Metabolic engineering of Escherichia coli for the production of benzoic acid from glucose
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Luo, Zi Wei (ORCID:0000000160189368)↗
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Corrigendum to "Engineering glucose metabolism for enhanced muconic acid production in Pseudomonas putida KT2440" [Metab. Eng. 59 (2020) 64-75]
The plasmid used to delete hexR, pGB022, in our Pseudomonas putida KT2440 strain engineered to produce cis,cis-muconic acid from glucose, GB062, inadvertently introduced two mutations: a point mutation in the zwf-1, encoding the glucose-6-phosphate 1-dehydrogenase, that results in a conservative, V157I replacement and a deletion of the last 8 bp of the glucose-6-phosphate 1-epimerase gene, yeaD, leading to a frame shift in this gene and, consequently, the replacement of the last two amino acids of the C-terminus (LS) with 56 amino acids (RGPWVCPWVGKTAGCVSSRLFARSSIVLSVRLTYHLSVTLVCNVVVFTTLSLENRV).
BIOMASS FUELS↗
Muconic acid production from methane using rationally-engineered methanotrophic biocatalysts
Here, we demonstrate bioconversion of methane to muconic acid, a dicarboxylic acid that can be upgraded to an array of platform chemicals, by three gammaproteobacterial methanotrophs.
09 BIOMASS FUELS↗
NEW PARTICLE WORKING STANDARDS FOR NWAL PARTICLE LABORATORY CALIBRATION AND QUALITY CONTROL - OPERATIONAL ENGINEERING FOR AN AEROSOL-BASED PRODUCTION PLATFORM FOR THE SYNTHESIS OF PLUTONIUM-CONTAINING REFERENCE PARTICULATE MATERIALS
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Scott, Spencer M.↗
Engineering biology approaches for food and nutrient production by cyanobacteria
Here, as photoautotrophic organisms, cyanobacteria capture and store solar energy in the form of biomass. Cyanobacterial biomass has been an important component of diet and nutrition in several regions for centuries. Synthetic biology strategies are currently being applied to increase the yield and productivity of cyanobacterial biomass by optimizing solar energy utilization and CO 2 fixation rates for carbon storage. Likewise, engineering cyanobacteria as cellular factories to synthesize carbohydrates, amino acids, proteins, lipids and fatty acids is providing an attractive way to sustainably produce food and nutrients for human consumption. In this review, we have summarized recent progress in both aspects and prospective trends under development.
59 BASIC BIOLOGICAL SCIENCES↗
Evaluation of engineered low-lignin poplar for conversion into advanced bioproducts
Lignocellulosic resources are promising feedstocks for the manufacture of bio-based products and bioenergy. However, the inherent recalcitrance of biomass to conversion into simple sugars currently hinders the deployment of advanced bioproducts at large scale. Lignin is a primary contributor to biomass recalcitrance as it protects cell wall polysaccharides from degradation and can inhibit hydrolytic enzymes via non-productive adsorption. Several engineering strategies have been designed to reduce lignin or modify its monomeric composition. For example, expression of bacterial 3-dehydroshikimate dehydratase (QsuB) in poplar trees resulted in a reduction in lignin due to redirection of metabolic flux toward 3,4-dihydroxybenzoate at the expense of lignin. This reduction was accompanied with remarkable changes in the pools of aromatic compounds that accumulate in the biomass. The impact of these modifications on downstream biomass deconstruction and conversion into advanced bioproducts was evaluated in the current study. Using ionic liquid pretreatment followed by enzymatic saccharification, biomass from engineered trees released more glucose and xylose compared to wild-type control trees under optimum conditions. Fermentation of the resulting hydrolysates using Rhodosporidium toruloides strains engineered to produce α-bisabolene, epi-isozizaene, and fatty alcohols showed no negative impact on cell growth and yielded higher titers of bioproducts (as much as + 58%) in the case of QsuB transgenics trees. Our data show that low-recalcitrant poplar biomass obtained with the QsuB technology has the potential to improve the production of advanced bioproducts.
