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Stereoselectivity of the Pictet–Spengler reaction catalyzed by KslB resolved by the crystal structure of enzyme-product complex.
Pyrone-2,4-dicarboxylic acid (PDC) is a valuable polymer precursor that can be derived from the microbial degradation of lignin. The key enzyme in the microbial production of PDC is 4-carboxy-2-hydroxymuconate-6-semialdehyde (CHMS) dehydrogenase, which acts on the substrate CHMS. We present the crystal structure of CHMS dehydrogenase (PmdC from Comamonas testosteroni) bound to the cofactor NADP, shedding light on its three-dimensional architecture, and revealing residues responsible for binding NADP. Using a combination of structural homology, molecular docking, and quantum chemistry calculations, we have predicted the binding site of CHMS. Key histidine residues in a conserved sequence are identified as crucial for binding the hydroxyl group of CHMS and facilitating dehydrogenation with NADP. Mutating these histidine residues results in a loss of enzyme activity, leading to a proposed model for the enzyme's mechanism. These findings are expected to help guide efforts in protein and metabolic engineering to enhance PDC yields in biological routes to polymer feedstock synthesis.
Soil Pseudomonas species, which thrive on lignin derivatives, are widely explored for biotechnology applications in lignin valorization. However, how the native metabolism coordinates phenolic carbon processing with required cofactor generation remains poorly understood. Here, we achieve quantitative understanding of this metabolic balance through a detailed multi-omics investigation of Pseudomonas putida KT2440 grown on four common phenolic acid substrates: ferulate, p-coumarate, vanillate, and 4-hydroxybenzoate. Relative to succinate, proteomics reveals > 140-fold increase in transport and catabolic proteins for aromatics, but metabolomics identifies bottlenecks in initial catabolism to maintain favorable cellular energy charge, which is compromised in mutants with resolved bottlenecks. Up to 30-fold increase in pyruvate carboxylase and glyoxylate shunt proteins implies a metabolic remodeling confirmed by kinetic 13 C-metabolomics. Quantitative analysis by 13 C-fluxomics demonstrates coupling of this remodeling with cofactor production. Specifically, anaplerotic carbon recycling through pyruvate carboxylase promotes tricarboxylic acid cycle fluxes to generate 50-60% NADPH yield and 60-80% NADH yield, resulting in up to 6-fold greater ATP surplus than with succinate metabolism; the glyoxylate shunt sustains cataplerotic flux through malic enzyme for the remaining NADPH yield. This quantitative blueprint affords cofactor imbalance predictions in proposed engineering of key metabolic nodes in lignin valorization pathways.
This project focused on developing cell-free systems to directly express multi-enzyme catalysts and perform CO2 bioconversions for industrial chemical production. The use of cell-free expression (CFE) systems derived from bacterial lysates is emerging as a promising approach for biomanufacturing. CFEs are genetically programmable, permit the expression of toxic enzymes, and allow for rapid prototyping of metabolic pathways. Research Contributions: 1. Understanding the Area Investigated: This research advances the understanding of cell-free systems by demonstrating their capability to perform complex multi-enzyme reactions. By directly expressing multi-gene systems, CFEs avoid the high costs and inefficiencies associated with producing and purifying enzymes for multi-step pathways. 2. Technical Effectiveness and Economic Feasibility: The project successfully engineered a CFE-based multienzyme biocatalyst for the de novo synthesis of serine and glycine from CO2 equivalents (formate and bicarbonate) and ammonia. This method achieved a 30% conversion rate of formate into these industrially important amino acids. Additionally, an 8-gene CFE biocatalyst was developed to produce malate, conserving 43% of carbon that would otherwise be lost as CO2. This approach has the potential to reach higher carbon efficiency than microbial production. 3. Public Benefit: The cell-free production of chemicals like serine, glycine, and malate using electrochemically generated formate could significantly reduce CO2 emissions. For example, satisfying the global malate market with this method could avoid approximately 400,000 tons of CO2 emissions annually. This work demonstrates the potential of CFE systems to produce platform chemicals, contributing to environmental sustainability and reducing reliance on petrochemicals. Future Prospects: The CFE-based biocatalyst process could be extended to produce a variety of chemicals, including other industrial di-acids, aromatics, terpenes, alcohols, and polymers. This project showcases the capabilities of cell-free expression systems for prototyping carbon-conserving pathways and sustainably bioproducing platform chemicals, marking a significant step towards economically-viable industrial processes.
