Opportunities and challenges in biological lignin valorization

Different lignin fraction extraction by pH fractionation for lignin microspheres preparation as UV-blocking PVA film

Kraft lignin (KL), a major by-product of the pulp and paper industry, has garnered significant research attention due to its abundant availability and distinctive chemical structure, making it a promising candidate for applications such as biofuels, carbon materials, and polymer composites. Despite these advantages, its utilization in fine chemical industries, including nanomaterials, is constrained by its inherent dark color and broad molecular weight distribution. Addressing these limitations has become a central focus in ongoing research efforts aimed at enhancing the functionality and commercial viability of KL. In this study, we fractionated KL from a paper-making enterprise using pH fractionation, and obtained four kinds of lignin with different molecular weights. Following that, lignin microspheres (LMPs) were formed by self-assembly from four sizes of KL. Analyzing the KL and LMP properties, the low molecular weight lignin, such as KL-2, exhibited good antioxidant properties (84.27 %, 5 mg/mL), high brightness (ISO% = 7.6), high L⁎ value (L⁎ = 86.2) and low polydispersity index (PDI = 1.19). The LMP showed a narrow size distribution (1.0-1.4 μm). When the LMP content is 5 %, the 5 % LMP/PVA film maintains high transparency and exhibits excellent UV protection, achieving a UV shielding rate of up to 94.6 %. Therefore, this study offered an effective way for the comprehensive utilization of pulping waste KL.

Characterization of a two-component kinase that initiates the bacterial catabolism of hydroxyphenylethanones

The prodigious ability of bacteria to catabolize aromatic compounds has sparked considerable efforts to engineer bacteria to valorize lignin, an under-utilized component of biomass. Despite decades of study, key catabolic pathways and enzymes remain poorly characterized. We recently identified the hydroxyphenylethanone (Hpe) pathway, which enables Rhodococcus rhodochrous GD02 and other bacteria to catabolize 4-hydroxyacetophenone (HAP) and acetovanillone (AV), which are generated in the catalytic fractionation of lignin. Catabolism is initiated by a two-component, ATP-dependent dikinase, HpeHI, homologs of which are involved in the catabolism of other aromatic compounds. In biochemical studies, the kinase activity of HpeHI was highest at low ionic strength and low concentrations of Mn2+. HpeHI had highest apparent specificity for HAP and AV (kcat/KM ≥ 250 mM-1 s-1) and had submicromolar KM values for these substrates, consistent with the enzyme acting as a scavenging system. The enzyme also transformed 4-hydroxybenzaldehyde, vanillin, acetosyringone, and phenol. A 1.8 Å crystal structure of HpeI revealed that it is homologous to the ATP-grasp domain of rifampin phosphotransferase (RPH) while an AlphaFold model of HpeH indicated that it is homologous to the swivel and rifampin-binding domains of RPH. Consistent with HpeHI using a similar mechanism where the swivel domain transits between the spatially distinct substrate-binding sites, substitution of the conserved His residue in HpeH abolished kinase activity. Moreover, the HpeH component alone catalyzed phosphotransfer from 4-phosphoacetophenone to AV. This study reveals a subfamily of small molecule dikinases that comprise two components, some of which are involved in aromatic compound catabolism.

Solid-state NMR at natural isotopic abundance for bioenergy applications

Lignocellulosic biomass offers a vast and renewable resource for biofuel production and carbon management solutions. The effective conversion of lignocellulosic biomass into economically competitive biofuels and bioproducts demands a comprehensive understanding of its complex structure and composition, often requiring a range of analytical tools to achieve meaningful insights. However, for the analysis of rigid solids, many traditional methods necessitate dissolution or chemical/physical modification of the sample, which limit our ability to capture an intact view of its structural components. This highlights the need for non-destructive approaches, such as solid-state nuclear magnetic resonance (ssNMR), which preserves the sample's natural state while providing deep, molecular-level insights. While advanced multi-dimensional ssNMR on 13C-enriched materials has recently proven exceptionally valuable for elucidating the complex macrostructure of biomass, isotopic enrichment is expensive, laborious and is clearly infeasible at large scales. In this review, we explore the role of solid-state NMR methods at natural isotopic abundance as essential tools for the non-destructive, in-depth characterization of lignocellulosic biomass and bioenergy materials in their native and unaltered state. After a brief introduction to the basic principles of solid-state NMR, we first describe the acquisition and interpretation of routine 1D 13C ssNMR spectra of lignocellulose and other related biopolymers and products. We then delve into more advanced ssNMR approaches, including key spectral editing techniques, probing polymer dynamics, and various 2D methods applicable at natural abundance. Understanding of domain miscibility as observed from proton-based spin diffusion effects is a theme throughout. Our aim is to highlight key examples where ssNMR provides valuable insights into the composition, structure, dynamics, and morphology of rigid biomaterials relevant to the bioenergy economy, revealing both the native structures and fundamental transformations that occur across conversion and decomposition pathways. We hope that this review encourages a broader adoption of ssNMR methods in bioenergy research, where it can serve as a pivotal analytical tool for achieving sustainable biomass utilization and advancing a carbon-efficient bioeconomy.

Lignin-Degrading Enzymes and the Potential of Pseudomonas putida as a Cell Factory for Lignin Degradation and Valorization

Efficient utilization of lignin, a complex polymer in plant cell walls, is one of the key strategies for developing a green and sustainable bioeconomy. However, bioconversion of lignin poses a significant challenge due to its recalcitrant nature. Microorganisms, particularly fungi and bacteria, play a crucial role in lignin biodegradation, using various enzymatic pathways. Among bacteria, Pseudomonas putida is considered a promising host for lignin degradation and valorization, due to its robust and flexible metabolism and its tolerance to many noxious and toxic compounds. This review explores the various mechanisms of lignin breakdown by microorganisms, with a focus on P. putida's metabolic versatility and genetic engineering potential. By leveraging advanced genetic tools and metabolic pathway optimization, P. putida can be engineered to efficiently convert lignin into valuable bioproducts, offering sustainable solutions for lignin valorization in industrial applications.

Microbial Upgrading of Lignin Depolymerization: Enhancing Efficiency with Lignin-First Catalysis

Chemical depolymerization of lignin is a non-selective process that often generates a wide distribution of product compounds, denoted herein as lignin breakdown products (LBPs). To address this limitation, we developed a hybrid lignin conversion process that employs a lignin-first catalytic approach on biomass and subsequent microbial upgrading. A Pd/C catalyst was used for reductive catalytic fractionation (RCF) of poplar biomass, and Rhodococcus opacus PD630 (R. opacus PD630) was then cultivated on the resulting LBPs. This RCF approach increases the total biomass utilization by R. opacus PD630 over base-catalyzed depolymerization (BCD) reactions that were performed in the absence of Pd/C and molecular hydrogen (H2). LBPs generated using RCF resulted in higher cell growth per gram of biomass. Cellulose in the residual biomass after RCF treatment also showed enhanced enzymatic digestibility due to saccharification yields over 40%. Techno-economic analysis (TEA) and life cycle analysis (LCA) of this hybrid lignin conversion scheme, integrated into a cellulosic bioethanol plant, decreased the minimum ethanol selling price from $4.07/gallon (base case) to $3.94/gallon. Global warming potentials ranged from 29 and 30.5 CO2,eq/MJ. These results highlight the potential for an industrial hybrid conversion-based biorefinery scheme that utilizes lignin-first catalytic deconstruction and R. opacus PD630 upgrading.

Recent advances in enzymes active on lignin-derived aromatic compounds

Lignin is an attractive alternative to fossil fuels as a feedstock for the sustainable manufacture of chemicals. Emergent strategies for lignin valorization include tandem processes whereby thermochemical fractionation of the biomass yields a mixture of lignin-derived aromatic compounds (LDACs), which are then transformed into target compounds by a microbial cell factory. Identifying LDAC-degrading pathways is critical to optimize carbon yield from diverse depolymerization mixtures. Characterizing enzymes - especially those that catalyze the rate-limiting steps of O-demethylation, hydroxylation, and decarboxylation - informs and enables biocatalyst design. Rational, structure-based engineering of key enzymes, as well as untargeted, evolution-based approaches, further optimize biocatalysis. In this review we outline recent advances in these fields which are critical in developing biocatalysts to efficiently synthesize lignin-based bioproducts.

