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At least 1,009 records · Page 56

Glucose assimilation rate determines the partition of flux at pyruvate between lactic acid and ethanol in Saccharomyces cerevisiae

Engineered Saccharomyces cerevisiae expressing a lactic acid dehydrogenase can metab- olize pyruvate into lactic acid. However, three pyruvate decarboxylase (PDC) isozymes drive most carbon flux toward ethanol rather than lactic acid. Deletion of endoge- nous PDCs will eliminate ethanol production, but the resulting strain suffers from C 2 auxotrophy and struggles to complete a fermentation. Engineered yeast assimilating xylose or cellobiose produce lactic acid rather than ethanol as a major product with- out the deletion of any PDC genes. We report here that sugar flux, but not sensing, contributes to the partition of flux at the pyruvate branch point in S. cerevisiae express- ing the Rhizopus oryzae lactic acid dehydrogenase (LdhA). While the membrane glucose sensors Snf3 and Rgt2 did not play any direct role in the option of predominant product, the sugar assimilation rate was strongly correlated to the partition of flux at pyruvate: fast sugar assimilation favors ethanol production while slow sugar assimilation favors lactic acid. Applying this knowledge, we created an engineered yeast capable of simultaneously converting glucose and xylose into lactic acid, increasing lactic acid production to approximately 17 g L –1 from the 12 g L –1 observed during sequential consumption of sugars. This work elucidates the carbon source-dependent effects on product selection in engineered yeast.

59 BASIC BIOLOGICAL SCIENCES↗

Enzyme selection, optimization, and production toward biodegradation of post–consumer poly(ethylene terephthalate) at scale

Poly(ethylene terephthalate) (PET) is one of the world's most widely used polyester plastics. Due to its chemical stability, PET is extremely difficult to hydrolyze in a natural environment. Recent discoveries in new polyester hydrolases and breakthroughs in enzyme engineering strategies have inspired enormous research on biorecycling of PET. This study summarizes our research efforts toward large-scale, efficient, and economical biodegradation of post-consumer waste PET, including PET hydrolase selection and optimization, high-yield enzyme production, and high-capacity enzymatic degradation of post-consumer waste PET. First, genes encoding PETase and MHETase from Ideonella sakaiensis and the ICCG variant of leaf-branch compost cutinase (LCC ICCG ) were codon-optimized and expressed in Escherichia coli BL21(DE3) for high-yield production. To further lower the enzyme production cost, a pelB leader sequence was fused to LCC ICCG so that the enzyme can be secreted into the medium to facilitate recovery. To help bind the enzyme on the hydrophobic surface of PET, a substrate-binding module in a polyhydroxyalkanoate depolymerase from Alcaligenes faecalis (PBM) was fused to the C-terminus of LCC ICCG . The resulting four different LCC ICCG variants (LCC, PelB-LCC, LCC-PBM, and PelB-LCC-PBM), together with PETase and MHETase, were compared for PET degradation efficiency. A fed-batch fermentation process was developed to produce the target enzymes up to 1.2 g L –1 . Finally, the best enzyme, PelB-LCC, was selected and used for the efficient degradation of 200 g L –1 recycled PET in a well-controlled, stirred-tank reactor. Furthermore, the results will help develop an economical and scalable biorecycling process toward a circular PET economy.

59 BASIC BIOLOGICAL SCIENCES↗

Anaerobic gut fungi: Advances in isolation, culture, and cellulolytic enzyme discovery for biofuel production

Anaerobic gut fungi are an early branching family of fungi that are commonly found in the digestive tract of ruminants and monogastric herbivores. It is becoming increasingly clear that they are the primary colonizers of ingested plant biomass, and that they significantly contribute to the decomposition of plant biomass into fermentable sugars. As such, anaerobic fungi harbor a rich reservoir of undiscovered cellulolytic enzymes and enzyme complexes that can potentially transform the conversion of lignocellulose into bioenergy products. Despite their unique evolutionary history and cellulolytic activity, few species have been isolated and studied in great detail. As a result, their life cycle, cellular physiology, genetics, and cellulolytic metabolism remain poorly understood compared to aerobic fungi. To help address this limitation, this work briefly summarizes the current body of knowledge pertaining to anaerobic fungal biology, and describes progress made in the isolation, cultivation, molecular characterization, and long-term preservation of these microbes. Finally, we also discuss recent cellulase- and cellulosome-discovery efforts from gut fungi, and how these interesting, non-model microbes could be further adapted for biotechnology applications.