Polyamides, such as nylons, are often used in multi-component materials, like textiles and packaging, and are accompanied with unique recycling challenges. Recently, autoxidation and bioconversion has emerged as a tandem approach for the conversion of mixed plastics waste to single products, however the fate of polyamides in these processes is unknown. Here, we optimized the autoxidation of nylon-6 and nylon-6,6 depolymerization, achieving >92 mol% nitrogen recovery from both substrates, predominantly as acetamide, and 20–27 mol% carbon recovery (not including acetamide). Experiments with 13 C-labeled acetic acid demonstrated that the carbon in acetamide was solvent derived. Autoxidation of mixed nylon-6 and poly(ethylene terephthalate) (PET) post-consumer fibers resulted in similar carbon and nitrogen recoveries from nylon, while PET was depolymerized to terephthalic acid (TPA) at >65 C-mol% recovery. Next, we engineered Pseudomonas putida KT2440 to utilize acetamide as the sole carbon and nitrogen source for growth through the constitutive expression of genes encoding amidase enzymes, including a native amidase (PP_0613) shown to be active on C 2 –C 4 amides. Heterologous chromosomal expression of amiE, encoding the amidase from P. aeruginosa, was found to be superior to PP_0613 constitutive expression in genome integrated strains. Prior engineering to enable TPA conversion to β-ketoadipate pathway intermediate protocatechuate was leveraged and combined with deletion of pcaD to produce muconolactone as a product. Finally, a stacked strain engineered for conversion of acetamide, TPA, and DCAs was evaluated on the reaction product from autoxidation of mixed post-consumer nylon and PET fibers without any supplemental nitrogen, achieving quantitative yields in the presence of supplemental carbon.
Rising concerns for sustainability and global climate change have driven the development of sustainable production pathways for biofuels and chemicals from lignocellulosic biomass via integrated biological and chemical processes. We constructed an engineered Saccharomyces cerevisiae capable of producing 2,3-butanediol (2,3-BDO) from glucose without accumulating ethanol and glycerol, which hinder downstream processing of 2,3-BDO, through extensive metabolic reprogramming. Specifically, we introduced heterologous 2,3-BDO biosynthetic enzymes and deleted the major isozymes of ethanol and glycerol biosynthetic enzymes. In addition, we introduced an NAD+ regenerating Pyruvate-Malate (PM) cycle and enhanced the NAD+ regenerating capability of the PM cycle to resolve the redox imbalance from the deletion of ethanol and glycerol production pathways. The resulting engineered yeast produced 109.9 g/L of 2,3-BDO with a productivity of 1.0 g/L/h and a yield of 0.36 g/g glucose in a fed-batch fermentation. We also conducted techno-economic analysis (TEA) and life cycle assessment (LCA) of the production of methyl ethyl ketone (MEK) through catalytic dehydration of 2,3-BDO. A TEA based on the experimental results indicated that the minimum product selling price (MPSP) was estimated to be $1.90/kg. Regarding cradle-to-grave LCA, 100-year global warming potential (GWP100) and fossil energy consumption (FEC) were found to be 0.37 kg CO2 eq/kg and 3.1 MJ/kg, respectively. These results demonstrated the feasibility of cost-competitive and sustainable bio-based MEK production via yeast fermentation. In addition, we explored the possibility of using the fermentation broth containing 2,3-BDO as a biostimulant inducing drought tolerance in plants. As a result, the yeast 2,3-BDO fermentation broth can induce drought tolerance in Arabidopsis thaliana without a complicated purification process.
