The document discusses diversifying isoprenoid platforms through the use of atypical carbon substrates and non-model microorganisms. Recent studies have expanded isoprenoid biosynthesis by using non-model organisms that can metabolize C1 substrates and atypical carbon sources. This provides metabolic advantages over conventional microbial chassis by addressing issues like substrate costs and emissions. Harnessing metabolic features of non-model organisms and substrates like lignocellulosic biomass and C1 compounds could reduce production costs and make isoprenoid platforms more commercially viable. Systems engineering strategies are particularly interesting for optimizing carbon 1 metabolism in non-model organisms.
This document discusses an integrated acetic acid based one-pot ethanolamine acetate pretreatment process for efficient depolymerization of poplar polysaccharides. Key points:
(1) The new process simultaneously removes 88% of hemicellulose and extracts up to 46% of lignin from poplar biomass.
(2) It yields over 80% enzyme-hydrolyzed glucose, attributed to increased accessible surface area of cellulose.
(3) Analysis indicates the ionic liquid component is a good lignin solvent, leading to higher delignification.
Overall, integrating ionic liquid with acid pretreatment is a promising strategy for effective pretreatment of woody lignocellulose.
The document describes a study that engineered the chemolithoautotrophic bacterium Thiobacillus denitrificans to enhance fatty acid production. A thioesterase gene from E. coli was integrated into the T. denitrificans chromosome under control of different promoters. This led to up to 52-fold higher fatty acid titers compared to the wild-type strain when the bacteria were grown anaerobically using reduced sulfur compounds, nitrate, and carbon dioxide. The results demonstrate the potential to engineer sulfur-oxidizing bacteria to produce renewable fuels from sulfide-containing waste streams.
This document summarizes three papers related to biological conversion of lignocellulosic biomass. The first paper evaluates two red yeast species for their ability to assimilate sugars and aromatics from engineered Arabidopsis plants and successfully converts these products into biofuel precursors. The second paper identifies small drug resistance pumps in Bacillus bacteria that confer tolerance to ionic liquids used in biomass pretreatment and characterizes riboswitches that regulate these pumps. The third paper finds that engineered Pseudomonas putida produces more methyl ketones, a promising diesel blendstock, when grown on plant hydrolysates compared to sugars, due to plant-derived amino acids.
The document describes three studies related to biofuels and bioproducts:
1) A study characterized a novel lactam biosensor from Pseudomonas putida with unprecedented sensitivity for valerolactam and caprolactam. Through engineering, they developed biosensors with a wide dynamic range.
2) A study used quantum calculations and simulations to understand how Keggin-type polyoxometalate ionic liquids dissolve lignin. Calculations showed interactions between the ionic liquid and lignin model compound.
3) A study determined the mechanism of regioselectivity in an unusual bacterial acyl-CoA dehydrogenase, TcsD, which catalyzes terminal alkene formation. Struct
This document summarizes key outcomes and challenges in using synthetic and systems biology approaches for the microbial production of commodity chemicals. Some of the main challenges discussed include balancing economic potential and biological feasibility when selecting target molecules, optimizing protein expression levels for maximum production, preventing toxicity from metabolic intermediates and proteins, and successfully scaling up laboratory processes to commercial volumes. Integrated approaches that combine pathway engineering with host engineering and process modeling are presented as promising ways to address these challenges. The review outlines the multi-step process from initial target selection to commercial scale-up and highlights ongoing needs in dynamic pathway regulation and scale-up capabilities.
The document describes the development of a high throughput platform for screening glycoside hydrolase enzymes based on oxime-NIMS. Key points:
1) JBEI developed an approach integrating oxime chemistries, acoustic printing and nanostructure-initiator mass spectrometry (Oxime-NIMS) to quantitatively analyze glycan products of GH reactions, including with complex biomass substrates.
2) They defined a standard panel of 12 substrates spanning plant cell wall linkages.
3) The platform was automated and tested by studying cellulases and their synergistic combinations across reaction conditions - generating datasets to enable enzyme cocktail design.
JBEI Research Highlights - October 2018 Irina Silva
This document discusses three approaches:
1) Engineering E. coli to modulate membrane lipid composition and control cellular respiration through changes in inner membrane viscosity.
2) Applying synthetic biology tools like promoter engineering and metabolic pathway construction to investigate fundamental biochemical questions that cannot be easily studied otherwise.
3) Outlining the background, approach, and outcomes of using E. coli to produce renewable jet fuel precursors like sesquiterpenes from isoprenoid pathways.
This document describes a study that evaluated two pretreatment methods - ionic liquid (IL) pretreatment and organosolv (OV) pretreatment - for producing ethanol from agave bagasse via sequential saccharification and fermentation (SESF). Both pretreatments significantly reduced lignin and xylan content. High sugar conversions over 18 hours and ethanol yields of 12.1-12.7 kg/100kg untreated bagasse were achieved. Compared to corn or sugarcane, agave bagasse pretreated in this way could produce comparable or higher ethanol yields per hectare, demonstrating its potential as a feedstock for biofuel production.
This document discusses an integrated acetic acid based one-pot ethanolamine acetate pretreatment process for efficient depolymerization of poplar polysaccharides. Key points:
(1) The new process simultaneously removes 88% of hemicellulose and extracts up to 46% of lignin from poplar biomass.
(2) It yields over 80% enzyme-hydrolyzed glucose, attributed to increased accessible surface area of cellulose.
(3) Analysis indicates the ionic liquid component is a good lignin solvent, leading to higher delignification.
Overall, integrating ionic liquid with acid pretreatment is a promising strategy for effective pretreatment of woody lignocellulose.
The document describes a study that engineered the chemolithoautotrophic bacterium Thiobacillus denitrificans to enhance fatty acid production. A thioesterase gene from E. coli was integrated into the T. denitrificans chromosome under control of different promoters. This led to up to 52-fold higher fatty acid titers compared to the wild-type strain when the bacteria were grown anaerobically using reduced sulfur compounds, nitrate, and carbon dioxide. The results demonstrate the potential to engineer sulfur-oxidizing bacteria to produce renewable fuels from sulfide-containing waste streams.
This document summarizes three papers related to biological conversion of lignocellulosic biomass. The first paper evaluates two red yeast species for their ability to assimilate sugars and aromatics from engineered Arabidopsis plants and successfully converts these products into biofuel precursors. The second paper identifies small drug resistance pumps in Bacillus bacteria that confer tolerance to ionic liquids used in biomass pretreatment and characterizes riboswitches that regulate these pumps. The third paper finds that engineered Pseudomonas putida produces more methyl ketones, a promising diesel blendstock, when grown on plant hydrolysates compared to sugars, due to plant-derived amino acids.
The document describes three studies related to biofuels and bioproducts:
1) A study characterized a novel lactam biosensor from Pseudomonas putida with unprecedented sensitivity for valerolactam and caprolactam. Through engineering, they developed biosensors with a wide dynamic range.
2) A study used quantum calculations and simulations to understand how Keggin-type polyoxometalate ionic liquids dissolve lignin. Calculations showed interactions between the ionic liquid and lignin model compound.