59 BASIC BIOLOGICAL SCIENCES↗

Insights into cellulase-lignin non-specific binding revealed by computational redesign of the surface of green fluorescent protein

Biological-mediated conversion of pretreated lignocellulosic biomass to biofuels and biochemicals is a promising avenue towards energy sustainability. However, a critical impediment to the commercialization of cellulosic biofuel production is the high cost of cellulase enzymes needed to deconstruct biomass into fermentable sugars. One major factor driving cost is cellulase adsorption and inactivation in the presence of lignin, yet we currently have a poor understanding of the protein structure-function relationships driving this adsorption. In this work, we have systematically investigated the role of protein surface potential on lignin adsorption using a model monomeric fluorescent protein. We have designed and experimentally characterized 16 model protein variants spanning the physiological range of net charge (-24 to +16 total charges) and total charge density (0.28 to 0.40 charges per sequence length) typical for natural proteins. Protein designs were expressed, purified, and subjected to in silico and in vitro biophysical measurements to evaluate the relationship between protein surface potential and lignin adsorption properties. The designs were comparable to model fluorescent protein in terms of thermostability and heterologous expression yield, although the majority of the designs unexpectedly formed homodimers. Protein adsorption to lignin was studied at two different temperatures using Quartz Crystal Microbalance with Dissipation Monitoring and a subtractive mass balance assay. We found a weak correlation between protein net charge and protein-binding capacity to lignin. No other single characteristic, including apparent melting temperature and 2nd virial coefficient, showed correlation with lignin binding. Analysis of an unrelated cellulase dataset with mutations localized to a family I carbohydrate-binding module showed a similar correlation between net charge and lignin binding capacity. Altogether, our study provides strategies to identify highly active, low lignin-binding cellulases by either rational design or by computational screening genomic databases.

09 BIOMASS FUELS↗

Engineered CRISPR/Cas9 system for multiplex genome engineering of polyploid industrial yeast strains

The CRISPR/Cas9 system has been widely used for multiplex genome engineering of Saccharomyces cerevisiae . Furthermore, its application in manipulating industrial yeast strains is less successful, probably due to the genome complexity and low copy numbers of gRNA expression plasmids. Here we developed an efficient CRISPR/Cas9 system for industrial yeast strain engineering by using our previously engineered plasmids with increased copy numbers. Four genes in both a diploid strain (Ethanol Red, 8 alleles in total) and a triploid strain (ATCC 4124, 12 alleles in total) were knocked out in a single step with 100% efficiency. This system was used to construct xylose-fermenting, lactate-producing industrial yeast strains, in which ALD6, PHO13, LEU2, and URA3 were disrupted in a single step followed by the introduction of a xylose utilization pathway and a lactate biosynthetic pathway on auxotrophic marker plasmids. The optimized CRISPR/Cas9 system provides a powerful tool for the development of industrial yeast based microbial cell factories.

59 BASIC BIOLOGICAL SCIENCES↗

Enhancing hydrogen‐dependent growth of and carbon dioxide fixation by Clostridium ljungdahlii through nitrate supplementation

Abstract Synthesis gas (syngas) fermentation via the Wood–Ljungdahl pathway is receiving growing attention as a possible platform for the fixation of and renewable production of fuels and chemicals. However, the pathway operates near the thermodynamic limit of life, resulting in minimal adenosine triphosphate (ATP) production and long doubling times. This calls into question the feasibility of producing high‐energy compounds at industrially relevant levels. In this study, we investigated the possibility of co‐utilizing nitrate as an inexpensive additional electron acceptor to enhance ATP production during ‐dependent growth of Clostridium ljungdahlii , Moorella thermoacetica , and Acetobacterium woodii . In contrast to other acetogens tested, growth rate and final biomass titer were improved for C. ljungdahlii growing on a mixture of and when supplemented with nitrate. Transcriptomic analysis, labeling, and an electron balance were used to understand how electron flux was partitioned between and nitrate. We further show that, with nitrate supplementation, the ATP/adenosine diphosphate (ADP) ratio and acetyl‐CoA pools were increased by fivefold and threefold, respectively, suggesting that this strategy could be useful for the production of ATP‐intensive heterologous products from acetyl‐CoA. Finally, we propose a pathway for enhanced ATP production from nitrate and use this as a basis to calculate theoretical yields for a variety of products. This study demonstrates a viable strategy for the decoupling of ATP production from carbon dioxide fixation, which will serve to significantly improve the fixation rate and the production metrics of other chemicals from and in this host.

