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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Biochemical and structural characterization of a sphingomonad diarylpropane lyase for cofactorless deformylation

Lignin valorization is being intensely pursued via tandem catalytic depolymerization and biological funneling to produce single products. In many lignin depolymerization processes, aromatic dimers and oligomers linked by carbon–carbon bonds remain intact, necessitating the development of enzymes capable of cleaving these compounds to monomers. Recently, the catabolism of erythro -1,2-diguaiacylpropane-1,3-diol ( erythro -DGPD), a ring-opened lignin-derived β-1 dimer, was reported in Novosphingobium aromaticivorans . The first enzyme in this pathway, LdpA (formerly LsdE), is a member of the nuclear transport factor 2 (NTF-2)-like structural superfamily that converts erythro -DGPD to lignostilbene through a heretofore unknown mechanism. In this study, we performed biochemical, structural, and mechanistic characterization of the N. aromaticivorans LdpA and another homolog identified in Sphingobium sp. SYK-6, for which activity was confirmed in vivo. For both enzymes, we first demonstrated that formaldehyde is the C 1 reaction product, and we further demonstrated that both enantiomers of erythro -DGPD were transformed simultaneously, suggesting that LdpA, while diastereomerically specific, lacks enantioselectivity. We also show that LdpA is subject to a severe competitive product inhibition by lignostilbene. Three-dimensional structures of LdpA were determined using X-ray crystallography, including substrate-bound complexes, revealing several residues that were shown to be catalytically essential. We used density functional theory to validate a proposed mechanism that proceeds via dehydroxylation and formation of a quinone methide intermediate that serves as an electron sink for the ensuing deformylation. Overall, this study expands the range of chemistry catalyzed by the NTF-2-like protein family to a prevalent lignin dimer through a cofactorless deformylation reaction.

09 BIOMASS FUELS↗
DOE OSTI2021

Metabolism of Syringyl Lignin-Derived Compounds in Pseudomonas putida Enables Convergent Production of 2-Pyrone-4,6-Dicarboxylic Acid

Valorization of lignin, an abundant component of plant cell walls, is critical to enabling the lignocellulosic bioeconomy. Biological funneling using microbial biocatalysts has emerged as an attractive approach to convert complex mixtures of lignin depolymerization products to value-added compounds. Ideally, biocatalysts would convert aromatic compounds derived from the three canonical types of lignin: syringyl (S), guaiacyl (G), and p-hydroxyphenyl (H). Pseudomonas putida KT2440 (hereafter KT2440) has been developed as a biocatalyst owing in part to its native catabolic capabilities but is not known to catabolize S-type lignin-derived compounds. Here, we demonstrate that syringate, a common S-type lignin-derived compound, is utilized by KT2440 only in the presence of another energy source or when vanAB was overexpressed, as syringate was found to be O-demethylated to gallate by VanAB, a two-component monooxygenase, and further catabolized via extradiol cleavage. Unexpectedly, the specificity (kcat/KM) of VanAB for syringate was within 25% that for vanillate and O-demethylation of both substrates was well-coupled to O2 consumption. However, the native KT2440 gallate-cleaving dioxygenase, GalA, was potently inactivated by 3-O-methylgallate. To engineer a biocatalyst to simultaneously convert S-, G-, and H-type monomers, we therefore employed VanAB from Pseudomonas sp. HR199, which has lower activity for 3MGA, and LigAB, an extradiol dioxygenase able to cleave protocatechuate and 3-O-methylgallate. This strain converted 93% of a mixture of lignin monomers to 2-pyrone-4,6-dicarboxylate, a promising bio-based chemical. Overall, this study elucidates a native pathway in KT2440 for catabolizing S-type lignin-derived compounds and demonstrates the potential of this robust chassis for lignin valorization.