Quantitative Analysis of Coupled Carbon and Energy Metabolism for Lignin Carbon Utilization in Pseudomonas putida

Soil Pseudomonas species, which can thrive on lignin-derived phenolic compounds, are widely explored for biotechnology applications. Yet, there is limited understanding of how the native metabolism coordinates phenolic carbon processing with cofactor generation. Here, we achieve quantitative understanding of this metabolic balance through a multi-omics investigation of Pseudomonas putida KT2440 grown on four common phenolic substrates: ferulate, p-coumarate, vanillate, and 4-hydroxybenzoate. Relative to succinate as a non-aromatic reference, proteomics data reveal >140-fold increase in proteins for transport and initial catabolism of each phenolic substrate, but metabolomics profiling reveals that bottleneck nodes in initial phenolic compound catabolism maintain more favorable cellular energy state. Up to 30-fold increase in pyruvate carboxylase and glyoxylate shunt proteins implies a metabolic remodeling confirmed by kinetic 13C-metabolomics. Quantitative analysis by 13C-fluxomics demonstrates coupling of this remodeling with cofactor production. Specifically, anaplerotic carbon recycling via pyruvate carboxylase promotes fluxes in the tricarboxylic acid cycle to provide 50-60% NADPH yield and 60-80% NADH yield, resulting in 2-fold higher ATP yield than for succinate metabolism; the glyoxylate shunt sustains cataplerotic flux through malic enzyme for the remaining NADPH yield. The quantitative blueprint elucidated here explains deficient versus sufficient cofactor rebalancing during manipulations of key metabolic nodes in lignin valorization.

One-Pot lignin bioconversion to polyhydroxyalkanoates based on hierarchical utilization of heterogeneous compounds

Pseudomonas putida degraded 35 % of compounds in alkali-pretreated lignin liquor under nitrogen-replete conditions but with low polyhydroxyalkanoates (PHA) production, while limiting nitrogen supplement improved PHA content (PHA/dry cell weight) to 43 % at the expense of decreased lignin degradation of 22 %. Increase of initial cell biomass (0.1-1.5 g/L) monotonically improved the lignin degradation from 22 % to 33 % under nitrogen-limited conditions. Hierarchical utilization of heterogenous compounds under cell growth restricted conditions has been unveiled - simple carbon sources were prioritized for valorization, followed by aromatic compounds bioconversion. Based on the results of hierarchy and leveraging the initial bacterial biomass, acetate was augmented to facilitate one-pot lignin bioconversion under nitrogen-limited conditions. This approach improved lignin bioconversion closer to its upper degradation limit of 35 %, concomitant with PHA yield of 39 mg/g-lignin. Anaerobic digestion of lignocellulose was redesigned to favor acetate-type fermentation, with acetate constituting 91 wt%, providing an economic source of acetate.

Enhanced physicochemical characteristics and biological activities of low-temperature ethylenediamine/urea pretreated lignin

Low-temperature ethylenediamine (EDA)/urea pretreatment had been demonstrated to be an efficient pretreatment method for enzymatic hydrolysis and bioethanol production. For high-value utilization of the third main components of lignocellulosic biomass, the physicochemical structure characteristics and biological activities of low-temperature EDA/urea pretreated lignin (EUL) were comprehensively investigated in the present study. The results demonstrated that the pretreatment process facilitated the depolymerization of lignin, resulting in notable reduction in molecular weight and polydispersity index from 2.32 to 1.42 kg/mol and 1.44 to 1.20, respectively. The EDA/urea pretreated lignin (EUL) exhibited enhanced ultraviolet absorption capacity and the most significant DPPH radical scavenging and inhibition of Staphylococcus aureus in comparison to the primary lignin (PL) and the NaOH pretreated lignin (NL). Enhanced physicochemical characteristics and biological activities of EUL make it more suitable to be developed as sunscreen ingredient or antioxidant and antimicrobial agent in food preservation and conservation.

Metabolic profiling of two white-rot fungi during 4-hydroxybenzoate conversion reveals biotechnologically relevant biosynthetic pathways

White-rot fungi are efficient organisms for the mineralization of lignin and polysaccharides into CO2 and H2O. Despite their biotechnological potential, WRF metabolism remains underexplored. Building on recent findings regarding the utilization of lignin-related aromatic compounds as carbon sources by WRF, we aimed to gain further insights into these catabolic processes. For this purpose, Trametes versicolor and Gelatoporia subvermispora were incubated in varying conditions - in static and agitation modes and different antioxidant levels - during the conversion of 4-hydroxybenzoic acid (a lignin-related compound) and cellobiose. Their metabolic responses were assessed via transcriptomics, proteomics, lipidomics, metabolomics, and microscopy analyses. These analyses reveal the significant impact of cultivation conditions on sugar and aromatic catabolic pathways, as well as lipid composition of the fungal mycelia. Additionally, this study identifies biosynthetic pathways for the production of extracellular fatty acids and phenylpropanoids - both products with relevance in biotechnological applications - and provides insights into carbon fate in nature.

The Pseudomonas ligninolytic catalytic network reveals the importance of auxiliary enzymes in lignin biocatalysts

Lignin degradation by biocatalysts is a key strategy to develop a plant-based sustainable carbon economy and thus alleviate global climate change. This process involves synergy between ligninases and auxiliary enzymes. However, auxiliary enzymes within secretomes, which are composed of thousands of enzymes, remain enigmatic, although several ligninolytic enzymes have been well characterized. Moreover, it is a challenge to understand synergistic lignin degradation via a diverse array of enzymes, especially in bacterial systems. In this study, the coexpression network of the periplasmic proteome uncovers potential accessory enzymes for B-type dye-decolorizing peroxidases (DypBs) in Pseudomonas putida A514. The catalytic network of the DypBs-based multienzyme complex is characterized. DypBs couple with quinone reductases and nitroreductase to participate in quinone redox cycling. They work with superoxide dismutase to induce Fenton reaction for lignin oxidation. A synthetic enzyme cocktail (SEC), recruiting 15 enzymes, was consequently designed with four functions. It overcomes the limitation of lignin repolymerization, exhibiting a capacity comparable to that of the native periplasmic secretome. Importantly, we reveal the synergistic mechanism of a SEC-A514 cell system, which incorporates the advantages of in vitro enzyme catalysis and in vivo microbial catabolism. Chemical analysis shows that this system significantly reduces the molecular weight of lignin, substantially extends the degradation spectra for lignin functional groups, and efficiently metabolizes lignin derivatives. As a result, 25% of lignin is utilized, and its average molecular weight is reduced by 27%. Our study advances the knowledge of bacterial lignin-degrading multienzymes and provides a viable lignin degradation strategy.

Comparative metagenomics reveals the metabolic flexibility of coastal prokaryotic microbiomes contributing to lignin degradation

Coastal wetlands are rich in terrestrial organic carbon. Recent studies suggest that microbial consortia play a role in lignin degradation in coastal wetlands, where lignin turnover rates are likely underestimated. However, the metabolic potentials of these consortia remain elusive. This greatly hinders our understanding of the global carbon cycle and the "bottom-up" design of synthetic consortia to enhance lignin conversion. Here, we developed two groups of lignin degrading consortia, L6 and L18, through the 6- and 18-month in situ lignin enrichments in the coastal East China Sea, respectively. Lignin degradation by L18 was 3.6-fold higher than L6. Using read-based analysis, 16S rRNA amplicon and metagenomic sequencing suggested that these consortia possessed varied taxonomic compositions, yet similar functional traits. Further comparative metagenomic analysis, based on metagenomic assembly, revealed that L18 harbored abundant metagenome-assembled genomes (MAGs) that encoded diverse and unique lignin degradation gene clusters (LDGCs). Importantly, anaerobic MAGs were significantly enriched in L18, highlighting the role of anaerobic lignin degradation. Furthermore, the generalist taxa, which possess metabolic flexibility, increased during the extended enrichment period, indicating the advantage of generalists in adapting to heterogenous resources. This study advances our understanding of the metabolic strategies of coastal prokaryotic consortia and lays a foundation for the design of synthetic communities for sustainable lignocellulose biorefining.