3) A study determined the mechanism of regioselectivity in an unusual bacterial acyl-CoA dehydrogenase, TcsD, which catalyzes terminal alkene formation. Struct
This document summarizes key outcomes and challenges in using synthetic and systems biology approaches for the microbial production of commodity chemicals. Some of the main challenges discussed include balancing economic potential and biological feasibility when selecting target molecules, optimizing protein expression levels for maximum production, preventing toxicity from metabolic intermediates and proteins, and successfully scaling up laboratory processes to commercial volumes. Integrated approaches that combine pathway engineering with host engineering and process modeling are presented as promising ways to address these challenges. The review outlines the multi-step process from initial target selection to commercial scale-up and highlights ongoing needs in dynamic pathway regulation and scale-up capabilities.
The document describes the development of a high throughput platform for screening glycoside hydrolase enzymes based on oxime-NIMS. Key points:
1) JBEI developed an approach integrating oxime chemistries, acoustic printing and nanostructure-initiator mass spectrometry (Oxime-NIMS) to quantitatively analyze glycan products of GH reactions, including with complex biomass substrates.
2) They defined a standard panel of 12 substrates spanning plant cell wall linkages.
3) The platform was automated and tested by studying cellulases and their synergistic combinations across reaction conditions - generating datasets to enable enzyme cocktail design.
JBEI Research Highlights - October 2018 Irina Silva
This document discusses three approaches:
1) Engineering E. coli to modulate membrane lipid composition and control cellular respiration through changes in inner membrane viscosity.
2) Applying synthetic biology tools like promoter engineering and metabolic pathway construction to investigate fundamental biochemical questions that cannot be easily studied otherwise.
3) Outlining the background, approach, and outcomes of using E. coli to produce renewable jet fuel precursors like sesquiterpenes from isoprenoid pathways.
This document describes a study that evaluated two pretreatment methods - ionic liquid (IL) pretreatment and organosolv (OV) pretreatment - for producing ethanol from agave bagasse via sequential saccharification and fermentation (SESF). Both pretreatments significantly reduced lignin and xylan content. High sugar conversions over 18 hours and ethanol yields of 12.1-12.7 kg/100kg untreated bagasse were achieved. Compared to corn or sugarcane, agave bagasse pretreated in this way could produce comparable or higher ethanol yields per hectare, demonstrating its potential as a feedstock for biofuel production.
This study analyzed changes in the bacterial and fungal microbiome of soil samples treated with biosolarization, which uses solar heating and organic amendments. Sequencing analysis found that biosolarization had a stronger impact on the relative abundance of bacterial phyla than fungi. Network analysis identified microbial clusters correlated with volatile fatty acid accumulation, suggesting genera like Clostridium, Weissella and Acetobacter can tolerate and potentially produce these compounds. The results provide insight into structural changes in the soil microbiome during biosolarization as related to volatile fatty acid levels.
- Researchers studied the roles of three major prolyl-4-hydroxylase (P4H) isoforms expressed in Arabidopsis roots.
- P4H5 was found to have an essential function different from P4H2 and P4H13, which are partly redundant.
- Protein-protein interaction studies revealed the P4H proteins form homodimers and heterodimers, and P4H5 is necessary for the targeting of P4H2 to the Golgi.
- Understanding the complex regulation and interactions of P4H isoforms impacts root hair expansion and cell wall formation.
JBEI Research Highlights - January 2017Irina Silva
The document describes a study that engineered E. coli strains to overexpress the ptsI gene involved in glucose uptake. The strains were cultivated under nitrogen starvation conditions to limit growth during production. Overexpression of ptsI maintained higher glucose uptake and metabolic rates under starvation, leading to a fourfold increase in fatty alcohol production compared to exponential growth. The results demonstrate the potential of limiting growth through nitrogen starvation coupled with ptsI overexpression to improve biofuel and bioproduct yields in E. coli.
JBEI Research Highlights - February 2017Irina Silva
This document summarizes a study investigating the enzymatic degradation of lignin model compounds by versatile peroxidase (VP). The key findings are:
1) VP can catalyze both the polymerization and depolymerization of lignin, with the reaction pathway depending on factors like pH, H2O2 concentration, and the functional groups on the lignin compounds.
2) Degradation of phenolic β-O-4 lignin dimers by VP proceeds through oxidation, followed by competing polymerization or depolymerization reactions depending on conditions.
3) The functional group at the 5 position of guaiacyl units influences whether polymerization or depolymerization occurs.
JBEI Research Highlight Slides - February 2021SaraHarmon4
This study analyzed goat gut microbiomes to understand lignocellulose breakdown. Researchers enriched over 400 microbial consortia from goat feces under different conditions. They assembled 719 high-quality genomes, including bacteria, archaea, and fungi. Anaerobic fungi dominated the most active consortia and outperformed bacterial consortia in degrading cellulose and producing methane. Metabolic pathway analysis suggested cross-domain partnerships between fungi and methanogens enabled different metabolic outputs than bacterial consortia. The findings provide insight into natural biomass breakdown that can inform industrial bioprocessing.
This document discusses several studies related to feedstocks for aviation biofuels. It provides an overview of major feedstock options globally, including their regional production, challenges to increasing production levels, and forecasts for bioenergy use to 2050. While multiple feedstocks will likely be required, the availability and logistics of feedstocks may be the main determinants in what fuels are produced and where. Significant research, development, and infrastructure investments are still needed to enable aviation biofuels to replace fossil fuels, but there is likely sufficient global feedstock potential if road transport biofuel demand decreases through electric vehicle advancements.
- The document discusses four types of forage sorghum (brown-midrib, non-brown-midrib, photoperiod sensitive, and photoperiod insensitive) and their potential impact on the minimum ethanol selling price at a biorefinery using ionic liquid pretreatment.
- Simulation results show that non-photoperiod sensitive sorghum may result in lower cost biofuels compared to high-yielding photoperiod sensitive varieties under certain conditions.
- If lignin value increases, non-brown-midrib varieties become the most attractive option due to their higher biomass yield outweighing the lower lignin content of brown-midrib varieties.
JBEI Research Highlights - October 2021SaraHarmon4
This document summarizes a study that evaluated the potential for nutrient recovery from wet organic waste processing facilities in California to offset synthetic fertilizer demand. The study found that recovering nitrogen and phosphorus from organic waste streams through anaerobic digestion and separation techniques could meet 11% of the state's nitrogen and 29% of phosphorus fertilizer needs. Recovered nutrients would be in the form of liquid fertilizer, struvite, and compost. The approach provides a foundation for analyzing national-level nutrient flows and recovery potentials from bioenergy production.
The document discusses several studies related to engineering plants for improved biomass composition for biofuel production. One study found that Arabidopsis plants engineered to have low lignin and xylan content showed increased drought tolerance compared to wild-type plants. The engineered plants exhibited lower water loss, up-regulation of drought response genes, and a stronger response to the plant hormone ABA. This demonstrates that modifying secondary cell walls to improve biomass composition does not necessarily compromise plant resilience to the environment.