2-pyrone-4,6-dicarboxylic acid↗
DOE OSTI2021

Accurate determination of genotypic variance of cell wall characteristics of a Populus trichocarpa pedigree using high-throughput pyrolysis-molecular beam mass spectrometry

Abstract Background Pyrolysis-molecular beam mass spectrometry (py-MBMS) analysis of a pedigree of Populus trichocarpa was performed to study the phenotypic plasticity and heritability of lignin content and lignin monomer composition. Instrumental and microspatial environmental variability were observed in the spectral features and corrected to reveal underlying genetic variance of biomass composition. Results Lignin-derived ions (including m/z 124, 154, 168, 194, 210 and others) were highly impacted by microspatial environmental variation which demonstrates phenotypic plasticity of lignin composition in Populus trichocarpa biomass. Broad-sense heritability of lignin composition after correcting for microspatial and instrumental variation was determined to be H 2 = 0.56 based on py-MBMS ions known to derive from lignin. Heritability of lignin monomeric syringyl/guaiacyl ratio ( S / G ) was H 2 = 0.81. Broad-sense heritability was also high (up to H 2 = 0.79) for ions derived from other components of the biomass including phenolics (e.g., salicylates) and C5 sugars (e.g., xylose). Lignin and phenolic ion abundances were primarily driven by maternal effects, and paternal effects were either similar or stronger for the most heritable carbohydrate-derived ions. Conclusions We have shown that many biopolymer-derived ions from py-MBMS show substantial phenotypic plasticity in response to microenvironmental variation in plantations. Nevertheless, broad-sense heritability for biomass composition can be quite high after correcting for spatial environmental variation. This work outlines the importance in accounting for instrumental and microspatial environmental variation in biomass composition data for applications in heritability measurements and genomic selection for breeding poplar for renewable fuels and materials.

09 BIOMASS FUELS↗
DOE OSTI2024

Catalytic carbon–carbon bond cleavage in lignin via manganese–zirconium-mediated autoxidation

Abstract Efforts to produce aromatic monomers through catalytic lignin depolymerization have historically focused on aryl–ether bond cleavage. A large fraction of aromatic monomers in lignin, however, are linked by various carbon–carbon (C–C) bonds that are more challenging to cleave and limit the yields of aromatic monomers from lignin depolymerization. Here, we report a catalytic autoxidation method to cleave C–C bonds in lignin-derived dimers and oligomers from pine and poplar. The method uses manganese and zirconium salts as catalysts in acetic acid and produces aromatic carboxylic acids as primary products. The mixtures of the oxygenated monomers are efficiently converted to cis,cis -muconic acid in an engineered strain of Pseudomonas putida KT2440 that conducts aromatic O -demethylation reactions at the 4-position. This work demonstrates that autoxidation of lignin with Mn and Zr offers a catalytic strategy to increase the yield of valuable aromatic monomers from lignin.

09 BIOMASS FUELS↗
DOE OSTI2022

Lignin Utilization

Valorization of lignin has massive potential economic and sustainability benefits for the lignocellulosic biorefinery. However, challenges remain to realize lignin conversion to coproducts, especially related to selective, high yield depolymerization to monomers and quantitative analytics on lignin, the latter of which is critical for accurate process modeling. Towards these goals, the Lignin Utilization project focuses on catalytic lignin deconstruction chemistries for C-O and C-C bond cleavage, development of analytical chemistry techniques to quantitatively characterize lignin, and syntheses of requisite model compounds for understanding lignin transformations. This work is done with and supports multiple BETO projects, including the Biological Lignin Valorization (BLV) project, the Separations Consortium, and others. Outcomes of Lignin Utilization for analytics and synthesis include 1) development of new mass spectrometry (MS) methods to characterize lignin dimers/oligomers in process streams, 2) deployment of a computational-experimental tool (with Biochemical Process Modeling and Simulation) to identify lignin-derived compounds with high fidelity from MS, and 3) delivery of >40 unique compounds. From a catalysis perspective, we have developed new oxidative approaches to cleave C-O and C-C bonds and produce >50% bio-available aromatic monomers for biological funneling for the BLV project and have developed recoverable bases for base-catalyzed deconstruction of lignin.