Biochemical and structural characterization of enzymes in the 4-hydroxybenzoate catabolic pathway of lignin-degrading white-rot fungi

White-rot fungi (WRF) are the most efficient lignin-degrading organisms in nature. However, their capacity to use lignin-related aromatic compounds, such as 4-hydroxybenzoate, as carbon sources has only been described recently. Previously, the hydroxyquinol pathway was proposed for the bioconversion of these compounds in fungi, but gene- and structure-function relationships of the full enzymatic pathway remain uncharacterized in any single fungal species. Here, we characterize seven enzymes from two WRF, Trametes versicolor and Gelatoporia subvermispora, which constitute a four-enzyme cascade from 4-hydroxybenzoate to β-ketoadipate via the hydroxyquinol pathway. Furthermore, we solve the crystal structure of four of these enzymes and identify mechanistic differences with the closest bacterial and fungal structural homologs. Overall, this research expands our understanding of aromatic catabolism by WRF and establishes an alternative strategy for the conversion of lignin-related compounds to the valuable molecule β-ketoadipate, contributing to the development of biological processes for lignin valorization.

A novel engineered strain of Methylorubrum extorquens for methylotrophic production of glycolic acid

The conversion of CO2 into methanol depicts one of the most promising emerging renewable routes for the chemical and biotech industry. Under this regard, native methylotrophs have a large potential for converting methanol into value-added products but require targeted engineering approaches to enhance their performances and to widen their product spectrum. Here we use a systems-based approach to analyze and engineer M. extorquens TK 0001 for production of glycolic acid. Application of constraint-based metabolic modeling reveals the great potential of M. extorquens for that purpose, which is not yet described in literature. In particular, a superior theoretical product yield of 1.0 C-molGlycolic acid C-molMethanol-1 is predicted by our model, surpassing theoretical yields of sugar fermentation. Following this approach, we show here that strain engineering is viable and present 1st generation strains producing glycolic acid via a heterologous NADPH-dependent glyoxylate reductase. It was found that lactic acid is a surprising by-product of glycolic acid formation in M. extorquens, most likely due to a surplus of available NADH upon glycolic acid synthesis. Finally, the best performing strain was tested in a fed-batch fermentation producing a mixture of up to total 1.2 g L-1 glycolic acid and lactic acid. Several key performance indicators of our glycolic acid producer strain are superior to state-of-the-art synthetic methylotrophs. The presented results open the door for further strain engineering of the native methylotroph M. extorquens and pave the way to produce two promising biopolymer building blocks from green methanol, i.e., glycolic acid and lactic acid.

Concatenating Microbial, Enzymatic, and Organometallic Catalysis for Integrated Conversion of Renewable Carbon Sources

The chemical industry can now seize the opportunity to improve the sustainability of its processes by replacing fossil carbon sources with renewable alternatives such as CO2, biomass, and plastics, thereby thinking ahead and having a look into the future. For their conversion to intermediate and final products, different types of catalysts-microbial, enzymatic, and organometallic-can be applied. The first part of this review shows how these catalysts can work separately in parallel, each route with unique requirements and advantages. While the different types of catalysts are often seen as competitive approaches, an increasing number of examples highlight, how combinations and concatenations of catalysts of the complete spectrum can open new roads to new products. Therefore, the second part focuses on the different catalysts either in one-step, one-pot transformations or in reaction cascades. In the former, the reaction conditions must be conflated but purification steps are minimized. In the latter, each catalyst can work under optimal conditions and the "hand-over points" should be chosen according to defined criteria like minimal energy usage during separation procedures. The examples are discussed in the context of the contributions of catalysis to the envisaged (bio)economy.

Lignin deoxygenation for the production of sustainable aviation fuel blendstocks

Lignin is an abundant source of renewable aromatics that has long been targeted for valorization. Traditionally, the inherent heterogeneity and reactivity of lignin has relegated it to direct combustion, but its higher energy density compared with polysaccharides makes it an ideal candidate for biofuel production. This Review critically assesses lignin's potential as a substrate for sustainable aviation fuel blendstocks. Lignin can generate the necessary cyclic compounds for a fully renewable, sustainable aviation fuel when integrated with current paraffinic blends and can meet the current demand 2.5 times over. Using an energy-centric analysis, we show that lignin conversion technologies have the near-term potential to match the enthalpic yields of existing commercial sustainable aviation fuel production processes. Key factors influencing the viability of technologies for converting lignin to sustainable aviation fuel include lignin structure, delignification extent, depolymerization performance, and the development of stable and tunable deoxygenation catalysts.

Increased Antioxidant Performance of Lignin by Biodegradation Obtained from an Extract of the Mushroom Pleurotus eryngii

The aim of this study was to evaluate the antioxidant properties of the products derived from the biodegradation of lignin by the ligninolytic enzymes present in an aqueous extract of the mushroom P. eryngii. A mixture obtained after the incubation of lignin for 18 h with P. eryngii extract was tested in vitro for its total polyphenol content, reducing power, and 1,1-diphenyl-2-picrylhydrazyl (DPPH) and hydroxyl (OH) radical-scavenging activities. The results showed that the enzymatic treatment of lignin enhanced its antioxidant performance. The biocompatibility of the products of lignin biodegradation and their ability to scavenge reactive oxygen species (ROS) were also tested on the astrocytic cell line DI-TNC1. The results obtained indicated that a lignin mixture incubated for 18 h does not affect cell viability or inhibit the H2O2-induced ROS production. These results suggest that the enzymatic degradation of lignin represents an efficient and ecofriendly approach to obtain lignin derivatives potentially useful for antioxidant applications.

Bacterial valorization of lignin for the sustainable production of value-added bioproducts

As the most abundant aromatic biopolymer in the biosphere, lignin represents a promising alternative feedstock for the industrial production of various value-added bioproducts with enhanced economical value. However, the large-scale implementation of lignin valorization remains challenging because of the heterogeneity and irregular structure of lignin. General fragmentation and depolymerization processes often yield various products, but these approaches necessitate tedious purification steps to isolate target products. Moreover, microbial biocatalytic processes, especially bacterial-based systems with high metabolic activity, can depolymerize and further utilize lignin in an eco-friendly way. Considering that wild bacterial strains have evolved several metabolic pathways and enzymatic systems for lignin degradation, substantial efforts have been made to exploit their potential for lignin valorization. This review summarizes recent advances in lignin valorization for the production of value-added bioproducts based on bacterial systems. Additionally, the remaining challenges and available strategies for lignin biodegradation processes and future trends of bacterial lignin valorization are discussed.

Characterization of a cytochrome P450 that catalyzes the O-demethylation of lignin-derived benzoates

Cytochromes P450 (P450s) are a superfamily of heme-containing enzymes possessing a broad range of monooxygenase activities. One such activity is O-demethylation, an essential and rate-determining step in emerging strategies to valorize lignin that employ carbon-carbon bond cleavage. We recently identified PbdA, a P450 from Rhodococcus jostii RHA1, and PbdB, its cognate reductase, which catalyze the O-demethylation of para-methoxylated benzoates (p-MBAs) to initiate growth of RHA1 on these compounds. PbdA had the highest affinity (Kd = 3.8 ± 0.6 μM) and apparent specificity (kcat/KM = 20,000 ± 3000 M-1 s-1) for p-MBA. The enzyme also O-demethylated two related lignin-derived aromatic compounds with remarkable efficiency: veratrate and isovanillate. PbdA also catalyzed the hydroxylation and dehydrogenation of p-ethylbenzoate even though RHA1 did not grow on this compound. Atomic-resolution structures of PbdA in complex with p-MBA, p-ethylbenzoate, and veratrate revealed a cluster of three residues that form hydrogen bonds with the substrates' carboxylate: Ser87, Ser237, and Arg84. Substitution of these residues resulted in lower affinity and O-demethylation activity on p-MBA as well as increased affinity for the acetyl analog, p-methoxyacetophenone. The S87A and S237A variants of PbdA also catalyzed the O-demethylation of an aldehyde analog of p-MBA, p-methoxy-benzaldehyde, while the R84M variant did not, despite binding this compound with high affinity. These results suggest that Ser87, Ser237, and Arg84 are not only important determinants of specificity but also help to orientate that substrate correctly in the active site. This study facilitates the design of biocatalysts for lignin valorization.