Emerson, David F.↗

Xylose Assimilation Enhances Production of Isobutanol in Engineered Saccharomyces cerevisiae

Bioconversion of xylose—the second most abundant sugar in nature—into high–value fuels and chemicals by engineered Saccharomyces cerevisiae has been a long–term goal of the metabolic engineering community. Although most efforts have heavily focused on the production of ethanol by engineered S. cerevisiae , yields and productivities of ethanol produced from xylose have remained inferior as compared to ethanol produced from glucose. However, this entrenched focus on ethanol has concealed the fact that many aspects of xylose metabolism favor the production of non–ethanol products. Through reduced overall metabolic flux, a more respiratory nature of consumption, and evading glucose signaling pathways, the bioconversion of xylose can be more amenable to redirecting flux away from ethanol towards a desired target product. In this report, we show that coupling xylose consumption via the oxidoreductive pathway with a mitochondrially–targeted isobutanol biosynthesis pathway leads to enhanced product yields and titers as compared to cultures utilizing glucose or galactose as a carbon source. Through optimization of culture conditions, we achieve 2.6 g/L of isobutanol in fed–batch flask and bioreactor fermentations. Furthermore, these results suggest that there may be synergistic benefits of coupling xylose assimilation with the production of non–ethanol value–added products.

59 BASIC BIOLOGICAL SCIENCES↗

Reduced type-A carbohydrate-binding module interactions to cellulose I leads to improved endocellulase activity

Dissociation of nonproductively bound cellulolytic enzymes from cellulose is hypothesized to be a key rate-limiting factor impeding cost-effective biomass conversion to fermentable sugars. However, the role of carbohydrate-binding modules (CBMs) in enabling nonproductive enzyme binding is not well understood. Here, we examine the subtle interplay of CBM binding and cellulose hydrolysis activity for three models type-A CBMs (Families 1, 3a, and 64) tethered to multifunctional endoglucanase (CelE) on two distinct cellulose allomorphs (i.e., cellulose I and III). We generated a small library of mutant CBMs with varying cellulose affinity, as determined by equilibrium binding assays, followed by monitoring cellulose hydrolysis activity of CelE–CBM fusion constructs. Finally, kinetic binding assays using quartz crystal microbalance with dissipation were employed to measure CBM adsorption and desorption rate constants kon and koff, respectively, towards nanocrystalline cellulose derived from both allomorphs. Overall, our results indicate that reduced CBM equilibrium binding affinity towards cellulose I alone, resulting from increased desorption rates (koff) and reduced effective adsorption rates (nkon), is correlated to overall improved endocellulase activity. Future studies could employ similar approaches to unravel the role of CBMs in nonproductive enzyme binding and develop improved cellulolytic enzymes for industrial applications.

59 BASIC BIOLOGICAL SCIENCES↗

Probing specificities of alcohol acyltransferases for designer ester biosynthesis with a high–throughput microbial screening platform

Alcohol acyltransferases (AATs) enables microbial biosynthesis of a large space of esters by condensing an alcohol and an acyl-CoA. However, substrate promiscuity of AATs prevents microbial biosynthesis of designer esters with high selectivity. Here, we developed a high-throughput microbial screening platform that facilitates rapid identification of AATs for designer ester biosynthesis. First, we established a microplate-based culturing technique with in situ fermentation and extraction of esters. We validated its capability in rapid profiling of the alcohol substrate specificity of 20 chloramphenicol acetyltransferase variants derived from Staphylococcus aureus (CAT Sa ) for microbial biosynthesis of acetate esters with various exogeneous alcohol supply. By coupling the microplate-based culturing technique with a previously established colorimetric assay, we developed a high-throughput microbial screening platform for AATs. We demonstrated that this platform could not only probe the alcohol substrate specificity of both native and engineered AATs but also identify the beneficial mutations in engineered AATs for enhanced ester synthesis. Here, we anticipate the high-throughput microbial screening platform provides a useful tool to identify novel wildtype and engineered AATs that have important roles in nature and industrial biocatalysis for designer bioester production.