BIOMASS FUELS↗
DOE OSTI2022

Biological Lignin Valorization

Given lignin's heterogeneity, catalytic depolymerization results in aromatic compound mixtures, and conversion of this complex substrate to a single product is challenging. To that end, the Biological Lignin Valorization (BLV) project is pursuing biological funneling, wherein aromatic catabolic microbes are engineered to convert a mixture of lignin-derived compounds to a single product. Namely, we employ Pseudomonas putida and pursue atom-efficient products, such as muconic acid, which can be further converted to direct replacements or used in performance-advantaged bioproducts. Overall, biological lignin conversion can make major contributions to reduce the minimum fuel selling price of the integrated biorefinery. Early industrial efforts in this area are also leading to value-added products, including in collaboration with the BLV project. Primary challenges associated with BLV efforts include accessing bio-available monomers from lignin (with the Lignin Utilization project), enabling commercial titers, rates, and yields of bioproducts from lignin-derived compounds, and overcoming substrate and product toxicity. To date, we have 1) demonstrated 49 g/L of muconate from aromatic compounds and 4 g/L of muconate from lignin, 2) improved the toxicity tolerance of P. putida to key aromatic substrates, 3) debottlenecked biological funneling for higher rates, and 4) engineered P. putida to convert S, G, and H-type lignin-derived compounds to a single product.

BIOMASS FUELS,INORGANIC, ORGANIC, PHYSICAL, AND AN↗
DOE OSTI2022

Dynamic and single cell characterization of a CRISPR-interference toolset in Pseudomonas putida KT2440 for β-ketoadipate production from p -coumarate

We report Pseudomonas putida KT2440 is a well-studied bacterium for the conversion of lignin-derived aromatic compounds to bioproducts. The development of advanced genetic tools in P. putida has reduced the turnaround time for hypothesis testing and enabled the construction of strains capable of producing various products of interest. Here, we evaluate an inducible CRISPR-interference (CRISPRi) toolset on fluorescent, essential, and metabolic targets. Nuclease-deficient Cas9 (dCas9) expressed with the arabinose (8K)-inducible promoter was shown to be tightly regulated across various media conditions and when targeting essential genes. In addition to bulk growth data, single cell time lapse microscopy was conducted, which revealed intrinsic heterogeneity in knockdown rate within an isoclonal population. The dynamics of knockdown were studied across genomic targets in exponentially-growing cells, revealing a universal 1.75 ± 0.38 hour quiescent phase after induction where 1.5 ± 0.35 doublings occur before a phenotypic response is observed. To demonstrate application of this CRISPRi toolset, β-ketoadipate, a monomer for performance-advantaged nylon, was produced at a 4.39 ± 0.5 g/L and yield of 0.76 ± 0.10 mol/mol from p-coumarate, a hydroxycinnamic acid that can be derived from grasses. These cultivation metrics were achieved by using the higher strength IPTG (1K)-inducible promoter to knockdown the pcaIJ operon in the βKA pathway during early exponential phase. This allowed the majority of the carbon to be shunted into the desired product while eliminating the need for a supplemental carbon and energy source to support growth and maintenance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Pathway discovery and engineering for cleavage of a β-1 lignin-derived biaryl compound

Lignin biosynthesis typically results in a polymer with several inter-monomer bond linkages, and the heterogeneity of linkages presents a challenge for depolymerization processes. While several enzyme classes have been shown to cleave common dimer linkages in lignin, the pathway of bacterial β-1 spirodienone linkage cleavage has not been elucidated. In this study, we identified a pathway for cleavage of 1,2-diguaiacylpropane-1,3-diol (DGPD), a β-1 linked biaryl representative of a ring-opened spirodienone linkage, in Novosphingobium aromaticivorans DSM12444. In vitro assays using cell lysates demonstrated that RS14230 (LsdE) converts DGPD to a lignostilbene intermediate, which the carotenoid oxygenase, LsdA, then converts to vanillin. A Pseudomonas putida KT2440 strain engineered with lsdEA expression catabolizes erythro-DGPD, but not threo-DGPD. We further engineered P. putida to convert DGPD to a product, cis,cis-muconic acid. Overall, this work demonstrates the potential to identify new enzymatic reactions in N. aromaticivorans and expands the biological funnel of P. putida for microbial lignin valorization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Chemical Diversity of Oligomers in Biomass Fast Pyrolysis Oils, Part 2: Heavy Lignin-Derived Molecules and Highly Dehydrated Sugars from Dichloromethane-Insoluble Pyrolytic Lignin

