathways, and Scavenging During ACTIVATE: Model Products and Research Projects
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Hongyu Liu↗
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Towards using bacterial microcompartments as a platform for spatial metabolic engineering in the industrially important and metabolically versatile Zymomonas mobilis
Advances in synthetic biology have enabled the incorporation of novel biochemical pathways for the production of high-value products into industrially important bacterial hosts. However, attempts to redirect metabolic fluxes towards desired products often lead to the buildup of toxic or undesirable intermediates or, more generally, unwanted metabolic cross-talk. The use of shells derived from self-assembling protein-based prokaryotic organelles, referred to as bacterial microcompartments (BMCs), as a scaffold for metabolic enzymes represents a sophisticated approach that can both insulate and integrate the incorporation of challenging metabolic pathways into industrially important bacterial hosts. Here we took a synthetic biology approach and introduced the model shell system derived from the myxobacterium Haliangium ochraceum (HO shell) into the industrially relevant organism Zymomonas mobilis with the aim of constructing a BMC-based spatial scaffolding platform. SDS-PAGE, transmission electron microscopy, and dynamic light scattering analyses collectively demonstrated the ability to express and purify empty capped and uncapped HO shells from Z. mobilis . As a proof of concept to internally load or externally decorate the shell surface with enzyme cargo, we have successfully targeted fluorophores to the surfaces of the BMC shells. Overall, our results provide the foundation for incorporating enzymes and constructing BMCs with synthetic biochemical pathways for the future production of high-value products in Z. mobilis .
59 BASIC BIOLOGICAL SCIENCES↗
Biosynthesis of natural and halogenated plant monoterpene indole alkaloids in yeast
Monoterpenoid indole alkaloids (MIAs) represent a large class of plant natural products with marketed pharmaceutical activities against a wide range of indications, including cancer, malaria and hypertension. Halogenated MIAs have shown improved pharmaceutical properties; however, synthesis of new-to-nature halogenated MIAs remains a challenge. Here we demonstrate a platform for de novo biosynthesis of two MIAs, serpentine and alstonine, in baker’s yeast Saccharomyces cerevisiae and deploy it to systematically explore the biocatalytic potential of refactored MIA pathways for the production of halogenated MIAs. From this, we demonstrate conversion of individual haloindole derivatives to a total of 19 different new-to-nature haloserpentine and haloalstonine analogs. Furthermore, by process optimization and heterologous expression of a modified halogenase in the microbial MIA platform, we document de novo halogenation and biosynthesis of chloroalstonine. Together, this study highlights a microbial platform for enzymatic exploration and production of complex natural and new-to-nature MIAs with therapeutic potential.
59 BASIC BIOLOGICAL SCIENCES↗
In vitro prototyping and rapid optimization of biosynthetic enzymes for cell design
The design and optimization of biosynthetic pathways for industrially relevant, non-model organisms is challenging due to transformation idiosyncrasies, reduced numbers of validated genetic parts and a lack of high-throughput workflows. Here we describe a platform for in vitro prototyping and rapid optimization of biosynthetic enzymes (iPROBE) to accelerate this process. In iPROBE, cell lysates are enriched with biosynthetic enzymes by cell-free protein synthesis and then metabolic pathways are assembled in a mix-and-match fashion to assess pathway performance. We demonstrate iPROBE by screening 54 different cell-free pathways for 3-hydroxybutyrate production and optimizing a six-step butanol pathway across 205 permutations using data-driven design. Observing a strong correlation (r = 0.79) between cell-free and cellular performance, we then scaled up our highest-performing pathway, which improved in vivo 3-HB production in Clostridium by 20-fold to 14.63 ± 0.48 g l -1 . Finally, we expect iPROBE to accelerate design–build–test cycles for industrial biotechnology.
