Effect of plant growth-promoting molecules on improving biomass productivity in DISCOVR production strains
Not Available
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Engineering topics
Dale, Taraka
Publications and source records attributed to Dale, Taraka.
Modified biosensors and biocatalysts and methods of use
Biosensors including a nucleic acid encoding a PcaU protein, a PobR protein, a CatM protein, a PcaR protein, or a TphR protein are provided. In some examples, the biosensors include a promoter regulated by the sensed molecule operably linked to a reporter gene. The biosensors may be included in a vector or in cells including one or more of the biosensors or vectors. Modified chorismate pyruvate lyase (UbiC) and modified paraoxonase (PON1) proteins including one or more amino acid substitutions are provided. Finally, methods of selecting biocatalysts with increased activity including transforming a library of cells expressing a biosensor with one or more nucleic acids encoding one or more mutations in a gene involved in a biosynthesis pathway, determining activity of the reporter protein; and selecting a cell with increased reporter protein activity as expressing a biocatalyst with increased activity are provided.
Jha, Ramesh K.↗
Targeted mutagenesis and high-throughput screening of diversified gene and promoter libraries for isolating gain-of-function mutations
Targeted mutagenesis of a promoter or gene is essential for attaining new functions in microbial and protein engineering efforts. In the burgeoning field of synthetic biology, heterologous genes are expressed in new host organisms. Similarly, natural or designed proteins are mutagenized at targeted positions and screened for gain-of-function mutations. Here, we describe methods to attain complete randomization or controlled mutations in promoters or genes. Combinatorial libraries of one hundred thousands to tens of millions of variants can be created using commercially synthesized oligonucleotides, simply by performing two rounds of polymerase chain reactions. With a suitably engineered reporter in a whole cell, these libraries can be screened rapidly by performing fluorescence-activated cell sorting (FACS). Within a few rounds of positive and negative sorting based on the response from the reporter, the library can rapidly converge to a few optimal or extremely rare variants with desired phenotypes. Library construction, transformation and sequence verification takes 6–9 days and requires only basic molecular biology lab experience. Screening the library by FACS takes 3–5 days and requires training for the specific cytometer used. Further steps after sorting, including colony picking, sequencing, verification, and characterization of individual clones may take longer, depending on number of clones and required experiments.
59 BASIC BIOLOGICAL SCIENCES↗
Development of integrated screening, cultivar optimization, and verification research (DISCOVR): A coordinated research-driven approach to improve microalgal productivity, composition, and culture stability for commercially viable biofuels production
To address major knowledge gaps and barriers to the commercial development of algal biomass for biofuels and co-products, a collaborative consortium, Development of Integrated Screening, Cultivar Optimization, and Verification Research (DISCOVR), was established in 2016. Funded by the U.S. Department of Energy (DOE) Bioenergy Technologies Office (BETO), this consortium constitutes a partnership between four DOE national laboratories - Pacific Northwest National Laboratory (PNNL), Los Alamos National Laboratory (LANL), the National Renewable Energy Laboratory (NREL), and Sandia National Laboratories (SNL) - and the Arizona Center for Algae Technology and Innovation (AzCATI) at Arizona State University. To address the barriers of strain selection for achieving high seasonal productivities with a suitable composition and culture resilience, a tiered strain down-selection pipeline is implemented. At Tier I, the temperature and salinity tolerance of strains is determined in flask cultures; at Tier II, the areal biomass productivity and composition is determined in climate-simulation photobioreactors; at Tier III, the productivity and culture stability are determined in outdoor raceways. The top performing strains move forward to long-term testing at the algae testbed site at AzCATI to generate annual biomass productivity data. Concurrent to the strain down-selection in the DISCOVR pipeline, hypotheses for increasing biomass productivity, shifting biomass composition to enhance intrinsic value, and improving culture stability and resistance to pests are also tested. Techno-economic analyses are carried out to determine whether promising findings from laboratory studies or proposed modifications in outdoor pond cultivation conditions translate into reductions in the minimum biomass selling price (MBSP). Notably, in the three years following the launch of DISCOVR, annual biomass productivity has increased from 11.7 to 17.6 g m -2 day -1 , resulting in an MBSP decrease from 824 to 611 $ ton -1 .