Accessing monomers from lignin through carbon-carbon bond cleavage

Lignin, the heterogeneous aromatic macromolecule found in the cell walls of vascular plants, is an abundant feedstock for the production of biochemicals and biofuels. Many valorization schemes rely on lignin depolymerization, with decades of research focused on accessing monomers through C-O bond cleavage, given the abundance of β-O-4 bonds in lignin and the large number of available C-O bond cleavage strategies. Monomer yields are, however, invariably lower than desired, owing to the presence of recalcitrant C-C bonds whose selective cleavage remains a major challenge in catalysis. In this Review, we highlight lignin C-C cleavage reactions, including those of linkages arising from biosynthesis (β-1, β-5, β-β and 5-5) and industrial processing (5-CH2-5 and α-5). We examine multiple approaches to C-C cleavage, including homogeneous and heterogeneous catalysis, photocatalysis and biocatalysis, to identify promising strategies for further research and provide guidelines for definitive measurements of lignin C-C bond cleavage.

Lignin valorization through the oxidative activity of β-etherases: Recent advances and perspectives

The increasing interest in lignin, a complex and abundant biopolymer, stems from its ability to produce environmentally beneficial biobased products. β-Etherases play a crucial role by breaking down the β-aryl ether bonds in lignin. This comprehensive review covers the latest advancements in β-etherase-mediated lignin valorization, focusing on substrate selectivity, enzymatic oxidative activity, and engineering methods. Research on the microbial origin, protein modification, and molecular structure determination of β-etherases has improved our understanding of their effectiveness. Furthermore, the use of these enzymes in biorefinery processes is promising for enhancing lignin breakdown and creating more valuable products. The review also discusses the challenges and future potential of β-etherases in advancing lignin valorization for biorefinery applications that are economically viable and environmentally sustainable.

Biomanufacturing of value-added chemicals from lignin

Lignin valorization faces persistent biomanufacturing challenges due to the heterogeneous and toxic carbon substrates derived from lignin depolymerization. To address the heterogeneous nature of aromatic feedstocks, plant cell wall engineering and 'lignin first' pretreatment methods have recently emerged. Next, to convert the resulting aromatic substrates into value-added chemicals, diverse microbial host systems also continue to be developed. This includes microbes that (1) lack aromatic metabolism, (2) metabolize aromatics but not sugars, and (3) co-metabolize both aromatics and sugars, each system presenting unique pros and cons. Considering the intrinsic complexity of lignin-derived substrate mixtures, emerging and non-model microbes with native metabolism for aromatics appear poised to provide the greatest impacts on lignin valorization via biomanufacturing.

Metabolic Engineering and Process Intensification for Muconic Acid Production Using Saccharomyces cerevisiae

The efficient production of biobased organic acids is crucial to move to a more sustainable and eco-friendly economy, where muconic acid is gaining interest as a versatile platform chemical to produce industrial building blocks, including adipic acid and terephthalic acid. In this study, a Saccharomyces cerevisiae platform strain able to convert glucose and xylose into cis,cis-muconic acid was further engineered to eliminate C2 dependency, improve muconic acid tolerance, enhance production and growth performance, and substantially reduce the side production of the intermediate protocatechuic acid. This was achieved by reintroducing the PDC5 gene and overexpression of QDR3 genes. The improved strain was integrated in low-pH fed-batch fermentations at bioreactor scale with integrated in situ product recovery. By adding a biocompatible organic phase consisting of CYTOP 503 and canola oil to the process, a continuous extraction of muconic acid was achieved, resulting in significant alleviation of product inhibition. Through this, the muconic acid titer and peak productivity were improved by 300% and 185%, respectively, reaching 9.3 g/L and 0.100 g/L/h in the in situ product recovery process as compared to 3.1 g/L and 0.054 g/L/h in the control process without ISPR.

Resolving the metabolism of monolignols and other lignin-related aromatic compounds in Xanthomonas citri

Lignin, a major plant cell wall component, has an important role in plant-defense mechanisms against pathogens and is a promising renewable carbon source to produce bio-based chemicals. However, our understanding of microbial metabolism is incomplete regarding certain lignin-related compounds like p-coumaryl and sinapyl alcohols. Here, we reveal peripheral pathways for the catabolism of the three main lignin precursors (p-coumaryl, coniferyl, and sinapyl alcohols) in the plant pathogen Xanthomonas citri. Our study demonstrates all the necessary enzymatic steps for funneling these monolignols into the tricarboxylic acid cycle, concurrently uncovering aryl aldehyde reductases that likely protect the pathogen from aldehydes toxicity. It also shows that lignin-related aromatic compounds activate transcriptional responses related to chemotaxis and flagellar-dependent motility, which might play an important role during plant infection. Together our findings provide foundational knowledge to support biotechnological advances for both plant diseases treatments and conversion of lignin-derived compounds into bio-based chemicals.

Improving the Monophenolic Yield of Lignin Depolymerization in Dualistic Aprotic Solvent System by Organic Solvent Fractionation

Converting lignin into aromatic chemicals is a promising strategy for the high-value utilization of lignocellulosic feedstock. However, the inherent heterogeneity of lignin poses a significant obstacle to achieving efficient conversion and optimal product yields within bio-refinery systems. Herein, we employed a one-step fractionation method to enhance lignin homogeneity and utilized the THF/DMSO-EtONa (tetrahydrofuran/dimethyl sulfoxide-sodium ethoxide) system to depolymerize the fractionated lignin. Three protic and three aprotic solvents were used for fractionation. The impact of the solvent properties on the structure and the depolymerization efficiency of the fractionated lignin was investigated. Methanol-fractionated lignin generated the benzoic acid compounds with a yield of 30 wt%, 50 % higher than that of the unfractionated lignin. The polarities (δP), hydrogen bonding abilities (δH), and viscosities (η) of selected protic solvents showed strong linear correlation with molecular weight (Mw), polymer dispersity index (PDI), and syringyl/guaiacyl ratio (S/G ratio) of the fractionated lignin, as well as the total yield of benzoic acid compounds derived from the β-O-4 bond cleavage. This study elucidates the relationship between solvent properties and lignin structure and proposes a promising approach for refining lignin to enhance utilization efficiency, thereby presenting a potential strategy for value-added application of complex lignin polymers.

Mechanistic insights and applications of lignin-based ultraviolet shielding composites: A comprehensive review

Lignin is a green aromatic polymer constructed from repeating phenylpropane units, incorporating features such as phenolic hydroxyl groups, carbonyl groups, and conjugated double bonds that serve as chromophores. These structural attributes enable it to absorb a wide spectrum of ultraviolet radiation within the 250-400 nm range. The resulting properties make lignin a material of considerable interest for its potential applications in polymers, packaging, architectural decoration, and beyond. By examining the structure of lignin, this research delves into the structural influence on its UV-shielding capabilities. Through a comparative analysis of lignin's use in various UV-shielding applications, the study explores the interplay between lignin's structure and its interactions with other materials. This investigation aims to elucidate the UV-shielding mechanism, thereby offering insights that could inform the development of high-value applications for lignin in UV-shielding composite materials.