36 MATERIALS SCIENCE↗
Metabolic engineering strategies for producing decanoic acid and related oleochemicals: 1-decanol, 2-nonanone, and poly(3-hydroxydecanoate) in Escherichia coli
Medium-chain (mc-) oleochemicals are an important class of renewable chemicals with broad industrial applications; however, their sustainable microbial production remains challenging. In this study, we developed a versatile metabolic engineering and fed-batch strategy to produce C 10 -oleochemicals in Escherichia coli. Central to this approach is an engineered mc-acyl-ACP thioesterase Cl FatB3-tr-D10S with C 10 species accounting for around 70% of the total fatty acids produced. To expand product diversity, we established a decanoyl-CoA pool through co-expression of fadD, enabling downstream conversion into multiple product classes. Through pathway tuning, enzyme bioprospecting, strain engineering and fermentation optimization strategies, we demonstrated selective production of 1-decanol, 2-nonanone and poly(3-hydroxydecanoate) (C 10 -PHA). Production of decanoic acid and 1-decanol were achieved by optimizing expression of Cl fatB3-tr-D10S and, Mt fadD6 and Ma acr, respectively. Leveraging β-oxidation enabled the production of β-ketoacyl-CoA intermediates, which were converted to 2-nonanone via heterologous Mlu fadE, Vf fadB and Ps fadM expression. Additionally, expression of phaJ2 and phaC2 facilitated the conversion of decanoyl-CoA pool into C 10 -PHA homopolymer. Altogether, this work demonstrates a versatile and tunable platform for medium-chain oleochemical production.
1-Decanol↗
Controlling selectivity of modular microbial biosynthesis of butyryl-CoA-derived designer esters
Short-chain esters have broad utility as flavors, fragrances, solvents, and biofuels. Controlling selectivity of ester microbial biosynthesis has been an outstanding metabolic engineering problem. In this study, we enabled the de novo fermentative microbial biosynthesis of butyryl-CoA-derived designer esters (e.g., butyl acetate, ethyl butyrate, butyl butyrate) in Escherichia coli with controllable selectivity. Using the modular design principles, we generated the butyryl-CoA-derived ester pathways as exchangeable production modules compatible with an engineered chassis cell for anaerobic production of designer esters. We designed these modules derived from an acyl-CoA submodule (e.g., acetyl-CoA, butyryl-CoA), an alcohol submodule (e.g., ethanol, butanol), a cofactor regeneration submodule (e.g., NADH), and an alcohol acetyltransferase (AAT) submodule (e.g., ATF1, SAAT) for rapid module construction and optimization by manipulating replication (e.g., plasmid copy number), transcription (e.g., promoters), translation (e.g., codon optimization), pathway enzymes, and pathway induction conditions. To further enhance production of designer esters with high selectivity, we systematically screened various strategies of protein solubilization using protein fusion tags and chaperones to improve the soluble expression of multiple pathway enzymes. Finally, our engineered ester-producing strains could achieve 19-fold increase in butyl acetate production (0.64 g/L, 96% selectivity), 6-fold increase in ethyl butyrate production (0.41 g/L, 86% selectivity), and 13-fold increase in butyl butyrate production (0.45 g/L, 54% selectivity) as compared to the initial strains. Altogether, this study presented a generalizable framework to engineer modular microbial platforms for anaerobic production of butyryl-CoA-derived designer esters from renewable feedstocks.
59 BASIC BIOLOGICAL SCIENCES↗
Development of Corynebacterium glutamicum as a monoterpene production platform
Monoterpenes are commonly known for their role in the flavors and fragrances industry and are also gaining attention for other uses like insect repellant and as potential renewable fuels for aviation. Corynebacterium glutamicum, a Generally Recognized as Safe microbe, has been a choice organism in industry for the annual million ton-scale bioproduction of amino acids for more than 50 years; however, efforts to produce monoterpenes in C. glutamicum have remained relatively limited. In this study, we report a further expansion of the C. glutamicum biosynthetic repertoire through the development and optimization of a mevalonate-based monoterpene platform. In the course of our plasmid design iterations, we increased flux through the mevalonate-based bypass pathway, measuring isoprenol production as a proxy for monoterpene precursor abundance and demonstrating the highest reported titers in C. glutamicum to date at 1504.6 mg/L. Our designs also evaluated the effects of backbone, promoter, and GPP synthase homolog origin on monoterpene product titers. Monoterpene production was further improved by disrupting competing pathways for isoprenoid precursor supply and by implementing a biphasic production system to prevent volatilization. With this platform, we achieved 321.1 mg/L of geranoids, 723.6 mg/L of 1,8-cineole, and 227.8 mg/L of linalool. Furthermore, we determined that C. glutamicum first oxidizes geraniol through an aldehyde intermediate before it is asymmetrically reduced to citronellol. Additionally, we demonstrate that the aldehyde reductase, AdhC, possesses additional substrate promiscuity for acyclic monoterpene aldehydes.