Enzymatic depolymerization has the potential to contribute to nylon waste recycling. However, the implementation of a viable industrial process still lags far behind progress in enzymatic polyester recycling. Here we review the current biocatalytic nylon recycling landscape, highlighting biochemical, structural, and materials science barriers that currently limit depolymerization extents. We detail efforts to identify, engineer, and characterize new nylon depolymerases, where currently even the best biocatalysts rarely exceed ~1 wt% conversion of solid polymer to products. Based on our analyses, we suggest that limited substrate accessibility due to substrate crystallinity and hydrogen bonding, rather than intrinsic enzyme inefficiency or instability, is the primary bottleneck to enhanced depolymerization. Guided by successes in polyester enzymatic recycling, we outline a research roadmap combining nylonase engineering with polymer pretreatment, chemo-enzymatic cascades, and process analyses to accelerate development of viable enzymatic nylon recycling processes.
Over the past three decades, efforts to decipher plant metabolism have shed light on key enzymes driving specialized metabolite biosynthesis. Although only few pathways have been completely investigated to date, their characterization paves the way for exploring the potential effects of specialized metabolites on plant physiology. Among them is the linear furanocoumarin pathway, which was recently completed to produce up to psoralen. In this study, we report the first metabolic engineering of the linear furanocoumarin pathway to enable artificial psoralen production in tomato, through the integration of four genes coding for the enzymes: Umbelliferone Synthase (PsDiox), Demethylsuberosin Synthase (PsPT1), Marmesin Synthase (FcCYP76F112) and Psoralen Synthase (PsCYP71AJ3). Metabolic analyses confirmed the detection of small quantities of psoralen in the transgenic tomato line, but also highlighted a larger accumulation of coumarins and particularly scopoletin. Using morphophysiological and multi-omics analyses, we explorate how such metabolic modifications, could impact growth and affect plant physiology.
The yeast Rhodotorula toruloides is a promising bioproduction organism due to its high lipid yields and ability to grow on cheap and abundant substrates. Quantitative, systems-level assessment of its metabolic activity is accordingly merited. Resource-balance analysis (RBA) models capture not only reaction stoichiometry but also enzyme requirements for catalysis, providing valuable tools for understanding metabolic trade-offs and optimizing metabolic engineering strategies. Here, in this work, we present systems-level measurements of R. toruloides metabolic flux based on isotope tracing and metabolic flux analysis. In combination with new proteomic measurements, these flux data are used to parameterize a genome-scale resource balance model rtRBA. We find that S. cerevisiae and R. toruloides grow at nearly indistinguishable rates using similar biosynthetic but dramatically different central metabolic programs. R. toruloides consumes one-fifth as much glucose, which it metabolizes primarily via the pentose phosphate pathway and TCA cycle unlike primarily glycolysis in S. cerevisiae . Overall, across these two divergent yeasts, protein abundances aligned more closely than metabolic flux. Resource balance modeling of these metabolic programs predicts superior theoretical yields but lower productivities in R. toruloides than S. cerevisiae for industrial chemicals, highlighting the value of rapid glucose uptake for productivity but respiratory metabolism for yields.