Insights on kraft lignin degradation in an anaerobic environment

Lignin is an aromatic macromolecule and one of the main constituents of lignocellulosic materials. Kraft lignin is generated as a residual by-product of the lignocellulosic biomass industrial process, and it might be used as a feedstock to generate low molecular weight aromatic compounds. In this study, we seek to understand and explore the potential of ruminal bacteria in the degradation of kraft lignin. We established two consortia, KLY and KL, which demonstrated significant lignin-degrading capabilities. Both consortia reached maximum growth after two days, with KLY showing a higher growth and decolorization rate. Additionally, SEM analysis revealed morphological changes in the residual lignin from both consortia, indicating significant degradation. This was further supported by FTIR spectra, which showed new bands corresponding to the C-H vibrations of guaiacyl and syringyl units, suggesting structural transformations of the lignin. Taxonomic analysis showed enrichment of the microbial community with members of the Dickeya genus. Seven metabolic pathways related to lignin metabolism were predicted for the established consortia. Both consortia were capable of consuming aromatic compounds such as 4-hydroxybenzoic acid, syringaldehyde, acetovanillone, and syringic acid, highlighting their capacity to convert aromatic compounds into commercially valuable molecules presenting antifungal activity and used as food preservatives as 4-hydroxyphenylacetic, 3-phenylacetic, and phenylacetic acids. Therefore, the microbial consortia shown in the present work are models for understanding the process of lignin degradation and consumption in bacterial anaerobic communities and developing biological processes to add value to industrial processes based on lignocellulosic biomass as feedstock.

Perspective on Lignin Conversion Strategies That Enable Next Generation Biorefineries

The valorization of lignin, a currently underutilized component of lignocellulosic biomass, has attracted attention to promote a stable and circular bioeconomy. Successful approaches including thermochemical, biological, and catalytic lignin depolymerization have been demonstrated, enabling opportunities for lignino-refineries and lignocellulosic biorefineries. Although significant progress in lignin valorization has been made, this review describes unexplored opportunities in chemical and biological routes for lignin depolymerization and thereby contributes to economically and environmentally sustainable lignin-utilizing biorefineries. This review also highlights the integration of chemical and biological lignin depolymerization and identifies research gaps while also recommending future directions for scaling processes to establish a lignino-chemical industry.

Blue valorization of lignin-derived monomers via reprogramming marine bacterium Roseovarius nubinhibens

Biological valorization of lignin, the second most abundant biopolymer on Earth, is an indispensable sector to build a circular economy and net-zero future. However, lignin is recalcitrant to bioupcycling, demanding innovative solutions. We report here the biological valorization of lignin-derived aromatic carbon to value-added chemicals without requesting extra organic carbon and freshwater via reprogramming the marine Roseobacter clade bacterium Roseovarius nubinhibens. We discovered the unusual advantages of this strain for the oxidation of lignin monomers and implemented a CRISPR interference (CRISPRi) system with the lacI-Ptrc inducible module, nuclease-deactivated Cas9, and programmable gRNAs. This is the first CRISPR-based regulatory system in R. nubinhibens, enabling precise and efficient repression of genes of interest. By deploying the customized CRISPRi, we reprogrammed the carbon flux from a lignin monomer, 4-hydroxybenzoate, to achieve the maximum production of protocatechuate, a pharmaceutical compound with antibacterial, antioxidant, and anticancer properties, with minimal carbon to maintain cell growth and drive biocatalysis. As a result, we achieved a 4.89-fold increase in protocatechuate yield with a dual-targeting CRISPRi system, and the system was demonstrated with real seawater. Our work underscores the power of CRISPRi in exploiting novel microbial chassis and will accelerate the development of marine synthetic biology. Meanwhile, the introduction of a new-to-the-field lineage of marine bacteria unveils the potential of blue biotechnology leveraging resources from the ocean.IMPORTANCEOne often overlooked sector in carbon-conservative biotechnology is the water resource that sustains these enabling technologies. Similar to the "food-versus-fuel" debate, the competition of freshwater between human demands and bioproduction is another controversial issue, especially under global water scarcity. Here, we bring a new-to-the-field lineage of marine bacteria with unusual advantages to the stage of engineering biology for simultaneous carbon and water conservation. We report the valorization of lignin monomers to pharmaceutical compounds without requesting extra organic substrate (e.g., glucose) or freshwater by reprogramming the marine bacterium Roseovarius nubinhibens with a multiplex CRISPR interference system. Beyond the blue lignin valorization, we present a proof-of-principle of leveraging marine bacteria and engineering biology for a sustainable future.

Evolution and engineering of pathways for aromatic O-demethylation in Pseudomonas putida KT2440

Biological conversion of lignin from biomass offers a promising strategy for sustainable production of fuels and chemicals. However, aromatic compounds derived from lignin commonly contain methoxy groups, and O-demethylation of these substrates is often a rate-limiting reaction that influences catabolic efficiency. Several enzyme families catalyze aromatic O-demethylation, but they are rarely compared in vivo to determine an optimal biocatalytic strategy. Here, two pathways for aromatic O-demethylation were compared in Pseudomonas putida KT2440. The native Rieske non-heme iron monooxygenase (VanAB) and, separately, a heterologous tetrahydrofolate-dependent demethylase (LigM) were constitutively expressed in P. putida, and the strains were optimized via adaptive laboratory evolution (ALE) with vanillate as a model substrate. All evolved strains displayed improved growth phenotypes, with the evolved strains harboring the native VanAB pathway exhibiting growth rates ∼1.8x faster than those harboring the heterologous LigM pathway. Enzyme kinetics and transcriptomics studies investigated the contribution of selected mutations toward enhanced utilization of vanillate. The VanAB-overexpressing strains contained the most impactful mutations, including those in VanB, the reductase for vanillate O-demethylase, PP_3494, a global regulator of vanillate catabolism, and fghA, involved in formaldehyde detoxification. These three mutations were combined into a single strain, which exhibited approximately 5x faster vanillate consumption than the wild-type strain in the first 8 h of cultivation. Overall, this study illuminates the details of vanillate catabolism in the context of two distinct enzymatic mechanisms, yielding a platform strain for efficient O-demethylation of lignin-related aromatic compounds to value-added products.

Increased triacylglycerol production in Rhodococcus opacus by overexpressing transcriptional regulators

Lignocellulosic biomass is currently underutilized, but it offers promise as a resource for the generation of commercial end-products, such as biofuels, detergents, and other oleochemicals. Rhodococcus opacus PD630 is an oleaginous, Gram-positive bacterium with an exceptional ability to utilize recalcitrant aromatic lignin breakdown products to produce lipid molecules such as triacylglycerols (TAGs), which are an important biofuel precursor. Lipid carbon storage molecules accumulate only under growth-limiting low nitrogen conditions, representing a significant challenge toward using bacterial biorefineries for fuel precursor production. In this work, we screened overexpression of 27 native transcriptional regulators for their abilities to improve lipid accumulation under nitrogen-rich conditions, resulting in three strains that accumulate increased lipids, unconstrained by nitrogen availability when grown in phenol or glucose. Transcriptomic analyses revealed that the best strain (#13) enhanced FA production via activation of the β-ketoadipate pathway. Gene deletion experiments confirm that lipid accumulation in nitrogen-replete conditions requires reprogramming of phenylalanine metabolism. By generating mutants decoupling carbon storage from low nitrogen environments, we move closer toward optimizing R. opacus for efficient bioproduction on lignocellulosic biomass.

Role of Deep Eutectic Solvent Precursors as Hydrotropes: Unveiling Synergism/Antagonism for Enhanced Kraft Lignin Dissolution

Lignin holds significant potential as a feedstock for generating valuable aromatic compounds, fuels, and functional materials. However, achieving this potential requires the development of effective dissolution methods. Previous works have demonstrated the remarkable capability of hydrotropes to enhance the aqueous solubility of lignin, an amphiphilic macromolecule. Notably, deep eutectic solvents (DESs) have exhibited hydrotropic behavior, significantly increasing the aqueous solubility of hydrophobic solutes, making them attractive options for lignin dissolution. This study aimed at exploring the influence of hydrogen bond acceptors (HBAs) and hydrogen bond donors (HBDs) on the performance of DESs as hydrotropes for lignin dissolution, while possible dissolution mechanisms in different water/DES compositions were discussed. The capacity of six alcohols (glycerol, ethylene glycol, 1,3-propanediol, 1,4-butanediol, 1,5-pentanediol, and 1,6-hexanediol) and cholinium chloride to enhance the solubility of Kraft lignin in aqueous media was investigated. A correlation between solubility enhancement and the alkyl chain length of the alcohol was observed. This was rationalized upon the competition between hydrotrope-hydrotrope and solute-hydrotrope aggregates with the latter being maximized for 1,4-butanediol. Interestingly, the hydrotropic effect of DESs on lignin solubility is well represented by the independent sum of the dissolving contributions from the corresponding HBAs and HBDs in the diluted region. Conversely, in the concentrated region, the solubility of lignin for a certain hydrotrope concentration was always found to be higher for the pure hydrotropes rather than their combined HBA/HBD counterparts.