This document summarizes a study that developed an optimized process for the sustainable bioproduction of the blue pigment indigoidine by the yeast Rhodosporidium toruloides. Key findings include:
- R. toruloides was engineered to produce indigoidine, achieving a high titer of 85 g/L from glucose and demonstrating production from renewable carbon sources like sorghum hydrolysates.
- This represents the first heterologous production of a non-ribosomal peptide (NRP) in R. toruloides, extending the range of microbial hosts that can produce NRPs sustainably.
- Production of indigoidine demonstrates an alternative biobased route
JBEI Research Highlight Slides - August 2022SaraHarmon4
The document discusses engineering yeast to produce the anti-cancer drug vinblastine through a long biosynthetic pathway involving 30 enzymatic steps from multiple plants. This provides an alternative microbial supply chain that does not rely on low-yielding extraction from plants. The engineered yeast is able to produce the vinblastine precursors catharanthine and vindoline, demonstrating the potential for sustainable production of complex plant metabolites through synthetic biology.
This document summarizes three papers related to biological and environmental research. The first paper discusses a review of scaling up ionic liquid-based biomass conversion processes and highlights their advantages for bioenergy. The second paper reviews applications of targeted proteomics in metabolic engineering and its potential integration with machine learning. The third paper describes a microfluidic system that automates CRISPR-based strain engineering at scale.
JBEI Research Highlights - November 2017 Irina Silva
This document summarizes the development and testing of a quorum sensing (QS)-mediated gene expression system to control bisabolene production in engineered E. coli. Researchers developed a QS system using the LuxI/R genes from Vibrio fischeri to induce expression of the bisabolene production pathway without the need for external inducers. The best QS strain, with the sensor genes integrated into the genome and an optimized response plasmid, produced 1.1 g/L of bisabolene, a 44% improvement over previous inducible systems. This QS-based system provided defined and homogeneous gene expression and production compared to inducible controls.
This document summarizes the key outcomes, background, significance, and approach of a study that investigated the effects of glycerol thermal processing (GTP) on lignin structure through NMR analysis. The main outcomes were that GTP effectively breaks bonds within lignin, generating smaller molecular weight lignin fragments that are thermally stable up to temperatures over 290°C. The background discusses utilizing lignin for specialty products. The significance is that GTP generates lignin suitable for use as a thermoplastic co-product. The approach involved comparing the properties of GTP lignin to lignin from other processes through structural analysis.
Ionic liquid pretreatment is an effective method for pretreating various biomass feedstocks. Ionic liquids can dissolve up to 20% cellulose at room temperature. Studies have shown that certain ionic liquids are highly effective at pretreating biomass like switchgrass, increasing enzyme accessibility and decreasing lignin content. Pretreatment with ionic liquids generates high sugar yields for both single and mixed feedstocks. Ionic liquid pretreatment of densified, mixed feedstocks performs as well as or better than untreated feedstocks.
Engineered Thiobacillus denitrificans produced up to 52 times more fatty acids than the wild-type strain when a modified thioesterase gene from E. coli was integrated into its chromosome under control of two native promoters. Fatty acid production was tested during growth of the engineered strains on thiosulfate, nitrate and carbon dioxide. This proof-of-principle study suggests engineering sulfur-oxidizing bacteria to overproduce fatty acid-derived products could simultaneously produce renewable fuels and remediate sulfide-contaminated wastewater.
This document summarizes several research studies:
1. One study investigated the metabolic flexibility of Pseudomonas taiwanensis VLB120 by knocking out NADH dehydrogenases and performing multi-omics analysis. It revealed the bacterium's high robustness and proposed a metabolic response to type-2 NADH dehydrogenase deficiency.
2. Another characterized the BorB thioesterase from Streptomyces parvulus, determining its structure provides a substrate binding site and specificity.
3. A third engineered Pseudomonas putida to produce bisdemethoxycurcumin by leveraging its native lignin catabolism pathways.
4. A fourth studied Aspergillus niger's
This study optimized terpene production in the yeast Rhodosporidium toruloides by engineering enzymes in the mevalonate pathway. Multi-omic analysis of bisabolene-producing strains identified specific enzymes for optimization, including HMG-CoA reductase and mevalonate kinases. Optimization of these enzymes for two terpenes, 1,8-cineole and bisabolene, improved titers to 1.4 g/L and 2.6 g/L respectively. The study demonstrates improving terpene production from lignocellulosic biomass in R. toruloides, an efficient host for converting renewable carbon sources.
This study evaluated methods for preserving microbial communities enriched on switchgrass biomass. High-throughput sequencing showed the communities shifted during initial enrichment but remained active after storage. Storage in liquid nitrogen without cryoprotectants resulted in variable preservation of dominant microbes, while cryopreservation with DMSO or glycerol provided consistent preservation. Despite shifts in relative abundance, the preserved samples retained an active community, suggesting the presence rather than abundance of microbes is important for activity.
JBEI Research Highlights Slides - October 2022SaraHarmon4
This document summarizes three research articles from the Office of Biological and Environmental Research.
The first article describes an approach to engineer permeability in microfluidic compartments, enabling sustained multi-cycle protein production in a cell-free system and enhanced environmental fitness for bacteria-enclosing compartments.
The second article examines carbon metabolism in soil by tracking stable isotope enrichment of metabolites from various carbon sources, finding profiles varied more by source than time and corresponded to differences in active microbial populations.
The third article compares performance of parallel microbiomes cultivated on sorghum, finding actinobacteria differentiated outcomes and network reconstructions revealed enzyme-linked processing stages.
JBEI Research Highlights Slides - September 2022SaraHarmon4
This study developed a method for in situ synthesis of protic ionic liquids (PILs) for lignocellulosic biomass pretreatment. By mixing the components of the PIL ethanolamine acetate directly with biomass prior to pretreatment, similar sugar yields were achieved as compared to using pure PIL, but at significantly lower cost. Techno-economic and life-cycle analyses indicated this approach promotes improved economic and environmental benefits compared to using pure PIL. The in situ PIL synthesis method provides a simple and effective way to lower the costs and impacts of ionic liquid based biomass processing.
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This study analyzed changes in the bacterial and fungal microbiome of soil samples treated with biosolarization, which uses solar heating and organic amendments. Sequencing analysis found that biosolarization had a stronger impact on the relative abundance of bacterial phyla than fungi. Network analysis identified microbial clusters correlated with volatile fatty acid accumulation, suggesting genera like Clostridium, Weissella and Acetobacter can tolerate and potentially produce these compounds. The results provide insight into structural changes in the soil microbiome during biosolarization as related to volatile fatty acid levels.
- Researchers studied the roles of three major prolyl-4-hydroxylase (P4H) isoforms expressed in Arabidopsis roots.
- P4H5 was found to have an essential function different from P4H2 and P4H13, which are partly redundant.