59 BASIC BIOLOGICAL SCIENCES↗
Nuclear-Driven Chemical Conversion Pathways
The purpose of this work is to explore the possibilities of using coal as a carbon resource by converting it to fuels and chemicals with heat from a nuclear power plant. While many previous studies have focused on coal gasification, this process requires combusting a portion of the coal and producing heat. By employing pyrolysis over gasification, the energy content in the coal can be preserved. Pyrolysis of coal also results in a large portion of solid char, which can be converted to activated carbon and sold to various markets. This model uses hydrogen produced by nuclear-supplied heat and electricity to convert the syngas stream to methanol, which has many pathways for further processing into fuels, chemicals, and plastics. Specifically, this project focuses on non-fuel products for methanol pathways. The CO2 captured within the refinery model can also be combined with hydrogen to produce more chemical products and reduce CO2 emissions.
01 COAL, LIGNITE, AND PEAT↗
Temperature-Dependent Reaction Pathways in FeS 2 : Reversibility and the Electrochemical Formation of Fe 3 S 4
The present study has used a variety of characterization techniques to determine the products and reaction pathways involved in the rechargeable Li–FeS 2 system. We revisit both the initial lithiation and subsequent cycling of FeS 2 employing an ionic liquid electrolyte to investigate the intermediate and final charge products formed under varying thermal conditions (room temperature to 100 °C). The detection of Li 2 S and hexagonal FeS as the intermediate phases in the initial lithiation and the electrochemical formation of greigite, Fe 3 S 4 , as a charge product in the rechargeable reaction differ significantly from previous reports. The conditions for Fe 3 S 4 formation are shown to be dependent on both the temperature (~60 °C) and the availability of sulfur to drive a FeS to Fe 3 S 4 transformation. Upon further cycling, Fe 3 S 4 transforms to a lower sulfur content iron sulfide phase, a process which coincides with the loss of sulfur based on the new reaction pathways established in this work. The connection between sulfur loss, capacity fade, and charge product composition highlights the critical need to retain sulfur in the active material upon cycling.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Cell-Free Protein Synthesis for High-Throughput Biosynthetic Pathway Prototyping
Biological systems provide a sustainable and complimentary approach to synthesizing useful chemical products. Metabolic engineers seeking to establish economically viable biosynthesis platforms strive to increase product titers, rates, and yields. Despite continued advances in genetic tools and metabolic engineering techniques, cellular workflows remain limited in throughput. It may take months to test dozens of unique pathway designs even in a robust model organism, such as Escherichia coli. In contrast, cell-free protein synthesis enables the rapid generation of enzyme libraries that can be combined to reconstitute metabolic pathways in vitro for biochemical synthesis in days rather than weeks. Cell-free reactions thereby enable comparison of hundreds to thousands of unique combinations of enzyme homologs and concentrations, which can quickly identify the most productive pathway variants to test in vivo or further characterize in vitro. Furthermore, this cell-free pathway prototyping strategy provides a complementary approach to accelerate cellular metabolic engineering efforts toward highly productive strains for metabolite production.
59 BASIC BIOLOGICAL SCIENCES↗
Techno-Economic Assessment for the Production of Hydrocarbon Fuels via Catalytic Upgrading of Furans
This technical report documents the techno-economic analysis (TEA) implications of a biochemical/catalytic pathway for the production of long-chain hydrocarbon fuels in support to the multi-lab Catalytic Upgrading of Biochemical Intermediates (CUBI) project within the Chemical Catalysis for Bioenergy Consortium (ChemCatBio). Two distinct conceptual biorefineries centered around the process encompassing sugar dehydration to furans, aldol condensation between furans and a ketone (methyl ethyl ketone [MEK]), and a final step of hydrotreating to obtain hydrocarbons in the C 14 -C 16 range are considered: an integrated plant that simultaneously produces both furans (furfural and HMF) and ketone (MEK via 2,3-butanediol [BDO]) from sugars and a dedicated facility focused on producing furans from corn stover hydrolysate and procuring the ketone externally. In either plant, the main coproducts are adipic acid (derived from lignin) and sodium sulfate. The results from the assessment are quite comparable to those reported in previous design case focused on biological conversion of sugars to fermentation intermediates with subsequent catalytic upgrading of those intermediates to hydrocarbon fuels, thus presenting another viable alternative pathway to achieve similar fuel cost targets through purely catalytic upgrading of sugars. Since this study considers long-term performance targets for the full pathway dedicated to sugar upgrading to fuels, the critical remaining research points needed to achieve future cost goals are also discussed. Finally, this report presents a single-point sensitivity analysis around selected parameters to identify the major cost drivers of the biorefineries and provides a qualitative discussion on additional opportunities for cost reduction within the proposed concepts, namely through adding value to furans, to coproducts that may be obtained following BDO dehydration, and to lignin through alternative pathways.