Carbon-wise utilization of lignin-related compounds by synergistically employing anaerobic and aerobic bacteria

BACKGROUND

Lignin is a highly abundant but strongly underutilized natural resource that could serve as a sustainable feedstock for producing chemicals by microbial cell factories. Because of the heterogeneous nature of the lignin feedstocks, the biological upgrading of lignin relying on the metabolic routes of aerobic bacteria is currently considered as the most promising approach. However, the limited substrate range and the inefficient catabolism of the production hosts hinder the upgrading of lignin-related aromatics. Particularly, the aerobic O-demethylation of the methoxyl groups in aromatic substrates is energy-limited, inhibits growth, and results in carbon loss in the form of CO2.

RESULTS

In this study, we present a novel approach for carbon-wise utilization of lignin-related aromatics by the integration of anaerobic and aerobic metabolisms. In practice, we employed an acetogenic bacterium Acetobacterium woodii for anaerobic O-demethylation of aromatic compounds, which distinctively differs from the aerobic O-demethylation; in the process, the carbon from the methoxyl groups is fixed together with CO2 to form acetate, while the aromatic ring remains unchanged. These accessible end-metabolites were then utilized by an aerobic bacterium Acinetobacter baylyi ADP1. By utilizing this cocultivation approach, we demonstrated an upgrading of guaiacol, an abundant but inaccessible substrate to most microbes, into a plastic precursor muconate, with a nearly equimolar yields (0.9 mol/mol in a small-scale cultivation and 1.0 mol/mol in a one-pot bioreactor cultivation). The process required only a minor genetic engineering, namely a single gene knock-out. Noticeably, by employing a metabolic integration of the two bacteria, it was possible to produce biomass and muconate by utilizing only CO2 and guaiacol as carbon sources.

CONCLUSIONS

By the novel approach, we were able to overcome the issues related to aerobic O-demethylation of methoxylated aromatic substrates and demonstrated carbon-wise conversion of lignin-related aromatics to products with yields unattainable by aerobic processes. This study highlights the power of synergistic integration of distinctive metabolic features of bacteria, thus unlocking new opportunities for harnessing microbial cocultures in upgrading challenging feedstocks.

Bioaugmentation of anaerobic digesters with the enriched lignin-degrading microbial consortia through a metagenomic approach

The recalcitrance of lignin impedes the efficient utilization of lignocellulosic biomass, hindering the efficient production of biogas and value-added materials. Despite the emergence of anaerobic digestion as a superior alternative to the aerobic method for lignin processing, achieving its feasibility requires thorough characterization of lignin-degrading anaerobic microorganisms, assessment of their biomethane production potential, and a comprehensive understanding of the degradation pathway. This study aimed to address the aforementioned necessities by bioaugmenting seed sludge with three distinct enriched lignin-degrading microbial consortia at both 25 °C and 37 °C. Enhanced biomethane yields was detected in the bioaugmented digesters, while the highest production was observed as 188 mLN CH4 gVS-1 in digesters operated at 37 °C. Moreover, methane yield showed a significant improvement in the samples at 37 °C ranging from 110% to 141% compared to the control, demonstrating the efficiency of the enriched lignin-degrading microbial community. Temperature and substrate were identified as key factors influencing microbial community dynamics. The observation that microbial communities tended to revert to the initial state after lignin depletion, indicating the stability of the overall microbiota composition in the digesters, is a promising finding for large-scale studies. Noteworthy candidates for lignin degradation, including Sporosarcina psychrophila, Comamonas aquatica, Shewanella baltica, Pseudomonas sp. C27, and Brevefilum fermentans were identified in the bioaugmented samples. PICRUSt2 predictions suggest that the pathway and specific proteins involved in anaerobic lignin degradation might share similarities with those engaged in the degradation of aromatic compounds.

The role of glycosylation in non-productive adsorption of cellulase to lignin isolated from pretreated corn stover

Glycosylation, a general post-translational modification for fungal cellulase, has been shown to affect cellulase binding to its substrate. However, the exact impact of glycosylation on cellulase-lignin interaction remain unclear. Here, we demonstrated that the lignin isolated from tetrahydrofuran-pretreated corn stover exhibits strong adsorption capability to cellulase due to its negatively charged and porous structure. For the cellulases with varying glycosylation levels, the less-glycosylated protein showed high adsorption capability to lignin, and that trend was observed for the main cellulase components secreted by Penicillium oxilicum, including endoglucanase PoCel5B, cellobiohydrolase PoCel7A-2, and β-glucosidase PoBgl1. Additionally, N-glycan sites and motifs were examined using mass spectrometry, and protein structures with N-glycans were constructed, where PoBgl1 and PoCel7A-2 contained 13 and 1 glycosylated sites respectively. The results of molecular dynamics simulations indicated that the N-glycans impacted on the solvent-accessible surface area and secondary structure of protein, and the binding conformation of lignin fragment on cellulase, resulting in a decrease in binding energy (14 kcal/mol for PoBgl1 and 13 kcal/mol for PoCel7A-2), particularly for van der Waals and electrostatic interaction. Those findings suggested that glycosylation negatively impacted the lignin-cellulase interaction, providing a theoretical basis for the rational engineering of enzymes to reduce lignin-enzyme interaction.

A model-driven approach to upcycling recalcitrant feedstocks in Pseudomonas putida by decoupling PHA production from nutrient limitation

Bacterial polyhydroxyalkanoates (PHAs) have emerged as promising eco-friendly alternatives to petroleum-based plastics since they are synthesized from renewable resources and offer exceptional properties. However, their production is limited to the stationary growth phase under nutrient-limited conditions, requiring customized strategies and costly two-phase bioprocesses. In this study, we tackle these challenges by employing a model-driven approach to reroute carbon flux and remove regulatory constraints using synthetic biology. We construct a collection of Pseudomonas putida-overproducing strains at the expense of plastics and lignin-related compounds using growth-coupling approaches. PHA production was successfully achieved during growth phase, resulting in the production of up to 46% PHA/cell dry weight while maintaining a balanced carbon-to-nitrogen ratio. Our strains are additionally validated under an upcycling scenario using enzymatically hydrolyzed polyethylene terephthalate as a feedstock. These findings have the potential to revolutionize PHA production and address the global plastic crisis by overcoming the complexities of traditional PHA production bioprocesses.

From 13C-lignin to 13C-mycelium: Agaricus bisporus uses polymeric lignin as a carbon source

Plant biomass conversion by saprotrophic fungi plays a pivotal role in terrestrial carbon (C) cycling. The general consensus is that fungi metabolize carbohydrates, while lignin is only degraded and mineralized to CO2. Recent research, however, demonstrated fungal conversion of 13C-monoaromatic compounds into proteinogenic amino acids. To unambiguously prove that polymeric lignin is not merely degraded, but also metabolized, carefully isolated 13C-labeled lignin served as substrate for Agaricus bisporus, the world's most consumed mushroom. The fungus formed a dense mycelial network, secreted lignin-active enzymes, depolymerized, and removed lignin. With a lignin carbon use efficiency of 0.14 (g/g) and fungal biomass enrichment in 13C, we demonstrate that A. bisporus assimilated and further metabolized lignin when offered as C-source. Amino acids were high in 13C-enrichment, while fungal-derived carbohydrates, fatty acids, and ergosterol showed traces of 13C. These results hint at lignin conversion via aromatic ring-cleaved intermediates to central metabolites, underlining lignin's metabolic value for fungi.