09 BIOMASS FUELS↗
Unleashing the power of energy storage: Engineering β-oxidation pathways for polyketide production
Not Available
25 ENERGY STORAGE↗
Data for Metabolic Engineering of Rhodotorula toruloides IFO0880 Improves C16 and C18 Fatty Alcohol Production from Synthetic Media
The oleaginous, carotenogenic yeast Rhodotorula toruloides has been increasingly explored as a platform organism for the production of terpenoids and fatty acid derivatives. Fatty alcohols, a fatty acid derivative widely used in the production of detergents and surfactants, can be produced microbially with the expression of a heterologous fatty acyl-CoA reductase. Due to its high lipid production, R. toruloides has high potential for fatty alcohol production, and in this study several metabolic engineering approaches were investigated to improve the titer of this product. Fatty acyl-CoA reductase from Marinobacter aqueolei was co-expressed with SpCas9 in R. toruloides IFO0880 and a panel of gene overexpressions and Cas9-mediated gene deletions were explored to increase the fatty alcohol production. Two overexpression targets (ACL1 and ACC1, improving cytosolic acetyl-CoA and malonyl-CoA production, respectively) and two deletion targets (the acyltransferases DGA1 and LRO1) resulted in significant (1.8 to 4.4-fold) increases to the fatty alcohol titer in culture tubes. Combinatorial exploration of these modifications in bioreactor fermentation culminated in a 3.7 g/L fatty alcohol titer in the LRO1Δ mutant. As LRO1 deletion was not found to be beneficial for fatty alcohol production in other yeasts, a lipidomic comparison of the DGA1 and LRO1 knockout mutants was performed, finding that DGA1 is the primary acyltransferase responsible for triacylglyceride production in R. toruloides , while LRO1 disruption simultaneously improved fatty alcohol production, increased diacylglyceride and triacylglyceride production, and increased glucose consumption. The fatty alcohol titer of fatty acyl-CoA reductase-expressing R. toruloides was significantly improved through the deletion of LRO1, or the deletion of DGA1 combined with overexpression of ACC1 and ACL1. Disruption of LRO1 surprisingly increased both lipid and fatty alcohol production, creating a possible avenue for future study of the lipid metabolism of this yeast.
Conversion↗
I.1 Heavy-Duty Diesel Combustion (Sandia National Laboratories)
Regulatory drivers and market demands for lower pollutant emissions, lower carbon dioxide emissions, and lower fuel consumption motivate the development of cleaner and more fuel-efficient engine operating strategies. Most current production heavy-duty diesel engines use a combination of both in-cylinder and exhaust emissions-control strategies to achieve these goals. The emissions and efficiency performance of in-cylinder strategies depend strongly on flow and mixing processes that can be influenced by using multiple fuel injections. Past work performed under this project showed that adding a second injection can reduce soot to levels below what would have been produced by an unchanged first injection, thereby increasing load while decreasing soot and potentially reducing brake specific fuel consumption. Information characterizing the important in-cylinder processes with multiple injections has been gleaned from ensemble-averaged planar laser-induced incandescence (PLII) imaging visualizing the soot cloud and planar induced fluorescence (PLIF) of OH characterizing the soot oxidation regions. PLII showed a consistent disruption of the first injection soot cloud by the second injection. In conjunction with OH-PLIF, differences in soot oxidation patterns for multiple injections compared to single injections were observed. This understanding was further enhanced in FY20, when high-speed imaging resolving the above-mentioned effects in a single cycle were combined with direct numerical simulations investigating the multiple-injection ignition process on the microscopic level of turbulence and chemistry interaction. In FY21, these findings in conjunction with findings from other researchers published in the scientific literature were composed into a preliminary multiple-injection conceptual model of fuel-mixing, injection and ignition processes. Remaining key research questions were also highlighted. In addition, wall heat flux was investigated experimentally and with numerical simulations to understand the potential of multiple injections to reduce the engine heat losses and further enhance the efficiency.