Acetyl-TAG (3-acetyl-1,2-diacylglycerol), unique triacylglycerols (TAG) possessing an acetate group at the sn -3 position, exhibit valuable properties, such as reduced viscosity and freezing points. Previous attempts to engineer acetyl-TAG production in oilseed crops did not achieve the high levels found in naturally producing Euonymus seeds. Here, we demonstrate the successful generation of camelina and pennycress transgenic lines accumulating nearly pure acetyl-TAG at 93 mol% and 98 mol%, respectively. These ultrahigh acetyl-TAG synthesizing lines were created using gene-edited FATTY ACID ELONGASE1 ( FAE1 ) mutant lines as an improved genetic background to increase levels of acetyl-CoA available for acetyl-TAG synthesis mediated by the expression of EfDAcT, a high-activity diacylglycerol acetyltransferase isolated from Euonymus fortunei . Combining EfDAcT expression with suppression of the competing TAG-synthesizing enzyme DGAT1 further enhanced acetyl-TAG accumulation. These ultrahigh levels of acetyl-TAG exceed those in earlier engineered oilseeds and are equivalent or greater than those in Euonymus seeds. Imaging of lipid localization in transgenic seeds revealed that the low amounts of residual TAG were mostly confined to the embryonic axis. Similar spatial distributions of specific TAG and acetyl-TAG molecular species, as well as their probable diacylglycerol (DAG) precursors, provide additional evidence that acetyl-TAG and TAG are both synthesized from the same tissue-specific DAG pools. Remarkably, this ultrahigh production of acetyl-TAG in transgenic seeds exhibited minimal negative effects on seed properties, highlighting the potential for production of designer oils required for economical biofuel industries.
ABSTRACT Cobamides, the vitamin B 12 (cobalamin) family of cofactors, are used by most organisms but produced by only a fraction of prokaryotes, and are thus considered key shared nutrients among microbes. Cobamides are structurally diverse, with multiple different cobamides found in most microbial communities. The ability to use different cobamides has been tested for several bacteria and microalgae, and nearly all show preferences for certain cobamides. This approach is limited by the commercial unavailability of cobamides other than cobalamin. Here, we have extracted and purified seven commercially unavailable cobamides to characterize bacterial cobamide preferences based on growth in specific cobamide-dependent conditions. The tested bacteria include engineered strains of Escherichia coli , Sinorhizobium meliloti , and Bacillus subtilis expressing native or heterologous cobamide-dependent enzymes, cultured under conditions that functionally isolate specific cobamide-dependent processes such as methionine synthesis. Comparison of these results to those of previous studies of diverse bacteria and microalgae revealed that a broad diversity of cobamide preferences exists not only across different organisms but also between different cobamide-dependent metabolic pathways within the same organism. The microbes differed in the cobamides that support growth most efficiently, cobamides that do not support growth, and the minimum cobamide concentrations required for growth. The latter differ by up to four orders of magnitude across organisms from different environments and by up to 20-fold between cobamide-dependent enzymes within the same organism. Given that cobamides are shared, required for use of specific growth substrates, and essential for central metabolism in certain organisms, cobamide preferences likely impact community structure and function. IMPORTANCE Nearly all bacteria are found in microbial communities with tens to thousands of other species. Molecular interactions such as metabolic cooperation and competition are key factors underlying community assembly and structure. Cobamides, the vitamin B 12 family of enzyme cofactors, are one such class of nutrients, produced by only a minority of prokaryotes but required by most microbes. A unique aspect of cobamides is their broad diversity, with nearly 20 structural forms identified in nature. Importantly, this structural diversity impacts growth as most bacteria that have been tested show preferences for specific cobamide forms. We measured cobamide-dependent growth in several model bacteria and compared the results to those of previous analyses of cobamide preference. We found that cobamide preferences vary widely across bacteria, showing the importance of characterizing these aspects of cobamide biology to understand the impact of cobamides on microbial communities.