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Engineered microorganisms for the production of intermediates and final products
The present disclosure relates to a non-naturally occurring microorganism that includes an endogenous genetic deletion that eliminates the expression of at least a pyruvate kinase, where the genetically modified prokaryotic microorganism is capable of producing 3-deoxy-D-arabino-heptulosonate-7-phosphate.
Johnson, Christopher W.↗
Bio-Optimized Technologies to Keep Thermoplastics out of Landfills and the Environment (BOTTLE)
Plastics have revolutionized modern life, but reliance on these fossil-based materials that persist for centuries is causing a pollution crisis and contributing to greenhouse gas (GHG) emissions. To develop new technologies to address this problem, the Bio-Optimized Technologies to keep Thermoplastics out of Landfills and the Environment (BOTTLE) Consortium will deliver selective, scalable technologies to enable cost-effective recycling, upcycling, and increased energy efficiency. BOTTLE is an interdisciplinary team of experts that aim to develop selective, scalable processes to deconstruct and upcycle today's plastics and thermosets, redesign tomorrow's plastics to be recyclable-by-design (RBD) and derived from both bio-based and plastic waste-based feedstocks, work with industrial partners across the value chain to catalyze the circular economy for plastics, and leverage AMO and BETO investments in analysis-guided R&D, integrated process development, chemical and biological catalysis, materials characterization, modeling, and data science. BOTTLE is guided by techno-economic analysis (TEA) and supply chain-based life-cycle assessment (LCA). BOTTLE comprises members from ten partner institutions. Primary outcomes to date include establishment of a full consortium, impactful, benchmarking analyses that will be important for the plastics recycling and upcycling community, and multiple impactful, high-impact publications across the breadth of our research portfolio.
bio-optimized↗
Precise Genomic Riboregulator Control of Metabolic Flux in Microbial Systems
Not Available
59 BASIC BIOLOGICAL SCIENCES↗
High-Quality Genome Assembly of Nannochloris desiccata 2437 and Its Associated Bacterial Community
High-quality genome sequences were generated for the nonaxenic marine microalga Nannochloris desiccata UTEX 2437 and eight of its associated environmental bacterial species. N. desiccata UTEX 2437 is diploid, and its 20.738-Mbp nuclear genome sequence is assembled in 29 contigs.
59 BASIC BIOLOGICAL SCIENCES↗
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).
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Gene Amplification, Laboratory Evolution, and Biosensor Screening Reveal MucK as a Terephthalic Acid Transporter in Acinetobacter baylyi ADP1
Microbial terephthalic acid (TPA) catabolic pathways are conserved among the few bacteria known to turnover this xenobiotic aromatic compound. However, to date there are few reported cases in which this pathway has been successfully expressed in heterologous hosts to impart efficient utilization of TPA as a sole carbon source. In this work, we aimed to engineer TPA conversion in Acinetobacter baylyi ADP1 via the heterologous expression of catabolic and transporter genes from a native TPA-utilizing bacterium. Specifically, we obtained ADP1-derived strains capable of growing on TPA as the sole carbon source using chromosomal insertion and targeted amplification of the tph catabolic operon from Comamonas sp. E6. Adaptive laboratory evolution was then used to improve growth on this substrate. TPA consumption rates of the evolved strains, which retained multiple copies of the tph genes, were ~0.2 g/L/h (or ~1 g TPA/g cells/h), similar to that of Comamonas sp. E6 and almost 2-fold higher than that of Rhodococcus jostii RHA1, another native TPA-utilizing strain. To evaluate TPA transport in the evolved ADP1 strains, we engineered a TPA biosensor consisting of the transcription factor TphR and a fluorescent reporter. In combination with whole-genome sequencing, the TPA biosensor revealed that transport of TPA was not mediated by the heterologous proteins from Comamonas sp. E6. Instead, the endogenous ADP1 muconate transporter MucK, a member of the major facilitator superfamily, was responsible for TPA transport in several evolved strains in which MucK variants were found to enhance TPA uptake. Furthermore, the IclR-type transcriptional regulator DcaS was identified as a repressor of mucK expression. Overall, this work presents an unexpected function of a native protein identified through gene amplification, adaptive laboratory evolution, and a combination of screening methods. This study also provides a TPA biosensor for application in ADP1 and identifies transporter variants for use in metabolic engineering applications focused on plastic upcycling of polyesters.