Here, this paper, the second in a series, investigates the water-insoluble, dichloromethane (DCM)-insoluble residue of BTG pyrolysis oil, also known in the literature as high-molecular-weight pyrolytic lignin (HMW-PL). HMW-PL accounts for 9.2 wt % of the original bio-oil, which is known to increase upon aging and contribute to coke formation during bio-oil upgrading. Understanding its composition is crucial for managing pyrolysis oil during the processing. The HMW-PL was fractionated using a silica gel column with solvents of increasing polarity: ethyl acetate (EA), acetone (AC), isopropanol (ISO), and methanol (MeOH), yielding 49.2, 19.9, 8.2, and 8.1 wt %, respectively. Each subfraction was characterized by UV-fluorescence, FTIR, HSQC NMR, and (−)APCI-FT-Orbitrap MS. Analysis revealed that the EA subfraction primarily contained aromatic dimers (C 19 –C 20 ) and trimers (C 17 –C 13 ), while the MeOH subfraction was rich in oxygenated aliphatic monomers (C 8 –C 16 ) likely derived from sugar dehydration products. The resulting fractions were further separated via preparatory HPLC. Fifty-five candidate molecular structures were proposed based on the Orbitrap MS data, supported by UV-fluorescence, FTIR, and NMR results. This fractionation strategy defined four distinct subfractions, enabling the proposal of surrogate molecular structures and advancing the molecular-level understanding of the HMW-PL fraction in the pyrolysis bio-oil.

High-Molecular-Weight PL↗
DOE OSTI2021

Oxidative Catalytic Fractionation and Depolymerization of Lignin in a One-Pot Single-Catalyst System

It has been known that the yield of lignin monomers during lignin depolymerization is limited by the irreversible condensations of lignin in the fractionation and/or depolymerization process. In this study, we report a new oxidative catalytic fractionation (OCF) process with a simple and effective one-pot but two-step approach to depolymerize lignin to lignin-derived chemicals (LDCs) using polyoxometalate (POM) as the only catalyst. First, the POM effectively catalyzed the methoxylation of the active a-OH groups of lignin in a methanol and water mixture at low temperature (100 °C), and 96% of the stabilized lignin in the lignocellulose sawdust was extracted to the solution simultaneously. Then the lignin solution was heated to an elevated temperature (140 °C) in the same solvent. As a result, 74.0 wt % of the lignin (based on the weight of the Klason lignin in the wood) was converted to LDCs, including 45.9 wt % aromatic monomers.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2025

Lignin-Derived Methoxyterephthalates for Performance-Advantaged Polymers and Plasticizers

Lignin-derived aromatic carboxylic acids can be produced from oxidative catalytic processes and are promising building blocks for performance-advantaged bioproducts that leverage their inherent heteroatom functionalities. Here, we synthesize 2-methoxyterephthalate and 2,6-dimethoxyterephthalate derivatives by electrochemical carboxylation of guaiacyl- and syringyl-derived lignin monomers obtained from the oxidative deconstruction of lignin. These methoxylated terephthalates are evaluated as comonomers in poly(ethylene terephthalate) (PET) and as plasticizers that could replace petrochemically-derived isophthalate and phthalate, respectively. Specifically, we copolymerize 2-methoxy- and 2,6-dimethoxyterephthalate with dimethyl terephthalate to form several PET copolymers, both of which enable the properties of PET to be tuned, with an incorporation beyond 25% producing amorphous polyesters. At 10 mol % loading in the copolymers, we demonstrate that the bioderived comonomers exhibit comparable behavior to isophthalic acid, a commonly used comonomer in PET, by lowering the crystallinity and melting temperature. Moreover, methoxyterephthalate esters (2-ethylhexyl and butyl) are compared to phthalate and terephthalate ester counterparts used as poly(vinyl chloride) (PVC) plasticizers. The bioderived plasticizers are comparable to the petroleum-derived incumbents in reducing the glass transition temperature and increasing the thermal stability of PVC. Furthermore, the dimethoxyterephthalic esters are expected to have an extended lifetime in the polymer matrix due to their lower volatility and lower diffusion coefficients calculated by molecular dynamic simulations. These results demonstrate that the isophthalate and phthalate components in polyesters and plasticizers, respectively, could be substituted with biobased methoxyterephthalate derivatives.