33 ADVANCED PROPULSION SYSTEMS↗
SyPro Poplar: Improving Poplar Biomass Production under Abiotic Stress Conditions: an Integrated Omics, Bioinformatics, Synthetic Biology and Genetic Engineering Approach (Final Report)
SyPro Poplar: Improving Poplar Biomass Production under Abiotic Stress Conditions: an Integrated Omics, Bioinformatics, Synthetic Biology and Genetic Engineering Approach In the SyPro Poplar project, we aimed to integrate omics, bioinformatics, synthetic biology, and genetic engineering approaches to develop transgenic poplar trees with sustained photosynthetic activity and increased biomass production under individual and the simultaneous occurrence of water deficit, increased soil salinity, and elevated temperatures. Specifically, we intended to (i) study the functions of selected stress-responsive genes at tissue and cell type-specific levels, (ii) discover novel motifs and construct stress-responsive synthetic promoters, and (iii) use these promoters to drive the expression of genes shown to confer abiotic stress tolerance in a variety of crops and develop abiotic stress-tolerant poplars in a coordinated fashion.
09 BIOMASS FUELS↗
Metabolic engineering of Rhodotorula toruloides IFO0880 improves C16 and C18 fatty alcohol production from synthetic media
Abstract Background The oleaginous, carotenogenic yeast Rhodotorula toruloides has been increasingly explored as a platform organism for the production of terpenoids and fatty acid derivatives. Fatty alcohols, a fatty acid derivative widely used in the production of detergents and surfactants, can be produced microbially with the expression of a heterologous fatty acyl-CoA reductase. Due to its high lipid production, R. toruloides has high potential for fatty alcohol production, and in this study several metabolic engineering approaches were investigated to improve the titer of this product. Results Fatty acyl-CoA reductase from Marinobacter aqueolei was co-expressed with SpCas9 in R. toruloides IFO0880 and a panel of gene overexpressions and Cas9-mediated gene deletions were explored to increase the fatty alcohol production. Two overexpression targets ( ACL1 and ACC1 , improving cytosolic acetyl-CoA and malonyl-CoA production, respectively) and two deletion targets (the acyltransferases DGA1 and LRO1 ) resulted in significant (1.8 to 4.4-fold) increases to the fatty alcohol titer in culture tubes. Combinatorial exploration of these modifications in bioreactor fermentation culminated in a 3.7 g/L fatty alcohol titer in the LRO1 Δ mutant. As LRO1 deletion was not found to be beneficial for fatty alcohol production in other yeasts, a lipidomic comparison of the DGA1 and LRO1 knockout mutants was performed, finding that DGA1 is the primary acyltransferase responsible for triacylglyceride production in R. toruloides , while LRO1 disruption simultaneously improved fatty alcohol production, increased diacylglyceride and triacylglyceride production, and increased glucose consumption. Conclusions The fatty alcohol titer of fatty acyl-CoA reductase-expressing R. toruloides was significantly improved through the deletion of LRO1 , or the deletion of DGA1 combined with overexpression of ACC1 and ACL1 . Disruption of LRO1 surprisingly increased both lipid and fatty alcohol production, creating a possible avenue for future study of the lipid metabolism of this yeast.
59 BASIC BIOLOGICAL SCIENCES↗
Genome-scale Design and Engineering of Non-model Yeast Organisms for Production of Biofuels and Bioproducts
The overall goal of this project was to develop genome-scale design and engineering tools for two non-model yeast organisms including Rhodotorula toruloides and Issatchenkia orientalis to produce high-levels of fatty acids-derived products and organic acids, respectively. The project was performed between 9/15/2017 and 9/14/2024 (the last two-years were no-cost extensions). The team consisted of Huimin Zhao (Lead PI) and Christopher Rao (Co-PI) from the University of Illinois at Urbana-Champaign (UIUC), Costas Maranas (Co-PI) from the Pennsylvania State University, Joshua Rabinowitz (Co-PI) and Martin Wuhr (Co-PI) from Princeton University, and Yasuo Yoshikuni (Co-PI) from the DOE Joint Genome Institute. The team has made great progress in both tool development and fundamental understanding of these two non-model yeasts. In total, there were 40 research publications (one of them is still under review) and one patent application as well as numerous oral presentations.