2-phenhylethyl acetate↗

Metabolic engineering of oleaginous yeast Rhodotorula toruloides for overproduction of triacetic acid lactone

Abstract The plant‐sourced polyketide triacetic acid lactone (TAL) has been recognized as a promising platform chemical for the biorefinery industry. However, its practical application was rather limited due to low natural abundance and inefficient cell factories for biosynthesis. Here, we report the metabolic engineering of oleaginous yeast Rhodotorula toruloides for TAL overproduction. We first introduced a 2‐pyrone synthase gene from Gerbera hybrida ( GhPS ) into R. toruloides and investigated the effects of different carbon sources on TAL production. We then systematically employed a variety of metabolic engineering strategies to increase the flux of acetyl‐CoA by enhancing its biosynthetic pathways and disrupting its competing pathways. We found that overexpression of ATP‐citrate lyase (ACL1) improved TAL production by 45% compared to the GhPS overexpressing strain, and additional overexpression of acetyl‐CoA carboxylase (ACC1) further increased TAL production by 29%. Finally, we characterized the resulting strain I12‐ ACL1‐ACC1 using fed‐batch bioreactor fermentation in glucose or oilcane juice medium with acetate supplementation and achieved a titer of 28 or 23 g/L TAL, respectively. This study demonstrates that R. toruloides is a promising host for the production of TAL and other acetyl‐CoA‐derived polyketides from low‐cost carbon sources.

2‐pyrone synthase↗

Metabolic Engineering of Nonmodel Yeast Issatchenkia orientalis SD108 for 5–Aminolevulinic Acid Production

Biological production of 5-aminolevulinic acid (5-ALA) has received growing attention over the years. However, there is the tradeoff between 5-ALA biosynthesis and cell growth because the fermentation broth will become acidic due to the production of 5-ALA. To address this limitation, we engineered an acid-tolerant yeast, Issatchenkia orientalis SD108, for 5-ALA production. We first discovered that the cell growth rate of I. orientalis SD108 was boosted by 5-ALA and its endogenous ALA synthetase (ALAS) showed higher activity than those homologs from other yeasts. The titer of 5-ALA was improved from 28 mg/L to 120-, 150-, and 300 mg/L, by optimizing plasmid design, overexpressing a transporter, and increasing gene copy number, respectively. After redirecting the metabolic flux using the pyruvate decarboxylase (PDC) knockout strain (SD108ΔPDC) and culturing with urea, we increased the titer of 5-ALA to 510 mg/L, a 13-fold enhancement, proving the importance of the newly identified IoALAS with higher activity and the strategic selection of nitrogen sources for knockout strains. This study demonstrates the acid-tolerant I. orientalis SD108ΔPDC has a high potential for 5-ALA production at a large scale in the future.

59 BASIC BIOLOGICAL SCIENCES↗

Quantitative Analysis of The High‐Yield Hydrolysis of Kelp by Laminarinase and Alginate Lyase

Abstract Kelp is an abundant, farmable biomass‐containing laminarin and alginate as major polysaccharides, providing an excellent model substrate to study their deconstruction by simple enzyme mixtures. Our previous study showed strong reactivity of the glycoside hydrolase family 55 during hydrolysis of purified laminarin, raising the question of its reactivity with intact kelp. In this study, we determined that a combination of a single glycoside hydrolase family 55 β‐1,3‐exoglucanase with a broad‐specificity alginate lyase from the polysaccharide lyase family 18 gives efficient hydrolysis of untreated kelp to a mixture of simple sugars, that is, glucose, gentiobiose, mannitol‐end glucose, and mannuronic and guluronic acids and their soluble oligomers. Quantitative assignments from nanostructure initiator mass spectrometry (NIMS) and 2D HSQC NMR spectroscopy and analysis of the reaction time‐course are provided. The data suggest that binary combinations of enzymes targeted to the unique polysaccharide composition of marine biomass are sufficient to deconstruct kelp into soluble sugars for microbial fermentation.