- Protein-protein interaction studies revealed the P4H proteins form homodimers and heterodimers, and P4H5 is necessary for the targeting of P4H2 to the Golgi.
- Understanding the complex regulation and interactions of P4H isoforms impacts root hair expansion and cell wall formation.
JBEI Research Highlights - January 2017Irina Silva
The document describes a study that engineered E. coli strains to overexpress the ptsI gene involved in glucose uptake. The strains were cultivated under nitrogen starvation conditions to limit growth during production. Overexpression of ptsI maintained higher glucose uptake and metabolic rates under starvation, leading to a fourfold increase in fatty alcohol production compared to exponential growth. The results demonstrate the potential of limiting growth through nitrogen starvation coupled with ptsI overexpression to improve biofuel and bioproduct yields in E. coli.
JBEI Research Highlights - February 2017Irina Silva
This document summarizes a study investigating the enzymatic degradation of lignin model compounds by versatile peroxidase (VP). The key findings are:
1) VP can catalyze both the polymerization and depolymerization of lignin, with the reaction pathway depending on factors like pH, H2O2 concentration, and the functional groups on the lignin compounds.
2) Degradation of phenolic β-O-4 lignin dimers by VP proceeds through oxidation, followed by competing polymerization or depolymerization reactions depending on conditions.
3) The functional group at the 5 position of guaiacyl units influences whether polymerization or depolymerization occurs.
JBEI Research Highlight Slides - February 2021SaraHarmon4
This study analyzed goat gut microbiomes to understand lignocellulose breakdown. Researchers enriched over 400 microbial consortia from goat feces under different conditions. They assembled 719 high-quality genomes, including bacteria, archaea, and fungi. Anaerobic fungi dominated the most active consortia and outperformed bacterial consortia in degrading cellulose and producing methane. Metabolic pathway analysis suggested cross-domain partnerships between fungi and methanogens enabled different metabolic outputs than bacterial consortia. The findings provide insight into natural biomass breakdown that can inform industrial bioprocessing.
This document discusses several studies related to feedstocks for aviation biofuels. It provides an overview of major feedstock options globally, including their regional production, challenges to increasing production levels, and forecasts for bioenergy use to 2050. While multiple feedstocks will likely be required, the availability and logistics of feedstocks may be the main determinants in what fuels are produced and where. Significant research, development, and infrastructure investments are still needed to enable aviation biofuels to replace fossil fuels, but there is likely sufficient global feedstock potential if road transport biofuel demand decreases through electric vehicle advancements.
- The document discusses four types of forage sorghum (brown-midrib, non-brown-midrib, photoperiod sensitive, and photoperiod insensitive) and their potential impact on the minimum ethanol selling price at a biorefinery using ionic liquid pretreatment.
- Simulation results show that non-photoperiod sensitive sorghum may result in lower cost biofuels compared to high-yielding photoperiod sensitive varieties under certain conditions.
- If lignin value increases, non-brown-midrib varieties become the most attractive option due to their higher biomass yield outweighing the lower lignin content of brown-midrib varieties.
JBEI Research Highlights - October 2021SaraHarmon4
This document summarizes a study that evaluated the potential for nutrient recovery from wet organic waste processing facilities in California to offset synthetic fertilizer demand. The study found that recovering nitrogen and phosphorus from organic waste streams through anaerobic digestion and separation techniques could meet 11% of the state's nitrogen and 29% of phosphorus fertilizer needs. Recovered nutrients would be in the form of liquid fertilizer, struvite, and compost. The approach provides a foundation for analyzing national-level nutrient flows and recovery potentials from bioenergy production.
The document discusses several studies related to engineering plants for improved biomass composition for biofuel production. One study found that Arabidopsis plants engineered to have low lignin and xylan content showed increased drought tolerance compared to wild-type plants. The engineered plants exhibited lower water loss, up-regulation of drought response genes, and a stronger response to the plant hormone ABA. This demonstrates that modifying secondary cell walls to improve biomass composition does not necessarily compromise plant resilience to the environment.
This document summarizes a study that developed an optimized process for the sustainable bioproduction of the blue pigment indigoidine by the yeast Rhodosporidium toruloides. Key findings include:
- R. toruloides was engineered to produce indigoidine, achieving a high titer of 85 g/L from glucose and demonstrating production from renewable carbon sources like sorghum hydrolysates.
- This represents the first heterologous production of a non-ribosomal peptide (NRP) in R. toruloides, extending the range of microbial hosts that can produce NRPs sustainably.
- Production of indigoidine demonstrates an alternative biobased route
JBEI Research Highlight Slides - August 2022SaraHarmon4
The document discusses engineering yeast to produce the anti-cancer drug vinblastine through a long biosynthetic pathway involving 30 enzymatic steps from multiple plants. This provides an alternative microbial supply chain that does not rely on low-yielding extraction from plants. The engineered yeast is able to produce the vinblastine precursors catharanthine and vindoline, demonstrating the potential for sustainable production of complex plant metabolites through synthetic biology.
This document summarizes three papers related to biological and environmental research. The first paper discusses a review of scaling up ionic liquid-based biomass conversion processes and highlights their advantages for bioenergy. The second paper reviews applications of targeted proteomics in metabolic engineering and its potential integration with machine learning. The third paper describes a microfluidic system that automates CRISPR-based strain engineering at scale.
JBEI Research Highlights - November 2017 Irina Silva
This document summarizes the development and testing of a quorum sensing (QS)-mediated gene expression system to control bisabolene production in engineered E. coli. Researchers developed a QS system using the LuxI/R genes from Vibrio fischeri to induce expression of the bisabolene production pathway without the need for external inducers. The best QS strain, with the sensor genes integrated into the genome and an optimized response plasmid, produced 1.1 g/L of bisabolene, a 44% improvement over previous inducible systems. This QS-based system provided defined and homogeneous gene expression and production compared to inducible controls.
This document summarizes the key outcomes, background, significance, and approach of a study that investigated the effects of glycerol thermal processing (GTP) on lignin structure through NMR analysis. The main outcomes were that GTP effectively breaks bonds within lignin, generating smaller molecular weight lignin fragments that are thermally stable up to temperatures over 290°C. The background discusses utilizing lignin for specialty products. The significance is that GTP generates lignin suitable for use as a thermoplastic co-product. The approach involved comparing the properties of GTP lignin to lignin from other processes through structural analysis.
Ionic liquid pretreatment is an effective method for pretreating various biomass feedstocks. Ionic liquids can dissolve up to 20% cellulose at room temperature. Studies have shown that certain ionic liquids are highly effective at pretreating biomass like switchgrass, increasing enzyme accessibility and decreasing lignin content. Pretreatment with ionic liquids generates high sugar yields for both single and mixed feedstocks. Ionic liquid pretreatment of densified, mixed feedstocks performs as well as or better than untreated feedstocks.
Engineered Thiobacillus denitrificans produced up to 52 times more fatty acids than the wild-type strain when a modified thioesterase gene from E. coli was integrated into its chromosome under control of two native promoters. Fatty acid production was tested during growth of the engineered strains on thiosulfate, nitrate and carbon dioxide. This proof-of-principle study suggests engineering sulfur-oxidizing bacteria to overproduce fatty acid-derived products could simultaneously produce renewable fuels and remediate sulfide-contaminated wastewater.
