Synergistic co-utilization of biomass-derived sugars enhances aromatic amino acid production by engineered Escherichia coli

Efficient co-utilization of mixed sugar feedstocks remains a biomanufacturing challenge, thus motivating ongoing efforts to engineer microbes for improved conversion of glucose-xylose mixtures. This study focuses on enhancing phenylalanine production by engineering Escherichia coli to efficiently co-utilize glucose and xylose. Flux balance analysis identified E4P flux as a bottleneck which could be alleviated by increasing the xylose-to-glucose flux ratio. A mutant copy of the xylose-specific activator (XylR) was then introduced into the phenylalanine-overproducing E. coli NST74, which relieved carbon catabolite repression and enabled efficient glucose-xylose co-utilization. Carbon contribution analysis through 13 C-fingerprinting showed a higher preference for xylose in the engineered strain (NST74X), suggesting superior catabolism of xylose relative to glucose. As a result, NST74X produced 1.76 g/L phenylalanine from a model glucose-xylose mixture; a threefold increase over NST74. Then, using biomass-derived sugars, NST74X produced 1.2 g/L phenylalanine, representing a 1.9-fold increase over NST74. Notably, and consistent with the carbon contribution analysis, the xylR* mutation resulted in a fourfold greater maximum rate of xylose consumption without significantly impeding the maximum rate of total sugar consumption (0.87 vs. 0.70 g/L-h). This study presents a novel strategy for enhancing phenylalanine production through the co-utilization of glucose and xylose in aerobic E. coli cultures, and highlights the potential synergistic benefits associated with using substrate mixtures over single substrates when targeting specific products.

Characterizing Escherichia coli's transcriptional response to different styrene exposure modes reveals novel toxicity and tolerance insights

The global transcriptional response of Escherichia coli to styrene and potential influence of exposure source was determined by performing RNA sequencing (RNA-seq) analysis on both styrene-producing and styrene-exposed cells. In both cases, styrene exposure appears to cause both cell envelope and DNA damage, to which cells respond by down-regulating key genes/pathways involved in DNA replication, protein production, and cell wall biogenesis. Among the most significantly up-regulated genes were those involved with phage shock protein response (e.g. pspABCDE/G), general stress regulators (e.g. marA, rpoH), and membrane-altering genes (notably, bhsA, ompR, ldtC), whereas efflux transporters were, surprisingly, unaffected. Subsequent studies with styrene addition demonstrate how strains lacking ompR [involved in controlling outer membrane (OM) composition/osmoregulation] or any of tolQ, tolA, or tolR (involved in OM constriction) each displayed over 40% reduced growth relative to wild-type. Conversely, despite reducing basal fitness, overexpression of plsX (involved in phospholipid biosynthesis) led to 70% greater growth when styrene exposed. These collective differences point to the likely importance of OM properties in controlling native styrene tolerance. Overall, the collective behaviours suggest that, regardless of source, prolonged exposure to inhibitory styrene levels causes cells to shift from'growth mode' to 'survival mode', redistributing cellular resources to fuel native tolerance mechanisms.

Catabolic Division of Labor Enhances Production of D-Lactate and Succinate From Glucose-Xylose Mixtures in Engineered Escherichia coli Co-culture Systems

Although biological upgrading of lignocellulosic sugars represents a promising and sustainable route to bioplastics, diverse and variable feedstock compositions (e.g., glucose from the cellulose fraction and xylose from the hemicellulose fraction) present several complex challenges. Specifically, sugar mixtures are often incompletely metabolized due to carbon catabolite repression while composition variability further complicates the optimization of co-utilization rates. Benefiting from several unique features including division of labor, increased metabolic diversity, and modularity, synthetic microbial communities represent a promising platform with the potential to address persistent bioconversion challenges. In this work, two unique and catabolically orthogonal Escherichia coli co-cultures systems were developed and used to enhance the production of D-lactate and succinate (two bioplastic monomers) from glucose-xylose mixtures (100 g L-1 total sugars, 2:1 by mass). In both cases, glucose specialist strains were engineered by deleting xylR (encoding the xylose-specific transcriptional activator, XylR) to disable xylose catabolism, whereas xylose specialist strains were engineered by deleting several key components involved with glucose transport and phosphorylation systems (i.e., ptsI, ptsG, galP, glk) while also increasing xylose utilization by introducing specific xylR mutations. Optimization of initial population ratios between complementary sugar specialists proved a key design variable for each pair of strains. In both cases, ∼91% utilization of total sugars was achieved in mineral salt media by simple batch fermentation. High product titer (88 g L-1 D-lactate, 84 g L-1 succinate) and maximum productivity (2.5 g L-1 h-1 D-lactate, 1.3 g L-1 h-1 succinate) and product yield (0.97 g g-total sugar-1 for D-lactate, 0.95 g g-total sugar-1 for succinate) were also achieved.