Negative emissions technologies will be essential for limiting anthropogenic global temperature increases to 2 °C in the later years of the 21st century. Carbonic anhydrase (CA) metalloenzymes catalyze the otherwise slow conversion of CO 2 into carbonic acid (H 2 CO 3 ), suggesting their utility in the rapid hydration and downstream capture of dissolved CO 2 in aqueous media for a variety of CO 2 capture methods, such as thermal and pH swings and mineralization. The possibility of driving the rapid capture of CO 2 by catalyzing the CO 2 hydration bottleneck carries real potential for realizing efficient direct air capture (DAC) and direct ocean capture (DOC) systems. However, scaled application of CAs will be dependent on some way of economically sourcing the enzymes at volumes relevant to scaled DAC/DOC operations. In this perspective, we consider the prospect of catalyzing CO 2 hydration using a CA that is bound to the outer membrane of a cyanobacterial host, engineered constructs we call CyCAMs. Coupling extracellular CA expression to a marine, photosynthetic cyanobacterial host results in a CO 2 hydration catalyst that is continuously refreshed during the bacterial growth cycle, without the need for enzyme purification or harvesting steps. In the case of marine cyanobacteria, sunlight and the solutes native to seawater provide the respective energy, nutrients and sources of inorganic carbon essential to maintaining the bacterial population. We consider the potential impact of CA-mediated CO 2 hydration on a variety of DAC processes, with CO 2 mineralization explored as a primary use case.
Biological plastics deconstruction and upcycling have emerged as sustainable alternatives to traditional recycling technologies for plastics waste. The discovery and engineering of efficient thermostable poly(ethylene terephthalate) (PET) hydrolases have made biological PET recycling possible at scale; however, enzymes for non-PET plastics, which account for approximately 70% of all plastics produced, remain largely undiscovered. To accelerate the discovery of such enzymes, we develop a high-throughput screen to detect initial polymer oxidation, specifically that of the C-H bond to an aldehyde. We test 4-hydrazino-7-nitro-2,1,3-benxoxadiozole hydrazine (NBD-H), which reacts with generated aldehydes to form a fluorescent hydrazone on plasma oxidized low-density polyethylene (LDPE) films. Hydrazone generation correlated well with the area of aldehyde peaks as measured by Fourier Transform Infrared Spectroscopy (FTIR) (R2 = 0.92). Moreover, we demonstrate that the probe reliably identifies LDPE-active dye decolorizing peroxidases (DyPs) that generate aldehydes on LDPE films (1.7 – 3.0 fold change relative to background), serving as an effective screen as demonstrated by receiver operating characteristic area under the curve of 0.95. Furthermore, this assay offers an LDPE oxidation screening platform that can be readily parallelized and automated for accelerated discovery of enzymes involved in polyolefin deconstruction.
Photosynthesis enables the conversion of one of the most abundant and free forms of energy, sunlight, into chemical bonds through the utilization of highly tailored protein complexes. These enzymes work in unison to absorb, convert, and transform light into high-energy electrons which are used for various functions important to metabolism and cellular protection. Over the last ∼50 years, photosynthetic organisms, such as cyanobacteria, have been adapted and engineered to produce valuable compounds like hydrogen and ethylene, among others. Often this is performed by removing native and/or adding in exogenous energy utilization pathways so that light energy is re-directed towards the synthesis of desired compounds. However, the interplay between primary light capture, conversion reactions, and the downstream electron utilization sinks is not fully understood. Further complicating these strategies are the plethora of compensatory mechanisms that facilitate steady electron flow and the maintenance of photosynthesis under dynamic conditions. This manifests as structural and functional plasticity of the photosynthetic machinery, often seen in modulations of oligomeric compositions or changes in protein-protein interactions and coupling with redox enzymes. Understanding these mechanisms is crucial to biotechnology applications because re-engineering electron utilization sinks has profoundly different effects on the light capture and conversion reactions of photosynthesis. Optimization requires a molecular-level understanding of the functional interrelationships between electron sinks and photosynthetic components that influence photosynthetic efficiencies to realize potential improvements in product yields. Here, we aim to highlight how perturbation of reductive reactions is revealing the functional plasticity in key components of the photosynthetic energy transduction pathway.