This document summarizes several research studies:
1. One study investigated the metabolic flexibility of Pseudomonas taiwanensis VLB120 by knocking out NADH dehydrogenases and performing multi-omics analysis. It revealed the bacterium's high robustness and proposed a metabolic response to type-2 NADH dehydrogenase deficiency.
2. Another characterized the BorB thioesterase from Streptomyces parvulus, determining its structure provides a substrate binding site and specificity.
3. A third engineered Pseudomonas putida to produce bisdemethoxycurcumin by leveraging its native lignin catabolism pathways.
4. A fourth studied Aspergillus niger's
This study optimized terpene production in the yeast Rhodosporidium toruloides by engineering enzymes in the mevalonate pathway. Multi-omic analysis of bisabolene-producing strains identified specific enzymes for optimization, including HMG-CoA reductase and mevalonate kinases. Optimization of these enzymes for two terpenes, 1,8-cineole and bisabolene, improved titers to 1.4 g/L and 2.6 g/L respectively. The study demonstrates improving terpene production from lignocellulosic biomass in R. toruloides, an efficient host for converting renewable carbon sources.
This study evaluated methods for preserving microbial communities enriched on switchgrass biomass. High-throughput sequencing showed the communities shifted during initial enrichment but remained active after storage. Storage in liquid nitrogen without cryoprotectants resulted in variable preservation of dominant microbes, while cryopreservation with DMSO or glycerol provided consistent preservation. Despite shifts in relative abundance, the preserved samples retained an active community, suggesting the presence rather than abundance of microbes is important for activity.
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JBEI Research Highlights Slides - October 2022SaraHarmon4
This document summarizes three research articles from the Office of Biological and Environmental Research.
The first article describes an approach to engineer permeability in microfluidic compartments, enabling sustained multi-cycle protein production in a cell-free system and enhanced environmental fitness for bacteria-enclosing compartments.
The second article examines carbon metabolism in soil by tracking stable isotope enrichment of metabolites from various carbon sources, finding profiles varied more by source than time and corresponded to differences in active microbial populations.
The third article compares performance of parallel microbiomes cultivated on sorghum, finding actinobacteria differentiated outcomes and network reconstructions revealed enzyme-linked processing stages.
JBEI Research Highlights Slides - September 2022SaraHarmon4
This study developed a method for in situ synthesis of protic ionic liquids (PILs) for lignocellulosic biomass pretreatment. By mixing the components of the PIL ethanolamine acetate directly with biomass prior to pretreatment, similar sugar yields were achieved as compared to using pure PIL, but at significantly lower cost. Techno-economic and life-cycle analyses indicated this approach promotes improved economic and environmental benefits compared to using pure PIL. The in situ PIL synthesis method provides a simple and effective way to lower the costs and impacts of ionic liquid based biomass processing.
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Anaerobic fungi produce a wealth of enzymes that can act on cellulose, hemicellulose, and lignin. These enzymes show promise for accelerating the breakdown of lignocellulose for industrial applications like chemical and fuel production. Molecular dynamics simulations provide insights into how these enzymes may interact with lignocellulose and enable its breakdown. This could allow enzymes from anaerobic fungi to be applied industrially.
This document summarizes a study that utilized computational sequence analysis to discover a new glycoside phosphorylase enzyme. The enzyme was found to synthesize the previously undescribed biopolymer poly-β-1,3-N-acetylglucosamine. This new biopolymer and the reverse phosphorolysis action of the enzyme provides an efficient method to produce acholetin, a new biodegradable polymeric material.
This document summarizes four research articles from the Office of Biological and Environmental Research.
The first article compares pretreatment processes using two ionic liquids to pretreat aspen and maple biomass for biofuel production. It finds one ionic liquid increased crystallinity while the other reduced it.
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JBEI Research Highlights - January 2022SaraHarmon4
The study investigated resistance to the parasitic plant field dodder (Cuscuta campestris) in some Heinz tomato cultivars. It was discovered that these resistant cultivars respond to dodder attachment by locally lignifying their stem cortex, preventing the parasite from entering the host plant. Three factors - LIF1, SlMYB55, and CuRLR1 - were identified as regulating this lignification-based resistance mechanism. This work demonstrates how lignification can be used by plants as a defense against parasitic plants like dodder, and could help develop resistance for other crops impacted by parasitic plants.
JBEI Research Highlights - November 2021SaraHarmon4
- Poplar sapling were grown in high or low growth temperatures with and without additions of methanol to the soil. Leaf gas exchange, metabolomic profiles and photochemistry were assessed throughout an 8 week incubation period. High growth temperature plants showed suppression of leaf water use, photosynthesis and transpiration, but an upregulation of isoprene emissions and an increased optimum temperature of electron transport rate. Metabolomics analysis revealed a substantial number of metabolites with altered abundance in heat stress, and distinct subsets altered by methanol treatment at both temperatures.
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The document describes a modular automated workflow for high-throughput proteomic sample preparation that improves reproducibility and flexibility. Key points:
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- It was demonstrated on bacteria and yeast samples, showing high reproducibility.
- Digital protocols were created to facilitate transferring the methods and allowing flexibility for future development.
The study identified and characterized a BAHD family acyltransferase in poplar, PtrPHBMT1, that transfers p-hydoxybenzoate from its thio-ester donor to the sinapyl alcohol monolignol. This results in the conjugate being incorporated into nascent lignin polymers, leading to ester-linked p-hydoxybenzoate pendant groups and altering lignin properties. Genetically manipulating this enzyme controlling lignin p-hydroxybenzoylation could allow accumulating this high-value chemical, p-hydoxybenzoate, in lignocellulosic biomass and improve biofuel production and timber dur
1. The document describes research characterizing the process of Non-Photochemical Quenching (NPQ) in the algae Nannochloropsis oceanica using time-correlated single photon counting (TCSPC) fluorescence measurements.
2. The results show N. oceanica has a rapid NPQ response to light fluctuations and reaches steady state within 20 minutes of fluctuating light exposure.
3. The Steen model was found to predict the overall trend of the NPQ response data but lacked specificity for N. oceanica; minor edits to the model inputs improved accuracy.
This paper reviews recent advances in engineering Streptomyces bacteria for the production of medicines and bioproducts. Key approaches discussed include using genome editing tools and laboratory automation to rapidly engineer Streptomyces metabolism. The review highlights how integrating these methods within a design-build-test-learn framework is accelerating the discovery of new bioactive compounds and engineered Streptomyces cell factories. It provides an overview of this iterative engineering cycle and how each stage contributes to continual improvements in metabolic engineering outcomes for these industrially important bacteria.