Muconic Acid Production via Alternative Pathways and a Synthetic "Metabolic Funnel"

Muconic acid is a promising platform biochemical and precursor to adipic acid, which can be used to synthesize various plastics and polymers. In this study, the systematic construction and comparative evaluation of a modular network of non-natural pathways for muconic acid biosynthesis was investigated in Escherichia coli, including via three distinct and novel pathways proceeding via phenol as a common intermediate. However, poor recombinant activity and high promiscuity of phenol hydroxylase ultimately limited "phenol-dependent" muconic acid production. A fourth pathway proceeding via p-hydroxybenzoate, protocatechuate, and catechol was accordingly developed, though with muconic acid titers by this route reaching just 819 mg/L, its performance lagged behind that of the established, "3-dehydroshikimiate-derived" route. Finally, these two most promising pathways were coexpressed in parallel to create a synthetic "metabolic funnel" that, by enabling maximal net precursor assimilation and flux while preserving native chorismate biosynthesis, nearly doubled muconic acid production to up to >3.1 g/L at a glucose yield of 158 mg/g while introducing only a single auxotrophy. This generalizable, "funneling" strategy is expected to have broad applications in metabolic engineering for further enhancing production of muconic acid, as well as other important bioproducts of interest.

Nonconvective mixing of miscible ionic liquids

Ionic liquids (ILs) are ionic compounds that are liquid at room temperature. We studied the spontaneous mixing behavior between two ILs, ethylammonium nitrate (EAN) and 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]), and observed notable phenomena. Experimental studies showed that the interface between the two ILs was unusually long-lived, despite the ILs being miscible with one another. Molecular dynamics (MD) simulations supported these findings and provided insight into the micromixing behavior of the ILs. We found that not only did the ions experience slow diffusion as they mix but also exhibited significant ordering into distinct regions. We suspect that this ordering disrupted concentration gradients in the direction normal to the interface, thus hindering diffusion in this direction and allowing the macroscopic interface to remain for long periods of time. Intermolecular interactions responsible for this behavior included the O-NH interaction between the EAN ions and the carbon chain-carbon chain interactions between the [BMIM](+) cations, which associate more strongly in the mixed state than in the pure IL state.

Molecular dynamics studies on the adaptability of an ionic liquid in the extraction of solid nanoparticles

Recently, a number of publications have suggested that ionic liquids (ILs) can absorb solid particles. This development may have implications in fields like oil sand processing, oil spill beach cleanup, and water treatment. In this Article, we provide a computational investigation of this phenomenon via molecular dynamics simulations. Two particle surface chemistries were investigated: (1) hydrocarbon-saturated and (2) silanol-saturated, representing hydrophobic and hydrophilic particles, respectively. Employing 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF(6)]) as a model IL, these nanoparticles were allowed to equilibrate at the IL/water and IL/hexane interfaces to observe the interfacial self-assembled structures. At the IL/water interface, the hydrocarbon-based nanoparticles were nearly completely absorbed by the IL, while the silica nanoparticles maintained equal volume in both phases. At the IL/hexane interface, the hydrocarbon nanoparticles maintained minimal interactions with the IL, whereas the silica nanoparticles were nearly completely absorbed by it. Studies of these two types of nanoparticles immersed in the bulk IL indicate that the surface chemistry has a great effect on the corresponding IL liquid structure. These effects include layering of the ions, hydrogen bonding, and irreversible absorption of some ions to the silica nanoparticle surface. We quantify these effects with respect to each nanoparticle. The results suggest that ILs likely exhibit this absorption capability because they can form solvation layers with reduced dynamics around the nanoparticles.