60 APPLIED LIFE SCIENCES↗
Metabolic engineering of Caldicellulosiruptor bescii for 2,3-butanediol production from unpretreated lignocellulosic biomass and metabolic strategies for improving yields and titers
ABSTRACT The platform chemical 2,3-butanediol (2,3-BDO) is used to derive products, such as 1,3-butadiene and methyl ethyl ketone, for the chemical and fuel production industries. Efficient microbial 2,3-BDO production at industrial scales has not been achieved yet for various reasons, including product inhibition to host organisms, mixed stereospecificity in product formation, and dependence on expensive substrates (i.e., glucose). In this study, we explore engineering of a 2,3-BDO pathway inCaldicellulosiruptor bescii, an extremely thermophilic (optimal growth temperature = 78°C) and anaerobic bacterium that can break down crystalline cellulose and hemicellulose into fermentable C 5 and C 6 sugars. In addition, C. besciigrows on unpretreated plant biomass, such as switchgrass. Biosynthesis of 2,3-BDO involves three steps: two molecules of pyruvate are condensed into acetolactate; acetolactate is decarboxylated to acetoin, and finally, acetoin is reduced to 2,3-BDO.C. besciinatively produces acetoin; therefore, in order to complete the 2,3-BDO biosynthetic pathway,C. besciiwas engineered to produce a secondary alcohol dehydrogenase (sADH) to catalyze the final step. Two previously characterized, thermostable sADH enzymes with high affinity for acetoin, one from a bacterium and one from an archaeon, were tested independently. When either sADH was present inC. bescii,the recombinant strains were able to produce up to 2.5-mM 2,3-BDO from crystalline cellulose and xylan and 0.2-mM 2,3-BDO directly from unpretreated switchgrass. This serves as the basis for higher yields and productivities, and to this end, limiting factors and potential genetic targets for further optimization were assessed using the genome-scale metabolic model ofC. bescii. IMPORTANCE Lignocellulosic plant biomass as the substrate for microbial synthesis of 2,3-butanediol is one of the major keys toward cost-effective bio-based production of this chemical at an industrial scale. However, deconstruction of biomass to release the sugars for microbial growth currently requires expensive thermochemical and enzymatic pretreatments. In this study, the thermo-cellulolytic bacteriumCaldicellulosiruptor besciiwas successfully engineered to produce 2,3-butanediol from cellulose, xylan, and directly from unpretreated switchgrass. Genome-scale metabolic modeling ofC. besciiwas applied to adjust carbon and redox fluxes to maximize productivity of 2,3-butanediol, thereby revealing bottlenecks that require genetic modifications.
Biotechnology & Applied Microbiology↗
Corrosion-Resistant Plug Materials for Geothermal Well Fluid Control
Conventional cements and plugs are challenged by corrosion in CO 2 -rich and extreme geothermal environments, due to the hostile chemistry and high temperatures. Thermite-based sealing and well intervention technologies are being applied in the oil and gas industry, combining the energy delivery capability of thermite materials with the sealing characteristics of low melt temperature alloys. The thermite reaction products (ceramics) and the sealing alloys used in these plugs both have very attractive corrosion properties, and their operating envelopes extend into geothermal conditions. Thermite plugs and platforms, without supplemental sealing materials, have been considered for nuclear waste isolation, carbon sequestration, and geothermal applications due to the geochemical stability of the ceramic product and its very high service temperature. This study addresses corrosion resistance of the thermite reaction products. A range of engineered thermite systems which yield thermite reaction products including pure aluminum oxide, feldspar, or aluminosilicate solid solutions (in addition to the iron produced in thermite reactions) was developed. These materials were evaluated for their strong acid resistance (pH 1), carbonate resistance (sodium carbonate) and thermal shock resistance (600 °C heating → cold water quenching repeated three times). Performance of different materials was evaluated based on the changes in mechanical properties, water-fillable porosity, phase changes under stress conditions. The aluminosilicate product exhibited very good corrosion resistance, both from material loss and strength perspectives, while the other products performed with varying degrees of stability. This paper presents the results of the thermite corrosion studies and describes the novel tools being deployed, and under development, to satisfy challenging barrier and intervention applications.