2D HSQC NMR↗

Bioderived Muconates by Cross-Metathesis and Their Conversion into Terephthalates

Polyethylene terephthalate that is 100 % bioderived is in great demand in the market guided by the ever-more exigent sustainability regulations with the challenge of producing renewable terephthalic acid remaining. Renewable terephthalic acid or its precursors can be obtained by Diels–Alder cycloaddition and further dehydrogenation of biomass-derived muconic acid. The cis,cis isomer of the dicarboxylic acid is typically synthesized by fermentation with genetically modified microorganisms, a process that requires complex separations to obtain a high yield of the pure product. Moreover, the cis isomer has to be transformed into the trans,trans form and has to be esterified before it is suitable for terephthalate synthesis. To overcome these challenges, we investigated the synthesis of dialkyl muconates by cross-metathesis. The Ru-catalyzed cross-coupling of sorbates with acrylates, which can be bioderived, proceeded selectively to yield diester muconates in up to 41 % yield by using very low catalyst amounts (0.5–3.0 mol %) and no solvent. In the optimized procedure, the muconate precipitated as a solid and was easily recovered from the reaction medium. Analysis by GC–MS and NMR spectroscopy showed that this method delivered exclusively the trans,trans isomer of dimethyl muconate. The Diels–Alder reaction of dimethyl muconate with ethylene was studied in various solvents to obtain 1,4-bis(carbomethoxy)cyclohexene. The cycloaddition proceeded with very high conversions (77–100 %) and yields (70–98 %) in all of the solvents investigated, and methanol and tetrahydrofuran were the best choices. Next, the aromatization of 1,4-bis(carbomethoxy)cyclohexene to dimethyl terephthalate over a Pd/C catalyst resulted in up to 70 % yield in tetrahydrofuran under an air atmosphere. Because of the high yield of the reaction of dimethyl muconate to 1,4-bis(carbomethoxy)cyclohexene, no separation step was needed before the aromatization. This is the first time that cross-metathesis is used to produce bioderived trans,trans-muconates as precursors to renewable terephthalates, important building blocks in the polymer industry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Engineered Sorghum Bagasse Enables a Sustainable Biorefinery with p-Hydroxybenzoic Acid-Based Deep Eutectic Solvent

Integrating multidisciplinary research in plant genetic engineering and renewable deep eutectic solvents (DESs) can facilitate a sustainable and economic biorefinery. In this work, we leveraged a plant genetic engineering approach to specifically incorporate C6C1 monomers into the lignin structure. By expressing the bacterial ubiC gene in sorghum, p-hydroxybenzoic acid (PB)-rich lignin was incorporated into the plant cell wall while this monomer was completely absent in the lignin of the wild-type (WT) biomass. A DES was synthesized with choline chloride (ChCl) and PB and applied to the pretreatment of the PB-rich mutant biomass for a sustainable biorefinery. The release of fermentable sugars was significantly enhanced (~190 % increase) compared to untreated biomass by the DES pretreatment. In particular, the glucose released from the pretreated mutant biomass was up to 12 % higher than that from the pretreated WT biomass. Lignin was effectively removed from the biomass with the preservation of more than half of the β-Ο-4 linkages without condensed aromatic structures. Hydrogenolysis of the fractionated lignin was conducted to demonstrate the potential of phenolic compound production. In addition, a simple hydrothermal treatment could selectively extract PB from the same engineered lignin, showing a possible circular biorefinery. These results suggest that the combination of PB-based DES and engineered PB-rich biomass is a promising strategy to achieve a sustainable closed-loop biorefinery.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Genetically engineered poplar wood effectively enhances the efficiency of deep eutectic solvent-mediated one-pot processing