09 BIOMASS FUELS↗
DOE OSTI2022

Catalytic conversion of high S-lignin to a sustainable tri-epoxide polymer precursor

More than 40 million tons of thermosetting plastics are produced annually and 70% of those are epoxy polymers. The synthesis of bio-based epoxide provides a pathway for making renewable thermoset plastics. We describe in this study the use of a genetically modified high-S poplar lignin to produce 4-propyl-2,6-dimethoxyphenol (DMPP), which is converted to the tri-functional compound propylpyrogallol (DMPPO) by a reaction catalysed by N 2 O 5 in the green solvent water. The resulting DMPPO can be converted to a novel tri-epoxide by reaction with epichlorohydrin. Native high-S lignin as well as several organosolv lignins extracted from this poplar biomass were investigated as feedstocks. Notably, direct reductive catalytic fractionation (RCF) of the high-S poplar wood over Pd–Zn/C catalyst with Pd : Zn ratio 1 : 10 at 225 °C under 35 bar H 2 in methanol gave the highest yield of biophenol monomers from the lignin present, the major product being DMPP. Under optimized conditions, conversion of DMPP to DMPPO over the Nb 2 O 5 was nearly quantitative (96% yield), and this conversion could be made without extensive prior purification of the DMPP. The Nb 2 O 5 catalyst could be recycled several times before significant deactivation. This sequence of two catalytic reactions demonstrates that the production of epoxides from lignin-derived DMPPO is a realistic strategy for making renewable polymer building blocks from biomass.

09 BIOMASS FUELS↗
DOE OSTI2024

The Catabolism of Lignin-Derived p-Methoxylated Aromatic Compounds by Rhodococcus jostii RHA1

Emergent strategies to valorize lignin, an abundant but underutilized aromatic biopolymer, include tandem processes that integrate chemical depolymerization and biological catalysis. To date, aromatic monomers from C-O bond cleavage of lignin have been converted to bioproducts, but the presence of recalcitrant C-C bonds in lignin limits the product yield. A promising chemocatalytic strategy that overcomes this limitation involves phenol methyl protection and autoxidation. Incorporating this into a tandem process requires microbial cell factories able to transform the p-methoxylated products in the resulting methylated lignin stream. In this study, we assessed the ability of Rhodococcus jostii RHA1 to catabolize the major aromatic products in a methylated lignin stream and elucidated the pathways responsible for this catabolism. RHA1 grew on a methylated pine lignin stream, catabolizing the major aromatic monomers: p-methoxybenzoate (p-MBA), veratrate, and veratraldehyde. Bioinformatic analyses suggested that a cytochrome P450, PbdA, and its cognate reductase, PbdB, are involved in p-MBA catabolism. Gene deletion studies established that both pbdA and pbdB are essential for growth on p-MBA and several derivatives. Furthermore, a deletion mutant of a candidate p-hydroxybenzoate (p-HBA) hydroxylase, ..delta..pobA, did not grow on p-HBA. Veratraldehyde and veratrate catabolism required both vanillin dehydrogenase (Vdh) and vanillate O-demethylase (VanAB), revealing previously unknown roles of these enzymes. Finally, a ..delta..pcaL strain grew on neither p-MBA nor veratrate, indicating they are catabolized through the ..beta..-ketoadipate pathway. This study expands our understanding of the bacterial catabolism of aromatic compounds and facilitates the development of biocatalysts for lignin valorization.