09 BIOMASS FUELS↗
Upgrading of C1 Building Blocks
This project is developing the centerpiece technology for a market-responsive, integrated biorefinery concept based on the conversion of renewable C1 intermediates (e.g., syngas, CO2, methanol) to a suite of fuels and co-products with improved carbon efficiency, reduced capital expense, and control of the product distribution to meet market demand. Advanced upgrading technologies of syngas are critically needed for the successful commercialization of fuel production at a scale relevant for biomass gasification. Research tasks within this project leverage complementary catalyst and process design for the conversion of CO2-rich syngas (15-20% CO2 in syngas) to achieve high carbon yields of gasoline and jet fuels as the major products. The conversion pathways generate high quality fuels (e.g., high octane gasoline with low aromatics, desirable jet-range hydrocarbons), and potential to achieve favorable cost targets by 2022. Research progress is compared against the Mobil Olefin to Gasoline and Distillate (MOGD) process, which also offers control over the gasoline and distillate products, as an industrial benchmark. The pathway for direct conversion of CO2-rich syngas to hydrocarbon fuels seeks to exceed the carbon efficiency of biomass-sourced MOGD (31.8%). Recent catalyst and process development achievements are highlighted by improvements in carbon-selectivity to fuels and carbon yields, along with evidence of incorporation of carbon from CO2 into the hydrocarbon products.
bioenergy↗
Screening and evaluation of biomass upgrading strategies for sustainable transportation fuel production with biomass-derived volatile fatty acids
Biomass conversion to fuels and chemicals is crucial to decarbonization, but choosing an advantageous upgrading pathway out of many options is challenging. Rigorously evaluating all candidate pathways (process simulation, product property testing) requires a prohibitive amount of research effort; even simple upgrading schemes have hundreds of possible permutations. We present a method enabling high-throughput screening by approximating upgrading unit operations and drop-in compatibility of products (e.g., fuel properties) and apply it to volatile fatty acid (VFA) conversion to liquid transportation fuels via a MATLAB script, VFA Upgrading to Liquid Transportation fUels Refinery Estimation (VULTURE). VULTURE selects upgrading configurations that maximize fuel blend bio-derived content. We validate VULTURE's approximations through surrogate fuel property testing and process simulation. Techno-economic and life cycle analyses suggest that VFA upgrading processes down-selected by VULTURE are profitable and have low carbon intensities, demonstrating the potential for the strategy to accelerate process development timelines at decreased costs.
09 BIOMASS FUELS↗
Stressing the importance of plant specialized metabolites: omics-based approaches for discovering specialized metabolism in plant stress responses
Plants produce a diverse range of specialized metabolites that play pivotal roles in mediating environmental interactions and stress adaptation. These unique chemical compounds also hold significant agricultural, medicinal, and industrial values. Despite the expanding knowledge of their functions in plant stress interactions, understanding the intricate biosynthetic pathways of these natural products remains challenging due to gene and pathway redundancy, multifunctionality of proteins, and the activity of enzymes with broad substrate specificity. In the past decade, substantial progress in genomics, transcriptomics, metabolomics, and proteomics has made the exploration of plant specialized metabolism more feasible than ever before. Notably, recent advances in integrative multi-omics and computational approaches, along with other technologies, are accelerating the discovery of plant specialized metabolism. In this review, we present a summary of the recent progress in the discovery of plant stress-related specialized metabolites. Emphasis is placed on the application of advanced omics-based approaches and other techniques in studying plant stress-related specialized metabolism. Additionally, we discuss the high-throughput methods for gene functional characterization. These advances hold great promise for harnessing the potential of specialized metabolites to enhance plant stress resilience in the future.