Although lignocellulosic biomass is a renewable resource with the potential to replace fossil-derived fuels and chemicals, its recalcitrance, largely due to lignin, limits its utilization. Recent advancements in genetic engineering have produced transgenic trees with reduced lignin content and/or modified lignin structure without compromising growth traits. Here, three engineered poplar varieties are evaluated as feedstocks using a biocompatible one-pot deep eutectic solvent-mediated process that integrates biomass fractionation and enzymatic saccharification within a single reactor, eliminating water washing and reconditioning. All transgenic poplars exhibit higher fermentable sugar yields than wild-type (WT) trees. Notably, QsuB poplar, incorporating 3,4-dihydroxybenzoate in lignin, achieves the highest glucose conversion yield of 91.3% (vs. 73.0% from WT). AT5 and MdCHS3 poplars, incorporating ferulate esters and naringenin, also demonstrate improved glucose yields (86.7 and 84.7%, respectively), confirming reduced biomass recalcitrance. Additionally, residual lignins are valorized via hydrogenolysis into phenolic compounds, with comparable alkylphenol production across all lines. These findings demonstrate that the transgenic poplar lines not only serve as superior feedstocks for sugar conversion but also provide a rich resource for phenolic compound production, enhancing the operational and economic viability of integrated biorefinery processes.

biomasses↗

Negative Emission Energy Production Technologies: A Techno‐Economic and Life Cycle Analyses Review

Negative emission technologies (NETs) are of growing importance for society to meet the atmospheric carbon levels required to maintain global temperatures under sustainable limits. A wide range of NETs have been proposed, but there are limited NET assessments that integrate life cycle analysis (LCA) and techno‐economic analysis (TEA). This Review gathers NET TEA/LCA findings and compares their costs and greenhouse gas emissions. Eight different NET‐producing transportation fuels and power‐generation technologies are considered: anaerobic digestion (lignocellulosic), fermentation, torrefaction, combustion, fast pyrolysis, gasification, and hydrothermal liquefaction. Most of these technologies sequester carbon either as carbon dioxide or as biochar. Some are carbon negative by virtue of avoided or displaced emissions. Overall, results indicate that NET energy production costs range between $20 and $80 GJ −1 and have emissions from −400 to 100 kg CO 2,eq GJ −1 . These results suggest that there are potential tradeoffs to consider when developing NETs. These results also show that future TEA/LCA studies of NETs are needed to decrease their uncertainty and improve their technology readiness level.

Li, Wenqin↗

Molecular simulation as a tool for studying lignin

Lignocellulosic biomass provides a sustainable source of sugars for biofuel and biomaterial production. However, biomass resistance to degradation imposes difficulties for economical conversion of plant carbohydrates to fermentable sugars. One of the key contributors to recalcitrance is lignin. Understanding the properties of lignin macromolecules in the cell wall matrix is useful for manipulating biomass structure to generate more easily degradable biomass. Along with experimental techniques such as 2D-NMR and mass spectrometry, computational techniques can be useful for characterizing the structural and energetic properties of the biomass assembly and its individual constituents. Here, we provide a brief introduction to lignin, review some of the recent, relevant scientific literature, and give our perspectives on the role of molecular simulation in understanding lignin structure.

09 BIOMASS FUELS↗

The Thermodynamic Links between Substrate, Enzyme, and Microbial Dynamics in Michaelis-Menten-Monod Kinetics

Accurate prediction of the temperature response of the velocity v of a biochemical reaction has wide applications in cell biology, reaction design, and biomass yield enhancement. Here in this study, we introduce a simple but comprehensive mechanistic approach that uses thermodynamics and biochemical kinetics to describe and link the reaction rate and Michaelis–Menten constants (k T and K T ) with the biomass yield and mortality rate (Y T and δ T ) as explicit functions of T . The temperature control is exerted by catabolic enthalpy at low temperatures and catabolic entropy at high temperatures, whereas changes in cell and enzyme–substrate heat capacity shift the anabolic electron use efficiency e A and the maximum reaction velocity v max . We show that cells have optimal growth when the catabolic (differential) free energy of activation decreases the cell free energy harvest required to duplicate their internal structures as long as electrons for anabolism are available. Lastly, with the described approach, we accurately predicted observed glucose fermentation and ammonium nitrification dynamics across a wide temperature range with a minimal number of thermodynamics parameters, and we highlight how kinetic parameters are linked to each other using first principles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