aromatic biopolymers↗
DOE OSTI2024

Catabolism of β-5 linked aromatics by Novosphingobium aromaticivorans

ABSTRACT Aromatic compounds are an important source of commodity chemicals traditionally produced from fossil fuels. Aromatics derived from plant lignin can potentially be converted into commodity chemicals through depolymerization followed by microbial funneling of monomers and low molecular weight oligomers. This study investigates the catabolism of the β-5 linked aromatic dimer dehydrodiconiferyl alcohol (DC-A) by the bacterium Novosphingobium aromaticivorans . We used genome-wide screens to identify candidate genes involved in DC-A catabolism. Subsequent in vivo and in vitro analyses of these candidate genes elucidated a catabolic pathway composed of four required gene products and several partially redundant dehydrogenases that convert DC-A to aromatic monomers that can be funneled into the central aromatic metabolic pathway of N. aromaticivorans . Specifically, a newly identified γ-formaldehyde lyase, PcfL, opens the phenylcoumaran ring to form a stilbene and formaldehyde. A lignostilbene dioxygenase, LsdD, then cleaves the stilbene to generate the aromatic monomers vanillin and 5-formylferulate (5-FF). We also showed that the aldehyde dehydrogenase FerD oxidizes 5-FF before it is decarboxylated by LigW, yielding ferulic acid. We found that some enzymes involved in the β-5 catabolism pathway can act on multiple substrates and that some steps in the pathway can be mediated by multiple enzymes, providing new insights into the robust flexibility of aromatic catabolism in N. aromaticivorans . A comparative genomic analysis predicted that the newly discovered β-5 aromatic catabolic pathway is common within the order Sphingomonadales. IMPORTANCE In the transition to a circular bioeconomy, the plant polymer lignin holds promise as a renewable source of industrially important aromatic chemicals. However, since lignin contains aromatic subunits joined by various chemical linkages, producing single chemical products from this polymer can be challenging. One strategy to overcome this challenge is using microbes to funnel a mixture of lignin-derived aromatics into target chemical products. This approach requires strategies to cleave the major inter-unit linkages of lignin to release monomers for funneling into valuable products. In this study, we report newly discovered aspects of a pathway by which the Novosphingobium aromaticivorans DSM12444 catabolizes aromatics joined by the second most common inter-unit linkage in lignin, the β-5 linkage. This work advances our knowledge of aromatic catabolic pathways, laying the groundwork for future metabolic engineering of this and other microbes for optimized conversion of lignin into products.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Understanding of bacterial lignin extracellular degradation mechanisms by Pseudomonas putida KT2440 via secretomic analysis

Abstract Background Bacterial lignin degradation is believed to be primarily achieved by a secreted enzyme system. Effects of such extracellular enzyme systems on lignin structural changes and degradation pathways are still not clearly understood, which remains as a bottleneck in the bacterial lignin bioconversion process. Results This study investigated lignin degradation using an isolated secretome secreted by Pseudomonas putida KT2440 that grew on glucose as the only carbon source. Enzyme assays revealed that the secretome harbored oxidase and peroxidase/Mn 2+ -peroxidase capacity and reached the highest activity at 120 h of the fermentation time. The degradation rate of alkali lignin was found to be only 8.1% by oxidases, but increased to 14.5% with the activation of peroxidase/Mn 2+ -peroxidase. Gas chromatography–mass spectrometry (GC–MS) and two-dimensional 1 H– 13 C heteronuclear single-quantum coherence (HSQC) NMR analysis revealed that the oxidases exhibited strong C–C bond ( β-β , β -5, and β -1) cleavage. The activation of peroxidases enhanced lignin degradation by stimulating C–O bond ( β -O-4) cleavage, resulting in increased yields of aromatic monomers and dimers. Further mass spectrometry-based quantitative proteomics measurements comprehensively identified different groups of enzymes particularly oxidoreductases in P. putida secretome, including reductases, peroxidases, monooxygenases, dioxygenases, oxidases, and dehydrogenases, potentially contributed to the lignin degradation process. Conclusions Overall, we discovered that bacterial extracellular degradation of alkali lignin to vanillin, vanillic acid, and other lignin-derived aromatics involved a series of oxidative cleavage, catalyzed by active DyP-type peroxidase, multicopper oxidase, and other accessory enzymes. These results will guide further metabolic engineering design to improve the efficiency of lignin bioconversion. Graphical Abstract

09 BIOMASS FUELS↗
DOE OSTI2025

The anaerobic fungus Neocallimastix californiae shifts metabolism and produces melanin in response to lignin-derived aromatic compounds