Autonomous molecular machines capable of converting chemical energy into mechanical motion are foundational components for synthetic nanoscale systems. Inspired by biological motors, we report the construction of a tunable, RNA-fueled DNA origami engine that drives the cyclic movement of a 500 nm-diameter particle at the microscale. The engine operates via sequential RNA–DNA hybridization and enzymatic cleavage by RNase H, enabling reversible switching between folded and unfolded conformations without external intervention. By modulating RNA and enzyme concentrations and controlling temperature, we achieve tunable switching kinetics, with transition periods as short as ~10 s. Kinetic modeling reveals that the folding pathway is governed by both productive RNA binding and the enzymatic clearance of misfolded intermediates, while unfolding is primarily controlled by RNase H activity. Since the RNA fuel binds specifically to the DNA strands, each engine is addressable simply by changing the sequences. This work demonstrates a programmable, self-resetting molecular actuator and offers a blueprint for building more complex nanomechanical systems with forces and energies comparable to molecular motors.
Transcriptional regulators play key roles in plant growth, development and environmental responses; however, understanding how their regulatory activity is encoded at the protein level has been hindered by a lack of multiplexed large-scale methods to characterize protein libraries in planta. Here we present enrichment of nuclear trans-elements reporter assay in plants with sequencing (ENTRAP-seq), a high-throughput method that introduces protein-coding libraries into plant cells to drive a nuclear magnetic sorting-based reporter, enabling multiplexed measurement of regulatory activity from thousands of protein variants. Using ENTRAP-seq and machine learning, we screen 1,495 plant viruses and identify hundreds of putative transcriptional regulatory domains found in structural proteins and enzymes not associated with gene regulation. In addition, we combine ENTRAP-seq with machine-guided design to engineer the activity of a plant transcription factor in a semirational fashion. Our findings demonstrate how scalable protein function assays deployed in planta will enable the characterization of natural and synthetic coding diversity in plants.
Abstract Modification of lignin in feedstocks via genetic engineering aims to reduce biomass recalcitrance to facilitate efficient conversion processes. These improvements can be achieved by expressing exogenous enzymes that interfere with native biosynthetic pathways responsible for the production of the lignin precursors. In planta expression of a bacterial 3-dehydroshikimate dehydratase in poplar trees reduced lignin content and altered the monomer composition, which enabled higher yields of sugars after cell wall polysaccharide hydrolysis. Understanding how plants respond to such genetic modifications at the transcriptional and metabolic levels is needed to facilitate further improvement and field deployment. In this work, we acquired fundamental knowledge on lignin-modified poplar expressing 3-dehydroshikimate dehydratase using RNA-seq and metabolomics. The data clearly demonstrate that changes in gene expression and metabolite abundance can occur in a strict spatiotemporal fashion, revealing tissue-specific responses in the xylem, phloem, or periderm. In the poplar line that exhibited the strongest reduction in lignin, we found that 3% of the transcripts had altered expression levels and ~19% of the detected metabolites had differential abundance in the xylem from older stems. The changes affected predominantly the shikimate and phenylpropanoid pathways as well as secondary cell wall metabolism, and resulted in significant accumulation of hydroxybenzoates derived from protocatechuate and salicylate.
Cyanobacterial production of a biofertilizer shows promise as an environmentally benign alternative to conventional nitrogen fertilizers, reducing environmental and energy burdens through light-driven nitrogen and carbon fixation. One route to realizing the potential for a nitrogen-rich, slow-releasing biofertilizer involves the genetic engineering of cyanobacteria to produce guanidine. Recent advances have demonstrated enzymatic guanidine production in cyanobacteria, but an understanding of cyanobacterial guanidine metabolism is still limited. This Perspective highlights strategies and opportunities for cyanobacterial guanidine production in a Design−Build−Test−Learn cycle. Exploring new guanidine-producing enzymes via phylogenetics could expand candidate enzymes, while understanding the metabolism of substrates can identify constraints and opportunities in substrate utilization. Additionally, guanidine sensing and export are crucial areas of study to enable continuous fertilizer production and stable nitrogen flux. These strategies will guide the development of advanced nitrogen biofertilizer strategies for the agricultural sector.