March 2021 - JBEI Research Highlight SlidesSaraHarmon4
This study evaluated the use of ionic liquids (ILs) for pretreatment of woody biomass to enable efficient deconstruction. Specifically, it compared protic and aprotic ILs for pretreatment of pine wood at the bench scale. Protic ILs like cholinium lysinate achieved 80% glucose and 70% xylose yields at high solids loading of 20%, representing an effective pretreatment. For the first time, an aprotic IL containing the ions 1-ethyl-3-methylimidazolium and acetate was shown to significantly improve the enzymatic digestibility of pine wood compared to untreated biomass. This work demonstrates the potential of developing new IL systems for low-cost and high-efficiency pret
Recent advances in technoeconomic analysis (TEA) were reviewed:
- TEA is useful for process design, cost estimation, and identifying bottlenecks early in research.
- Studies now enable faster iteration, robust uncertainty analysis, and open-source platforms.
- Trends include more expansive system boundaries and potential integration with high-throughput experiments.
Overexpression of four previously uncharacterized poplar transcription factors produced enhanced saccharification of plant biomass in poplar. Two transcription factors, PtxtERF123 and PtxtZHD14, significantly improved both glucan and xylan release from plant cell walls. These transcription factors regulate groups of genes involved in xylem cell wall biosynthesis and are potential targets for improving biomass digestibility in poplar and other bioenergy feedstocks.
An automated workflow to screen alkene reductases using high-throughput thin layer chromatography
1) Researchers developed an automated 96-well screening platform using thin layer chromatography (TLC) to monitor the in vitro activity of an enzyme called geranylgeranyl reductase from Sulfolobus acidocaldarius. 2) The platform uses TLC to separate enzyme variants with unique product distributions or enhanced reductase activity. 3) Testing this workflow on a library of enzyme mutants, researchers could distinguish 4-fold differences in enzyme activity for some mutants and validated results with another method.
This study developed genetic tools for the thermophilic fungus Thermoascus aurantiacus, including a transformation system, CRISPR/Cas9 gene editing, and sexual crossing protocol. The transformation system was used to overexpress a transcriptional regulator of xylanase, increasing xylanase activity by up to 500%. CRISPR/Cas9 was shown to successfully delete a target gene with 10-35% efficiency. A sexual crossing protocol allowed crossing and isolation of progeny within a week, enabling strain engineering in this industrially relevant fungus. These tools open new possibilities for engineering thermostable enzyme production in T. aurantiacus.
This document summarizes three papers related to engineering plant metabolism and microbial physiology.
The first paper describes engineering the brassinin biosynthetic pathway in plants to produce novel antifungal compounds called crucifalexins. Two of the new compounds showed stronger antifungal activity than brassinin.
The second paper discusses using solid-state NMR to characterize the native architecture of plant cell walls without disruption. This provides information to engineer bioenergy crops.
The third paper combines mechanistic and machine learning models to predictively engineer and optimize tryptophan metabolism in microbes. This approach increased tryptophan titer and productivity by up to 74% and 43% compared to an improved reference strain.
PPT on Direct Seeded Rice presented at the three-day 'Training and Validation Workshop on Modules of Climate Smart Agriculture (CSA) Technologies in South Asia' workshop on April 22, 2024.
Travis Hills of MN is Making Clean Water Accessible to All Through High Flux ...Travis Hills MN
By harnessing the power of High Flux Vacuum Membrane Distillation, Travis Hills from MN envisions a future where clean and safe drinking water is accessible to all, regardless of geographical location or economic status.
The technology uses reclaimed CO₂ as the dyeing medium in a closed loop process. When pressurized, CO₂ becomes supercritical (SC-CO₂). In this state CO₂ has a very high solvent power, allowing the dye to dissolve easily.
The binding of cosmological structures by massless topological defectsSérgio Sacani
Assuming spherical symmetry and weak field, it is shown that if one solves the Poisson equation or the Einstein field
equations sourced by a topological defect, i.e. a singularity of a very specific form, the result is a localized gravitational
field capable of driving flat rotation (i.e. Keplerian circular orbits at a constant speed for all radii) of test masses on a thin
spherical shell without any underlying mass. Moreover, a large-scale structure which exploits this solution by assembling
concentrically a number of such topological defects can establish a flat stellar or galactic rotation curve, and can also deflect
light in the same manner as an equipotential (isothermal) sphere. Thus, the need for dark matter or modified gravity theory is
mitigated, at least in part.
(June 12, 2024) Webinar: Development of PET theranostics targeting the molecu...Scintica Instrumentation
Targeting Hsp90 and its pathogen Orthologs with Tethered Inhibitors as a Diagnostic and Therapeutic Strategy for cancer and infectious diseases with Dr. Timothy Haystead.
When I was asked to give a companion lecture in support of ‘The Philosophy of Science’ (https://shorturl.at/4pUXz) I decided not to walk through the detail of the many methodologies in order of use. Instead, I chose to employ a long standing, and ongoing, scientific development as an exemplar. And so, I chose the ever evolving story of Thermodynamics as a scientific investigation at its best.
Conducted over a period of >200 years, Thermodynamics R&D, and application, benefitted from the highest levels of professionalism, collaboration, and technical thoroughness. New layers of application, methodology, and practice were made possible by the progressive advance of technology. In turn, this has seen measurement and modelling accuracy continually improved at a micro and macro level.
Perhaps most importantly, Thermodynamics rapidly became a primary tool in the advance of applied science/engineering/technology, spanning micro-tech, to aerospace and cosmology. I can think of no better a story to illustrate the breadth of scientific methodologies and applications at their best.
Current Ms word generated power point presentation covers major details about the micronuclei test. It's significance and assays to conduct it. It is used to detect the micronuclei formation inside the cells of nearly every multicellular organism. It's formation takes place during chromosomal sepration at metaphase.
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...Leonel Morgado
Current descriptions of immersive learning cases are often difficult or impossible to compare. This is due to a myriad of different options on what details to include, which aspects are relevant, and on the descriptive approaches employed. Also, these aspects often combine very specific details with more general guidelines or indicate intents and rationales without clarifying their implementation. In this paper we provide a method to describe immersive learning cases that is structured to enable comparisons, yet flexible enough to allow researchers and practitioners to decide which aspects to include. This method leverages a taxonomy that classifies educational aspects at three levels (uses, practices, and strategies) and then utilizes two frameworks, the Immersive Learning Brain and the Immersion Cube, to enable a structured description and interpretation of immersive learning cases. The method is then demonstrated on a published immersive learning case on training for wind turbine maintenance using virtual reality. Applying the method results in a structured artifact, the Immersive Learning Case Sheet, that tags the case with its proximal uses, practices, and strategies, and refines the free text case description to ensure that matching details are included. This contribution is thus a case description method in support of future comparative research of immersive learning cases. We then discuss how the resulting description and interpretation can be leveraged to change immersion learning cases, by enriching them (considering low-effort changes or additions) or innovating (exploring more challenging avenues of transformation). The method holds significant promise to support better-grounded research in immersive learning.