59 BASIC BIOLOGICAL SCIENCES↗
Salt supplementation-induced metabolic reprogramming in Streptomyces coelicolor
Members of the genus Streptomyces are major producers of a wide variety of secondary metabolites that serve as bioactive compounds. Many secondary metabolites are produced in response to environmental signals such as biotic and abiotic stresses. In this study, we identified salt supplementation as one of the stimuli activating secondary metabolism in the model Streptomyces species, Streptomyces coelicolor. Comparative metabolomics revealed overproduction of several known secondary metabolites, most notably undecylprodigiosin and coelimycin P1, in addition to their biosynthetic intermediates and derivatives, as well as many unknown metabolites. Transcriptomic analysis revealed activation of diverse biological processes including cation uptake, compatible solute production, and the phosphate limitation stress response through conserved and species-specific mechanisms, presumably to overcome the increased salinity. This response leads to activation of a variety of regulatory and metabolic pathways required for production of secondary metabolites including activation of conserved metabolic pathways for energy and substrate supply and species-specific secondary metabolite biosynthetic gene clusters. Furthermore, several promoter sequences contributing to upregulation of secondary metabolism induced by salt supplementation were identified. Overall, our data show how S. coelicolor copes with the increased salinity and tailors the cellular metabolism toward secondary metabolism in a conserved and species-specific manner.
Otani, Hiroshi [USDOE Joint Genome Institute (JGI)↗
Electrifying the production of sustainable aviation fuel: the risks, economics, and environmental benefits of emerging pathways including CO 2
Emerging CO 2 to SAF pathways facilitates diversification of fuel production with the potential for a near carbon neutral footprint.
09 BIOMASS FUELS↗
Activation of the plant mevalonate pathway by extracellular ATP
The mevalonate pathway plays a critical role in multiple cellular processes in both animals and plants. In plants, the products of this pathway impact growth and development, as well as the response to environmental stress. A forward genetic screen of Arabidopsis thaliana using Ca 2+ -imaging identified mevalonate kinase (MVK) as a critical component of plant purinergic signaling. MVK interacts directly with the plant extracellular ATP (eATP) receptor P2K1 and is phosphorylated by P2K1 in response to eATP. Mutation of P2K1-mediated phosphorylation sites in MVK eliminates the ATP-induced cytoplasmic calcium response, MVK enzymatic activity, and suppresses pathogen defense. The data demonstrate that the plasma membrane associated P2K1 directly impacts plant cellular metabolism by phosphorylation of MVK, a key enzyme in the mevalonate pathway. The results underline the importance of purinergic signaling in plants and the ability of eATP to influence the activity of a key metabolite pathway with global effects on plant metabolism.
59 BASIC BIOLOGICAL SCIENCES↗
Metabolic engineering of Zymomonas mobilis for anaerobic isobutanol production
Biofuels and value-added biochemicals derived from renewable biomass via biochemical conversion have attracted considerable attention to meet global sustainable energy and environmental goals. Isobutanol is a four-carbon alcohol with many advantages that make it attractive as a fossil-fuel alternative. Zymomonas mobilis is a highly efficient, anaerobic, ethanologenic bacterium making it a promising industrial platform for use in a biorefinery. In this study, the effect of isobutanol on Z. mobilis was investigated, and various isobutanol-producing recombinant strains were constructed. The results showed that the Z. mobilis parental strain was able to grow in the presence of isobutanol below 12 g/L while concentrations greater than 16 g/L inhibited cell growth. Integration of the heterologous gene encoding 2-ketoisovalerate decarboxylase such as kdcA from Lactococcus lactis is required for isobutanol production in Z. mobilis. Moreover, isobutanol production increased from nearly zero to 100-150 mg/L in recombinant strains containing the kdcA gene driven by the tetracycline-inducible promoter Ptet. In addition, we determined that overexpression of a heterologous als gene and two native genes (ilvC and ilvD) involved in valine metabolism in a recombinant Z. mobilis strain expressing kdcA can divert pyruvate from ethanol production to isobutanol biosynthesis. This engineering improved isobutanol production to above 1 g/L. Finally, recombinant strains containing both a synthetic operon, als-ilvC-ilvD, driven by Ptet and the kdcA gene driven by the constitutive strong promoter, Pgap, were determined to greatly enhance isobutanol production with a maximum titer about 4.0 g/L. Finally, isobutanol production was negatively affected by aeration with more isobutanol being produced in more poorly aerated flasks. This study demonstrated that overexpression of kdcA in combination with a synthetic heterologous operon, als-ilvC-ilvD, is crucial for diverting pyruvate from ethanol production for enhanced isobutanol biosynthesis. Moreover, this study also provides a strategy for harnessing the valine metabolic pathway for future production of other pyruvate-derived biochemicals in Z. mobilis.
09 BIOMASS FUELS↗