02 PETROLEUM↗
Phenylpropanoid methyl esterase unlocks catabolism of aromatic biological nitrification inhibitors
Microbial nitrification of fertilizers represents is a significant global source of greenhouse gas emissions. This process increases emissions, fosters toxic algal blooms, and raises crop production costs. Some plants naturally release biological nitrification inhibitors to suppress ammonium-oxidizing microbes and reduce nitrification. Engineering nitrification inhibitor production into food and bioenergy crops via synthetic biology offers a promising mitigation strategy, but its success depends on addressing gaps in our understanding of inhibitor degradation in soil. This study begins to fill this gap by identifying a previously unknown microbial pathway for degrading phenylpropanoid methyl esters, a key class of aromatic nitrification inhibitors. Using transcriptomics and high-throughput functional genomics, we discovered genes essential for phenylpropanoid methyl ester degradation. Genetic and biochemical analyses revealed two novel enzymes, including a newly identified phenylpropanoid methyl esterase, that direct phenylpropanoid methyl esters into known metabolic pathways. Importantly, transferring these genes into bacteria capable of metabolizing other phenylpropanoids enabled them to use the methyl esters as a carbon source. This work provides critical insights into microbial nitrification inhibitor degradation, a poorly understood element of the nitrification cycle.
Genetic Engineering↗
Electrochemical CO2 conversion to formic acid through the Andora Process
Electrochemical utilization or conversion of CO2 can be used to convert waste CO2 into targeted high-value and cost-effective commercial products. Conventional processes for CO2 conversion to fuel sources are challenging and expensive due to their requirement for high temperatures and pressures. Electrochemically, a catalyst can be used at a fixed applied potential to reduce CO2 to form a desired product with less competition at modest operating conditions. Formic acid (FA) has recently become a product of interest for CO2 conversion due to its potential for hydrogen storage and fuel cell applications. Electrochemically, FA is produced through a direct two-electron transfer process involving CO2 with a proton source, requiring less energy input and fewer reaction steps than traditional processes. However, there remain significant obstacles for the broader-scale implementation of CO2 on the market, including competition with unwanted CO and H, the presence of molecular oxygen, and stability of the electrocatalyst. In order to overcome some of these challenges, a new continuous flow Andora Process was developed consisting of two separate cells to decouple electrochemical reduction of the charge carrier with the FA production via an engineered catalyst. Recent experimental results show that with appropriate design changes and operating conditions to the flow system, FA production above 500 mM can be achieved along with efficiencies above 80%. TEA and LCA assessments of the Andora Process show a potential for the reduction in the GWP potential and cost saving compared to the current comparative formic acid production process.
60 APPLIED LIFE SCIENCES↗
Effective Mechanisms for Improving Seed Oil Production in Pennycress (Thlaspi arvense L.) Highlighted by Integration of Comparative Metabolomics and Transcriptomics
Pennycress is a potentially lucrative biofuel crop due to its high content of long-chain unsaturated fatty acids, and because it uses non-conventional pathways to achieve efficient oil production. However, metabolic engineering is required to improve pennycress oilseed content and make it an economically viable source of aviation fuel. Research is warranted to determine if further upregulation of these non-conventional pathways could improve oil production within the species even more, which would indicate these processes serve as promising metabolic engineering targets and could provide the improvement necessary for economic feasibility of this crop. To test this hypothesis, we performed a comparative biomass, metabolomic, and transcriptomic analyses between a high oil accession (HO) and low oil accession (LO) of pennycress to assess potential factors required to optimize oil content. An evident reduction in glycolysis intermediates, improved oxidative pentose phosphate pathway activity, malate accumulation in the tricarboxylic acid cycle, and an anaplerotic pathway upregulation were noted in the HO genotype. Additionally, higher levels of threonine aldolase transcripts imply a pyruvate bypass mechanism for acetyl-CoA production. Nucleotide sugar and ascorbate accumulation also were evident in HO, suggesting differential fate of associated carbon between the two genotypes. An altered transcriptome related to lipid droplet (LD) biosynthesis and stability suggests a contribution to a more tightly-packed LD arrangement in HO cotyledons. In addition to the importance of central carbon metabolism augmentation, alternative routes of carbon entry into fatty acid synthesis and modification, as well as transcriptionally modified changes in LD regulation, are key aspects of metabolism and storage associated with economically favorable phenotypes of the species.
59 BASIC BIOLOGICAL SCIENCES↗