Authoring a personal GPT for your research and practice: How we created the Q...Leonel Morgado
Thematic analysis in qualitative research is a time-consuming and systematic task, typically done using teams. Team members must ground their activities on common understandings of the major concepts underlying the thematic analysis, and define criteria for its development. However, conceptual misunderstandings, equivocations, and lack of adherence to criteria are challenges to the quality and speed of this process. Given the distributed and uncertain nature of this process, we wondered if the tasks in thematic analysis could be supported by readily available artificial intelligence chatbots. Our early efforts point to potential benefits: not just saving time in the coding process but better adherence to criteria and grounding, by increasing triangulation between humans and artificial intelligence. This tutorial will provide a description and demonstration of the process we followed, as two academic researchers, to develop a custom ChatGPT to assist with qualitative coding in the thematic data analysis process of immersive learning accounts in a survey of the academic literature: QUAL-E Immersive Learning Thematic Analysis Helper. In the hands-on time, participants will try out QUAL-E and develop their ideas for their own qualitative coding ChatGPT. Participants that have the paid ChatGPT Plus subscription can create a draft of their assistants. The organizers will provide course materials and slide deck that participants will be able to utilize to continue development of their custom GPT. The paid subscription to ChatGPT Plus is not required to participate in this workshop, just for trying out personal GPTs during it.
Immersive Learning That Works: Research Grounding and Paths ForwardLeonel Morgado
We will metaverse into the essence of immersive learning, into its three dimensions and conceptual models. This approach encompasses elements from teaching methodologies to social involvement, through organizational concerns and technologies. Challenging the perception of learning as knowledge transfer, we introduce a 'Uses, Practices & Strategies' model operationalized by the 'Immersive Learning Brain' and ‘Immersion Cube’ frameworks. This approach offers a comprehensive guide through the intricacies of immersive educational experiences and spotlighting research frontiers, along the immersion dimensions of system, narrative, and agency. Our discourse extends to stakeholders beyond the academic sphere, addressing the interests of technologists, instructional designers, and policymakers. We span various contexts, from formal education to organizational transformation to the new horizon of an AI-pervasive society. This keynote aims to unite the iLRN community in a collaborative journey towards a future where immersive learning research and practice coalesce, paving the way for innovative educational research and practice landscapes.
Juaristi, Jon. - El canon espanol. El legado de la cultura española a la civi...
JBEI Research Highlights - December 2021
1. Diversifying isoprenoid platforms via atypical carbon
substrates and non-model microorganisms
Background
• Isoprenoid production has been largely successful in E. coli and S.
cerevisiae with metabolic engineering of the mevalonate (MVA) and
methylerythritol phosphate (MEP) pathways coupled with the
expression of heterologous terpene synthases.
• Conventional microbial chassis pose several major obstacles to
successful commercialization including the affordability of sugar
substrates at scale, precursor flux limitations, and intermediate
feedback-inhibition.
Approach
• Recent studies have challenged typical isoprenoid paradigms by
expanding the boundaries of terpene biosynthesis and using non-
model organisms including those metabolizing C1 substrates.
• We highlights the advances in isoprenoid biosynthesis with specific
focus on the synergy between model and non-model organisms
that may elevate the commercial viability of isoprenoid platforms by
addressing the dichotomy between high titer production and
inexpensive substrates.
Outcomes and Impacts
• Atypical carbon sources and non-model organisms harbor
metabolic advantages that could be harnessed to reduce substrate
costs and the associated emissions of bioproduction.
• Co-substrate utilization by certain organisms as in the case of R.
toruloides and P. putida has the potential to unlock lignocellulosic
biomass and many methylotrophs could tap into inexpensive and
highly abundant substrates.
• Systems engineering strategies are of particular interest for C1
metabolism. The translation of successful whole systems
engineering strategies from E. coli and S. cerevisiae to non-model
organisms will prove useful in further optimization.
Carruthers and Lee (2021) Frontiers Microbiology, doi: 10.3389/fmicb.2021.791089
Figure 1. A depiction of isoprenoid synthesis through the core 6
enzyme MVA and 7 enzyme MEP pathways. Also depicted are
the newly discovered archaeal branches from the MVA
pathway. The thermoarchaeal-type branch begins with
mevalonic acid whereas the archaeal and haloarchaeal-type
branches stem from MVAP.
2. Managing soil organic carbon for climate change
mitigation and food security
Background
• Soil organic carbon (SOC) determines the sustainability and
resilience of agroecosystems under changing climate
• Soil functions, such as climate change mitigation and food
production, are regulated by different properties of individual
SOC pools
Approach
• We review the literature and provide empirical evidence on the
functions of different SOC fractions, and their management
strategies to mitigate climate change impacts and ensure food
security
Outcomes and Impacts
• A new input of organic carbon is partially decomposed by soil
microbes and released back into the atmosphere, while some
C can be stored in the soil for decades to millennia. The
residence time of SOC is mainly determined by biochemical
recalcitrance, chemical stabilization, and physical protection.
• Conservation tillage sequestered more SOC and total nitrogen
in the soil than conventional tillage.
• Agroforestry and organic amendments increase crop
production through supplying more nutrients by increasing the
dissolved organic matter and free particulate organic matter
pools.
• Biochar showed the most favorable effect on soil C
sequestration and pore formation with its inherent porous
structure and recalcitrance, as well as its interaction with soil
particles and aggregates.
Kim et al. (2021). Managing Soil Organic Carbon for Climate Change Mitigation and Food
Security, doi: 10.1201/9781003243090-2.
Figure 1. Relations of soil organic carbon pools with soil
functions
Figure 2. Response ratios of soil organic amendments to no
addition for soil organic carbon (SOC), total nitrogen (TN), total
soil porosity (Porosity), and crop yield (Yield)
3. Lignin p-Hydroxybenzoate Decoration Regulates
Gravitropic Response of Poplar
Background
• Angiosperm woody species display gravitropic response in respect to
gravity and produce tension wood.
• Despite the long history of recognition of p-hydroxybenzoate
decoration in cell wall lignin, our understandings on its biological
significance remain largely elusive.
• This study explores physiological effects of lignin p-
hydroxybenzoylation on gravitropic response of poplar.
Approach
• Lignin p-hydroxybenzoate deficient and hyperaccumulating poplar
transgenic lines were treated with mechanical bending and/or
gravistimulation.
• The autotropism and gravitropism behaviors of the treated plantlets
were observed and recorded.
• The expression of secondary cell wall biosynthetic genes and the
alteration in cell wall composition were determined in the generated
tension wood, opposite wood and normal wood of the plants.
Outcomes and Impacts
• Mechanical bending or gravistimulation significantly enhances the
expression of PHBMT1 and the accumulation of p-hydroxybenzoates
in tension wood.
• Paradoxically, hyperaccumulation of p-hydroxybenzoates mitigates
gravitropism and/or enhances autotropism of the plants. Thus, lignin
p-hydroxybenzoylation negatively coordinates with the action of
tension wood cellulose fibers to control poplar wood deformation and
plant growth.