Statistical optimization of cellulase production from Bacillus sp. YE16 isolated from yak dung of the Sikkim Himalayas for its application in bioethanol production using pretreated sugarcane bagasse

Cellulolytic bacteria were isolated from yak dung samples collected from different habitats of Sikkim, India. Isolate YE16 from the Yumthang Valley sample showed highest enzyme activity of 7.68 U/mL and was identified as Bacillus sp., which has a sequence similarity of 96.15% with B. velezensis. One factor at a time (OFAT) analysis revealed that an acidic pH of 5 with 37 °C temperature was optimum for maximum enzyme production after 36 hrs of incubation (13.88 U/mL), which was further increased after statistical optimization (34.70 U/mL). Media optimization based on response surface methodology predicted that Carboxymethyl cellulose (CMC) and MgSO4 at concentrations of 30 g/L and 0.525 g/L, respectively, at pH 5.5 to show CMCase activity of 30.612 U/mL, which was consistent with the observed value of 30.25 U/mL and confirmed the model. The crude enzyme also efficiently hydrolyzed alkaline pretreated sugarcane bagasse, releasing 7.09 g/L of glucose equivalent with an ethanol production of 3.05 g.

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, ΔpobA, 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 ΔpcaL strain grew on neither p-MBA nor veratrate, indicating they are catabolized through the β-ketoadipate pathway. This study expands our understanding of the bacterial catabolism of aromatic compounds and facilitates the development of biocatalysts for lignin valorization.IMPORTANCELignin, an abundant aromatic polymer found in plant biomass, is a promising renewable replacement for fossil fuels as a feedstock for the chemical industry. Strategies for upgrading lignin include processes that couple the catalytic fractionation of biomass and biocatalytic transformation of the resulting aromatic compounds with a microbial cell factory. Engineering microbial cell factories for this biocatalysis requires characterization of bacterial pathways involved in catabolizing lignin-derived aromatic compounds. This study identifies new pathways for lignin-derived aromatic degradation in Rhodococcus, a genus of bacteria well suited for biocatalysis. Additionally, we describe previously unknown activities of characterized enzymes on lignin-derived compounds, expanding their utility. This work advances the development of strategies to replace fossil fuel-based feedstocks with sustainable alternatives.

Machine learning analysis of RB-TnSeq fitness data predicts functional gene modules in Pseudomonas putida KT2440

There is growing interest in engineering Pseudomonas putida KT2440 as a microbial chassis for the conversion of renewable and waste-based feedstocks, and metabolic engineering of P. putida relies on the understanding of the functional relationships between genes. In this work, independent component analysis (ICA) was applied to a compendium of existing fitness data from randomly barcoded transposon insertion sequencing (RB-TnSeq) of P. putida KT2440 grown in 179 unique experimental conditions. ICA identified 84 independent groups of genes, which we call fModules ("functional modules"), where gene members displayed shared functional influence in a specific cellular process. This machine learning-based approach both successfully recapitulated previously characterized functional relationships and established hitherto unknown associations between genes. Selected gene members from fModules for hydroxycinnamate metabolism and stress resistance, acetyl coenzyme A assimilation, and nitrogen metabolism were validated with engineered mutants of P. putida. Additionally, functional gene clusters from ICA of RB-TnSeq data sets were compared with regulatory gene clusters from prior ICA of RNAseq data sets to draw connections between gene regulation and function. Because ICA profiles the functional role of several distinct gene networks simultaneously, it can reduce the time required to annotate gene function relative to manual curation of RB-TnSeq data sets.

IMPORTANCE

This study demonstrates a rapid, automated approach for elucidating functional modules within complex genetic networks. While Pseudomonas putida randomly barcoded transposon insertion sequencing data were used as a proof of concept, this approach is applicable to any organism with existing functional genomics data sets and may serve as a useful tool for many valuable applications, such as guiding metabolic engineering efforts in other microbes or understanding functional relationships between virulence-associated genes in pathogenic microbes. Furthermore, this work demonstrates that comparison of data obtained from independent component analysis of transcriptomics and gene fitness datasets can elucidate regulatory-functional relationships between genes, which may have utility in a variety of applications, such as metabolic modeling, strain engineering, or identification of antimicrobial drug targets.

A green pathway for lignin valorization: Enzymatic lignin depolymerization in biocompatible ionic liquids and deep eutectic solvents

Lignin depolymerization, which enables the breakdown of a complex and heterogeneous aromatic polymer into relatively uniform derivatives, serves as a critical process in valorization of lignin. Enzymatic lignin depolymerization has become a promising biological strategy to overcome the heterogeneity of lignin, due to its mild reaction conditions and high specificity. However, the low solubility of lignin compounds in aqueous environments prevents efficient lignin depolymerization by lignin-degrading enzymes. The employment of biocompatible ionic liquids (ILs) and deep eutectic solvents (DESs) in lignin fractionation has created a promising pathway to enzymatically depolymerize lignin within these green solvents to increase lignin solubility. In this review, recent research progress on enzymatic lignin depolymerization, particularly in a consolidated process involving ILs/DESs is summarized. In addition, the interactions between lignin-degrading enzymes and solvent systems are explored, and potential protein engineering methodology to improve the performance of lignin-degrading enzymes is discussed. Consolidation of enzymatic lignin depolymerization and biocompatible ILs/DESs paves a sustainable, efficient, and synergistic way to convert lignin into value-added products.

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

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.

Engineering Novosphingobium aromaticivorans to produce cis,cis-muconic acid from biomass aromatics

The platform chemical cis,cis-muconic acid (ccMA) provides facile access to a number of monomers used in the synthesis of commercial plastics. It is also a metabolic intermediate in the β-ketoadipic acid pathway of many bacteria and, therefore, a current target for microbial production from abundant renewable resources via metabolic engineering. This study investigates Novosphingobium aromaticivorans DSM12444 as a chassis for the production of ccMA from biomass aromatics. The N. aromaticivorans genome predicts that it encodes a previously uncharacterized protocatechuic acid (PCA) decarboxylase and a catechol 1,2-dioxygenase, which would be necessary for the conversion of aromatic metabolic intermediates to ccMA. This study confirmed the activity of these two enzymes in vitro and compared their activity to ones that have been previously characterized and used in ccMA production. From these results, we generated one strain that is completely derived from native genes and a second that contains genes previously used in microbial engineering synthesis of this compound. Both of these strains exhibited stoichiometric production of ccMA from PCA and produced greater than 100% yield of ccMA from the aromatic monomers that were identified in liquor derived from alkaline pretreated biomass. Our results show that a strain completely derived from native genes and one containing homologs from other hosts are both capable of stoichiometric production of ccMA from biomass aromatics. Overall, this work combines previously unknown aspects of aromatic metabolism in N. aromaticivorans and the genetic tractability of this organism to generate strains that produce ccMA from deconstructed biomass.IMPORTANCEThe production of commodity chemicals from renewable resources is an important goal toward increasing the environmental and economic sustainability of industrial processes. The aromatics in plant biomass are an underutilized and abundant renewable resource for the production of valuable chemicals. However, due to the chemical composition of plant biomass, many deconstruction methods generate a heterogeneous mixture of aromatics, thus making it difficult to extract valuable chemicals using current methods. Therefore, recent efforts have focused on harnessing the pathways of microorganisms to convert a diverse set of aromatics into a single product. Novosphingobium aromaticivorans DSM12444 has the native ability to metabolize a wide range of aromatics and, thus, is a potential chassis for conversion of these abundant compounds to commodity chemicals. This study reports on new features of N. aromaticivorans that can be used to produce the commodity chemical cis,cis-muconic acid from renewable and abundant biomass aromatics.

Genetic Code Expansion in Pseudomonas putida KT2440

Emerging microorganism Pseudomonas putida KT2440 is utilized for the synthesis of biobased chemicals from renewable feedstocks and for bioremediation. However, the methods for analyzing, engineering, and regulating the biosynthetic enzymes and protein complexes in this organism remain underdeveloped.Such attempts can be advanced by the genetic code expansion-enabled incorporation of noncanonical amino acids (ncAAs) into proteins, which also enables further controls over the strain's biological processes. Here, we give a step-by-step account of the incorporation of two ncAAs into any protein of interest (POI) in response to a UAG stop codon by two commonly used orthogonal archaeal tRNA synthetase and tRNA pairs. Using superfolder green fluorescent protein (sfGFP) as an example, this method lays down a solid foundation for future work to study and enhance the biological functions of KT2440.