Biological deconstruction of lignocellulose for sustainable chemical production offers an opportunity to harness evolutionarily specialized enzymes and organisms for industrial bioprocessing. While hydrolysis of cellulose and hemicellulose by CAZymes yields fermentable sugars, ligninolysis releases a heterogeneous mix of aromatic compounds that likely play a crucial role in shaping microbial communities and microbial metabolism. Here, we interrogated the metabolomic and transcriptomic response of a lignocellulolytic anaerobic fungus, Neocallimastix californiae, to a heterogeneous mixture of aromatic compounds derived from lignin. Through exposing the fungus to both a concentration it might experience in its native environment and an elevated concentration of alkaline lignin, we observe that N. californiae transforms vanillin and that supplying alkaline lignin at 0.125 g/L, alongside cellulose, enhances the growth and polysaccharide-degrading activity of N. californiae. Altogether, our results further suggest that vanillin consumption, increased polymer-degrading activity, increased metabolic activity, and transcriptomic remodeling of amino acid synthesis genes all coincide with increased melanin production by fungal cells. These observations challenge previous notions that aromatics from lignocellulose only inhibit the growth and polymer deconstruction capabilities of the biomass-degrading anaerobic fungi (Neocallimastigomycetes). This study demonstrates that anaerobic fungi have a complex relationship with aromatic chemicals derived from lignin and hemicellulose and shift their metabolism in response to the addition of lignocellulose-derived aromatics to their growth medium. Further, as no known pathways for the biochemical transformation of aromatics were detected in these organisms despite observed transcriptome remodeling in the presence of aromatics, we suggest they might encode novel biochemical routes for scavenging amino acid building blocks from aromatic monomers derived from hemicellulose side chains and lignin.

Anaerobic fungi↗
DOE OSTI2023

Characterizing and Engineering Trehalose Biosynthesis Pathways to Improve Acetate Tolerance in Pseudomonas putida KT2440

Alkaline pretreatment can depolymerize lignin into a diverse mixture of monomers and smaller compounds, enabling bioconversion of these compounds to value-added chemicals in engineered bacterial hosts such as Pseudomonas putida KT2440. Acetate and salts comprise approximately 8% and 32% of the lignin stream, respectively. High concentrations of these components can cause cell death in P. putida, so lignin-derived streams must be fed in lower amounts to decrease stress. Investigation of the mechanisms of bacterial tolerance to chemicals in lignin-rich substrates is therefore required to overcome this obstacle in lignin bioconversion. Previous work has shown that trehalose, an endogenously produced disaccharide, is involved in tolerance to heat, cold, and osmotic stress, as well as implicated in acid stress in other bacteria. As such, trehalose biosynthesis presents a useful target to increase acetate and osmotic tolerance in P. putida. This work investigates the native TreSA, TreSB, and TreY/TreZ trehalose biosynthesis pathways in this bacterial strain as well as the OtsAB pathway of Sphingobium sp. SYK-6. Overexpression of the OtsAB pathway in P. putida increased tolerance to acetate relative to wild-type. Additionally, functional knockouts of treSA, treSB, treY, and treZ in P. putida showed that interruption of any trehalose biosynthesis pathway, and, in the case of TreY/TreZ, interruption of the pathway at any point, significantly hindered growth in acetate as well as on glucose and LB broth. Each trehalose biosynthesis pathway was then engineered for overexpression in P. putida to determine whether overexpression of these genes conferred additional tolerance to acetate. The TreSA, TreSB, OtsA, and OtsB enzymes were also expressed and purified to determine the reaction rates and kinetics of these pathways. The hypothetical glycoside hydrolase family 15 protein, encoded in the gene located in between otsB and otsA in the Sphingobium operon, was purified as well to investigate its potential involvement in the OtsAB pathway. The findings of this work illuminated the mechanisms of trehalose biosynthesis in P. putida and identified genetic targets to improve strain tolerance to common components of alkaline-pretreated lignin streams. These findings could ultimately improve yields of desired products from lignin in engineered strains of P. putida.

alkaline pretreatment↗