Zhao et al. (2021) Front Plant Sci 12, 755576, doi: 10.3389/fpls.2021.755576
The larger secant bending angle and more obvious
upward curving at the basal internodes were observed in
the PHBMT1 knockout plants, where the lignin-bound
pBAs are eliminated; by contrast, when pBAs were
hyper-accumulated in the stem cell walls of the PHBMT1
OE plants, smaller secant bending angle exhibited and
the stem upward curving occurred at the apical
internodes. The PHBMT1-mediated monolignol p-
hydroxybenzoylation and the subsequent accumulation
of lignin-bound pBAs play observable roles in the
regulation of poplar gravitropic response.
WT g1-8 g1-9 OE1 OE2
WT g1-8 g1-9 OE1 OE2
0.0
0.5
1.0
1.5
2.0
Top
length/
bottom
length
**
*
WT g1-8 g1-9 OE1 OE2
0.0
0.5
1.0
1.5
2.0
Relative
secant
bending
angle
**
*
4. Prediction of Solubility Parameters for Lignin and Ionic
Liquids Using Multi-resolution Simulation Approaches
Background
• The solubility parameters of a molecular species is a vital
feature that evaluates polarity and quantifies the ‘like-seeks-
like' principle.
• The performance of Hansen solubility parameters (HSP) has
previously been demonstrated for lignin solubility using different
solvent systems.
Approach
• The objective of this study is to evaluate the Hansen solubility
parameters of lignin, ILs, and DESs using multi-resolution
simulation approaches.
Outcomes and Impacts
• The SPs of lignin were obtained in the range of 23‒27 MPa1/2
,
which is close to the polymeric lignin solubility parameters.
• The correlation between experimental lignin dissolution in ILs
and DESs and predicted REDs of lignin had shown an
excellent agreement.
• The SPs of ILs namely [Ch][Lys], [Ch][Oct], and [Emim][Lys]
were predicted to be ~26 MPa1/2, which is close to lignin’s SPs
and resulted in increased biomass delignification.
• The molecular dynamics simulated SPs were validated by both
the COSMO-RS model and experimental investigations, with
the results showing a close agreement between predicted and
experimental solubility parameters.
• The predicted solubility parameters were applicable for
hardwood and grassy-type biomass, whereas the softwood
biomass has a different set of SPs for lignin
Mohan et al. (2021) Green Chemistry, https://doi.org/10.1039/D1GC03798F
Biomass
Type
Ionic Liquid
Lignin
removal (%)
RED Reference
Kraft lignin [Ch][For] 28.3 1.04
Hou et al.
(2015)
[Ch][Ace] 31 0.83
[Ch][But] 32.5 0.59
[Ch][Hex] 37.2 0.41
[Ch][Oct] 39.5 0.28
Sorghum
(grass)
[Ch][Ace] 45 0.83
Yao et al.
(2021)
[Ch][Oct] 51.86 0.28
[Ch][Lys] 77.41 0.34
Switchgrass
(grass)
[Emim][Ace] 16.5, 48.9 0.91
Sun et al.
(2014)
[Ch][Ace] 17.0, 50.2 0.83
[Ch][Lys] 69.3, 85.1 0.34
[Emim][Lys] 80.3, 86.6 0.28
Switchgrass
(grass)
[Ch][Lys] 74 0.34
Dutta et al.
(2018)
Eucalyptus
(hardwood)
[Ch][Lys] 70 0.34
Dutta et al.
(2018)
Pine
(softwood)
[Ch][Lys] 20 -
Dutta et al.
(2018)
Table : Correlation between RED values of solvent (ILs)−lignin
interaction and experimental lignin solubility or biomass
delignification
5. Genomics Characterization of an Engineered
Corynebacterium glutamicum in Bioreactor Cultivation
Under Ionic Liquid Stress
Background
• Ionic liquids (ILs) are potent reagents that can extract sugars from
renewable carbon streams for downstream bioconversion processes.
One emerging ionic liquid with favorable properties is cholinium lysinate
([Ch][Lys]).
• C. glutamicum shows a subtle growth defect at high concentrations of
[Ch][Lys] which suggested potential changes to its physiology in
response; a fundamental understanding of this microbe’s cellular
response to [Ch][Lys] stirred tank bioreactors during bioproduction could
inform future production strategies.
Approach
• We generated a new PacBio genome assembly of an engineered
isoprenol producing C. glutamicum strain BRC-JBEI 1.1.2 using whole-
genome sequencing.
• Differential gene expression profiling during isoprenol production in a
fed-batch bioreactor revealed the cellular response in the presence and
absence of [Ch][Lys].
Outcomes and Impacts
• This analysis identified genetic differences in C. glutamicum BRC-JBEI
1.1.2 isolate compared to the reference C. glutamicum genome.
• Transcriptomics analysis implicated ectP, a BCCT family transporter
similar to the E. coli betT and P. putida betT-III, as a transporter for
[Ch][Lys]; ectP was overexpressed in the presence of [Ch][Lys].
• This transcriptomics analysis of an isoprenol producing C. glutamicum
strain proposes several actionable targets including gltA, brnF for future
DBTL cycles that may lead to improved isoprenol production.
Banerjee et al. (2021) Front. Bioeng. Biotechnol., doi: 10.3389/fbioe.2021.766674
(A) Glucose and organic acids profiles in the 2-L stirred tank
bioreactor cultivation in the presence of 50 mM [Ch][Lys].
(B) Venn diagrams indicating the number of upregulated (left)
and downregulated (right) DEGs in response to [Ch][Lys]. (C)
Differential transcript profiles of C. glutamicum BRC-JBEI 1.1.2
under three discrete conditions, during scale transition (ST),
bioreactor cultivation in the absence of IL (BR) and presence of
IL (IL).
A B
C
6. Comparative genomics reveals a novel gene whose
product is involved in cyclization of a polyketide
Background
• Fungal genome sequencing has identified a tremendous
diversity of secondary metabolite gene clusters encoding a
huge breadth of biochemical reactions
• This study is the first functional study of a snoaL domain
cyclase (otaY) that is essential for the production of a
fungal polyketide, ochratoxin A, produced by Aspergillus
carbonarius
Approach
• A gene deletion approach was utilized to show the
essentiality of a polyketide cyclase for production of a
known polyketide
Outcomes and Impacts
• The cyclization process of the heterocyclic structure of
OTβ, in the first steps of OTA biosynthesis pathway had not
previously been associated with an enzyme
• Complete deletion of otaY gene demonstrated the inability
of ΔotaY mutant to synthesize the OTA molecule
• Defining the biochemical reactions performed by individual
enzymes in secondary metabolite biosynthetic pathways is
critical for growing the enzymatic “parts list” that may be
used to create novel pathways and compounds
Ferrara et al, Toxins 2021, 13(12), 892; https://doi.org/10.3390/toxins13120892
UPLC-FLD chromatograms of OTA standard
solution (1018 ng/g) (blue trace), extract of A.
carbonarius wild-type strain ITEM 5010 (6467
ng/g) (black trace), and extract of A.
carbonarius ∆otaY deletion mutant strain
AC2021 (red trace).