Unleashing the capacity of Rhodococcus for converting lignin into lipids

Bioconversion of bioresources/wastes (e.g., lignin, chemical pulping byproducts) represents a promising approach for developing a bioeconomy to help address growing energy and materials demands. Rhodococcus, a promising microbial strain, utilizes numerous carbon sources to produce lipids, which are precursors for synthesizing biodiesel and aviation fuels. However, compared to chemical conversion, bioconversion involves living cells, which is a more complex system that needs further understanding and upgrading. Various wastes amenable to bioconversion are reviewed herein to highlight the potential of Rhodococci for producing lipid-derived bioproducts. In light of the abundant availability of these substrates, Rhodococcus' metabolic pathways converting them to lipids are analyzed from a "beginning-to-end" view. Based on an in-depth understanding of microbial metabolic routes, genetic modifications of Rhodococcus by employing emerging tools (e.g., multiplex genome editing, biosensors, and genome-scale metabolic models) are presented for promoting the bioconversion. Co-solvent enhanced lignocellulose fractionation (CELF) strategy facilitates the generation of a lignin-derived aromatic stream suitable for the Rhodococcus' utilization. Novel alkali sterilization (AS) and elimination of thermal sterilization (ETS) approaches can significantly enhance the bioaccessibility of lignin and its derived aromatics in aqueous fermentation media, which promotes lipid titer significantly. In order to achieve value-added utilization of lignin, biodiesel and aviation fuel synthesis from lignin and lipids are further discussed. The possible directions for unleashing the capacity of Rhodococcus through synergistically modifying microbial strains, substrates, and fermentation processes are proposed toward a sustainable biological lignin valorization.

Green and sustainable production of high-purity lignin microparticles with well-preserved substructure and enhanced anti-UV/oxidant activity using peroxide-promoted alkaline deep eutectic solvent

Deep eutectic solvents (DESs) have emerged as promising and eco-friendly solvents for the efficient extraction of lignin from biomass due to their low cost and environmental benefits. Nevertheless, the prevalent use of acidic DESs in lignin extraction often results in excessive depolymerization and recondensation of lignin, thereby impeding its downstream applications. In this study, we developed a range of alkaline DESs (ADESs), both pure and peroxide-containing, for the extraction of high-quality lignin from bamboo. Moreover, carbon dioxide (CO2) was employed for the precipitation and regeneration of the extracted lignin. The obtained lignin fractions were comprehensively characterized in terms of yield, purity, morphology, solubility, structural features, and anti-UV/oxidant activity. The results showed that the monoethanolamine-based ADES demonstrated superior performance among the pure ADESs. Structural analysis confirmed the well-preserved substructures of lignin fractions obtained using ADESs, with β-O-4 bond retention ranging from 49.8 % to 68.4 %. The incorporation of a suitable amount of peroxide improved lignin yield, morphology, solubility, and anti-UV/oxidant activity. Additionally, the anti-UV/oxidant activity of lignin exhibited a positive correlation with its phenolic hydroxyl content. This study provides a valuable reference for the green and sustainable production and valorization of lignin within the existing biorefinery framework.

Autoxidation Catalysis for Carbon-Carbon Bond Cleavage in Lignin

Selective lignin depolymerization is a key step in lignin valorization to value-added products, and there are multiple catalytic methods to cleave labile aryl-ether bonds in lignin. However, the overall aromatic monomer yield is inherently limited by refractory carbon-carbon linkages, which are abundant in lignin and remain intact during most selective lignin deconstruction processes. In this work, we demonstrate that a Co/Mn/Br-based catalytic autoxidation method promotes carbon-carbon bond cleavage in acetylated lignin oligomers produced from reductive catalytic fractionation. The oxidation products include acetyl vanillic acid and acetyl vanillin, which are ideal substrates for bioconversion. Using an engineered strain of Pseudomonas putida, we demonstrate the conversion of these aromatic monomers to cis,cis-muconic acid. Overall, this study demonstrates that autoxidation enables higher yields of bioavailable aromatic monomers, exceeding the limits set by ether-bond cleavage alone.

Catabolic System of 5-Formylferulic Acid, a Downstream Metabolite of a β-5-Type Lignin-Derived Dimer, in Sphingobium lignivorans SYK-6

Sphingobium lignivorans SYK-6 can assimilate various lignin-derived aromatic compounds, including a β-5-type (phenylcoumaran-type) dimer, dehydrodiconiferyl alcohol (DCA). SYK-6 converts DCA to a stilbene-type intermediate via multiple reaction steps and then to vanillin and 5-formylferulic acid (FFA). Here, we first elucidated the catabolic pathway of FFA, which is the only unknown pathway in DCA catabolism. Then, we identified and characterized the enzyme-encoding genes responsible for this pathway. Analysis of the metabolites revealed that FFA was converted to 5-carboxyferulic acid (CFA) through oxidation of the formyl group, followed by conversion to ferulic acid by decarboxylation. A comprehensive analysis of the aldehyde dehydrogenase genes in SYK-6 indicated that NAD+-dependent FerD (SLG_12800) is crucial for the conversion of FFA to CFA. LigW and LigW2, which are 5-carboxyvanillic acid decarboxylases involved in the catabolism of a 5,5-type dimer, were found to be involved in the conversion of CFA to ferulic acid, and LigW2 played a significant role. The ligW2 gene forms an operon with ferD, and their transcription was induced during growth in DCA.

Construction of a synthetic microbial community based on multiomics linkage technology and analysis of the mechanism of lignocellulose degradation

The efficient degradation of lignocellulose is a bottleneck for its integrated utilization. This research performed species analysis and made functional predictions in various ecosystems using multiomics coupling to construct a core synthetic microbial community with efficient lignocellulose degradation function. The synthetic microbial community was employed to degrade corn straw via solid-state fermentation. The degradation mechanisms were resolved using proteomics. The optimum culture conditions included 10% inoculum level (w/v), 4% nitrogen source ratio and a fermentation time of 23 d. Under these conditions, the degradation rates of cellulose, hemicellulose, and lignin were 34.91%, 45.94%, and 23.34%, respectively. Proteomic analysis revealed that lignin 1,4-β-xylanase, β-xylosidase and endo-1,4-β-xylanase were closely related to lignocellulose degradation. The metabolic pathways involved in lignocellulose degradation and the functional roles of eight strains were obtained. The synthesis of a microbial community via multiomics linkage technology can effectively decompose lignocellulose, which is useful for their further utilization.

Lignocellulosic biomass-based glycoconjugates for diverse biotechnological applications

Glycoconjugates are the ubiquitous components of mammalian cells, mainly synthesized by covalent bonds of carbohydrates to other biomolecules such as proteins and lipids, with a wide range of potential applications in novel vaccines, therapeutic peptides and antibodies (Ab). Considering the emerging developments in glycoscience, renewable production of glycoconjugates is of importance and lignocellulosic biomass (LCB) is a potential source of carbohydrates to produce synthetic glycoconjugates in a sustainable pathway. In this review, recent advances in glycobiology aiming on glycoconjugates production is presented together with the recent and cutting-edge advances in the therapeutic properties and application of glycoconjugates, including therapeutic glycoproteins, glycosaminoglycans (GAGs), and nutraceuticals, emphasizing the integral role of glycosylation in their function and efficacy. Special emphasis is given towards the potential exploration of carbon neutral feedstocks, in which LCB has an emerging role. Techniques for extraction and recovery of mono- and oligosaccharides from LCB are critically discussed and influence of the heterogeneous nature of the feedstocks and different methods for recovery of these sugars in the development of the customized glycoconjugates is explored. Although reports on the use of LCB for the production of glycoconjugates are scarce, this review sets clear that the potential of LCB as a source for the production of valuable glycoconjugates cannot be underestimated and encourages that future research should focus on refining the existing methodologies and exploring new approaches to fully realize the potential of LCB in glycoconjugate production.