59 BASIC BIOLOGICAL SCIENCES↗
DISCOVR: Development of Integrated Screening, Cultivar Optimization, and Verification Research
The DISCOVR consortium has developed and is applying an integrated platform and workflow for standardized, deep characterization of highly productive and resilient microalgae strains. New strains are screened using three consecutive tiers in a conceptual down-selection funnel to arrive at the most promising strains. At tier I, strains are screened on gradient incubators to determine their temperature and salinity tolerance range, and to evaluate their resistance to infectious agents (e.g., chytrids). At tier II, the strains’ winter and summer season biomass productivities are quantified in Laboratory Environmental Algae Pond Simulator (LEAPS) photobioreactors, and biomass composition is determined under N-replete and N-deplete conditions. At tier III, the best winter and summer season strains are evaluated in indoor crash ponds to determine their resilience to induced infections, and strains are tested in outdoor raceway ponds to confirm high biomass productivity and culture stability. The top strains are then evaluated in seasonal SOT outdoor pond culture trials at AzCATI, the dedicated Department of Energy SOT (State of Technology) testbed. Additional research is carried out on evaluating growth promoting molecules, reducing the impact of oxygen inhibition, optimizing pond operational conditions, measuring compositional shift dynamics, developing integrated pest management strategies, analysing culture health using 96 well-plate tools, implementing spectroradiometric monitoring and using machine learning to predict culture crashes.
Huesemann, Michael H↗
Bioprocessing Separations Consortium Three-Year Overview: Technical Advances, Process Economics Influence, and State of the Science
The Bioprocessing Separations Consortium solves separations challenges that are unique to bioprocessing. To do this, the Consortium uses two methods: applying existing technologies to new challenges and developing new technologies that may address these unique challenges better than today’s commercial technologies. In its research and development, the Consortium leverages its three core capabilities: materials development and evaluation, process development, and analysis and computation. In its first three years, from 2016 to 2019, the Consortium addressed four critical challenges in biochemical and thermochemical processing. First, the Consortium targeted the fractionation of lignin to enable valorization of this portion of biomass that offers diverse, complex, and valuable building blocks and products. Second, Consortium researchers developed technologies to enable process intensification, which can reduce equipment needs, energy consumption, and waste generation, thereby cutting bioprocessing capital costs and rendering processes more efficient. Third, the Consortium sought to recover carbon from dilute aqueous streams that are common to bioprocessing; recovering dilute carbon can improve process efficiency and economics. Finally, Consortium researchers designed and developed new materials and catalysts to reduce targeted foulants and poisons in bioprocessing streams that can limit the lifetime of downstream catalysts or fermenting microorganisms. Table 1 lists the technologies that were examined and places them in the context of the Consortium’s capabilities, types of bioprocesses, and critical challenges in bioprocessing separations. Overall, across these projects, we have developed separations technologies for 10 bioprocesses, addressed 9 target compounds in bioprocessing, developed 10 materials, and evaluated 4 processes for cost and sustainability.
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Bioprocessing Separations Consortium: Three-Year Overview - Technical Advances, Process Economics Influence, and State of the Science
The Bioprocessing Separations Consortium solves separations challenges that are unique to bioprocessing. To do this, the Consortium uses two methods: applying existing technologies to new challenges and developing new technologies that may address these unique challenges better than today’s commercial technologies. In its research and development, the Consortium leverages its three core capabilities: materials development and evaluation, process development, and analysis and computation. In its first three years, from 2016 to 2019, the Consortium addressed four critical challenges in biochemical and thermochemical processing. First, the Consortium targeted the fractionation of lignin to enable valorization of this portion of biomass that offers diverse, complex, and valuable building blocks and products. Second, Consortium researchers developed technologies to enable process intensification, which can reduce equipment needs, energy consumption, and waste generation, thereby cutting bioprocessing capital costs and rendering processes more efficient. Third, the Consortium sought to recover carbon from dilute aqueous streams that are common to bioprocessing; recovering dilute carbon can improve process efficiency and economics. Finally, Consortium researchers designed and developed new materials and catalysts to reduce targeted foulants and poisons in bioprocessing streams that can limit the lifetime of downstream catalysts or fermenting microorganisms. Table 1 lists the technologies that were examined and places them in the context of the Consortium’s capabilities, types of bioprocesses, and critical challenges in bioprocessing separations. Overall, across these projects, we have developed separations technologies for 10 bioprocesses, addressed 9 target compounds in bioprocessing, developed 10 materials, and evaluated 4 processes for cost and sustainability.
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