Microbial demethylation of lignin: Evidence of enzymes participating in the removal of methyl/methoxyl groups

Pre-biodrying enhanced lignin degradation to promote aromatic macromolecular humic acid formation in double-phase composting

A 24-h pre-biodrying phase was introduced in 10-d double-phase biodrying-enhanced composting (BEC) to accelerate the humification of kitchen waste by promoting the generation of phenolic-rich aromatic skeletons, key humic precursors for the lignin-protein and polyphenol pathways. To explore how biodrying promotes phenolic hydroxyl accumulation, macromolecule decomposition, particularly lignin, was investigated. Compared to day 9 of 15-d conventional bioaugmented mechanical composting (BMC) without pre-biodrying, BEC achieved 78.32 ± 15.96 % higher lignin degradation by day 9 (p < 0.001), with stronger correlations to humification indicators and greater explanatory power (91 %) for humic acid UV-vis indices than other macromolecules. Structural analysis showed enhanced lignin demethoxylation (minimum 3.92/Ar) and β-O-4 cleavage (minimum 51.69 %), increasing phenolic hydroxyl accumulation (maximum 4.34 mmol·g-1). Microbial analysis further revealed that oxygen availability, improved by frequent stirring and aeration during biodrying, enriched Bacillaceae and Issatchenkia, which accelerated bioheat generation and created thermophilic conditions favorable for Bacillus and Saccharomonospora capable of lignin demethoxylation (via vanAB, ligM) and β-O-4 cleavage (via ligD, ligL, ligE, ligF, ligG). High temperatures also enhanced microbial cooperation, enabling the lignin degraders to obtain nutrients, cofactors, and detoxification agents for basal metabolism and lignin degradation from Oceanobacillus, Gracilibacillus, Sinibacillus, Georgenia, Nigrospora, and Aspergillus, thereby reducing their metabolic burden and allowing them to focus on lignin degradation. This study is the first to unveil the humification mechanism during composting from the perspective of macromolecule decomposition, especially lignin, for the generation of phenolic-rich aromatic skeletons as key humic precursors, providing theoretical support for developing simple, effective strategies to accelerate composting.

Flavonoid Stability and Biotransformation in Agricultural Soils: Effects of Hydroxylation, Methoxylation, and Glycosylation

Stricter pesticide regulations are increasing the demand for environmentally acceptable alternatives with flavonoids seen as promising candidates for use as biopesticides. However, the current limited understanding of the environmental fate of flavonoids in soils restricts their assessment as active pesticide ingredients. To address this knowledge gap, we conducted laboratory incubation experiments with LC-MS-based quantification to determine the half-lives of 18 structurally related flavonoids in three agricultural soils. Hydroxylated flavonoids were rapidly transformed (t1/2: 3-12 h), while methoxylated derivatives exhibited substantially longer half-lives, which increased with the number of methoxy groups (t1/2: 5-460 h). Glycosylated flavonoids were primarily transformed into their aglycones (t1/2: 0.5-5 h). Incubation experiments with autoclaved soil indicated that biotic processes primarily catalyzed the observed transformations. All trends were consistent across different soil types and pH values. This study provides a comprehensive overview of flavonoid stability in agricultural soils, enhancing our understanding of their potential as alternative pesticides.

Chemistry of lignin and condensed tannins as aromatic biopolymers

Aromatic biopolymers are the second largest group of biopolymers after polysaccharides. Depolymerization of aromatic biopolymers, as cheap and renewable substitutes for fossil-based resources, has been used in the preparation of biofuels, and a range of aromatic and aliphatic small molecules. Additionally, these polymers exhibit a robust UV-shielding function due to the high content of aromatic groups. Meanwhile, the abundance of phenolic groups in their structures gives these compounds outstanding antioxidant capabilities, making them well-suited for a diverse array of anti-UV and medical applications. Nevertheless, these biopolymers possess inherent drawbacks in their pristine states, such as rigid structure, low solubility, and lack of desired functionalities, which hinder their complete exploitation across diverse sectors. Thus, the modification and functionalization of aromatic biopolymers are essential to provide them with specific functionalities and features needed for particular applications. Aromatic biopolymers include lignins, tannins, melanins, and humic acids. The objective of this review is to offer a thorough reference for assessing the chemistry and functionalization of lignins and condensed tannins. Lignins represent the largest and most prominent category of aromatic biopolymers, typically distinguishable as either softwood-derived or hardwood-derived lignins. Besides, condensed tannins are the most investigated group of the tannin family. The electron-rich aromatic rings, aliphatic hydroxyl groups, and phenolic groups are the main functional groups in the structure of lignins and condensed tannins. Methoxy groups are also abundant in lignins. Each group displays varying chemical reactivity within these biopolymers. Therefore, the selective and specific functionalization of lignins and condensed tannins can be achieved by understanding the chemistry behavior of these functional groups. Targeted applications include biomedicine, monomers and surface active agents for sustainable plastics.

Enhanced Antioxidation and UV-Absorption Ability of Industrial Lignin via Promoting Phenolic Contents and Hydrophilicity

Lignin possesses unique natural antioxidation and UV-absorption abilities, making it a promising ingredient for sunscreen. However, the industrial lignin produced from pulping or bioethanol production generally shows low efficiency due to the limited phenolic hydroxyl content and poor compatibility with sunscreen, respectively. To address this issue, a molten salt hydrate treatment process was carried out for the selective cleavage of ether bonds in industrial lignin. After treatment, a 2-fold increase in phenolic hydroxyl content was observed, and lignin antioxidation efficiency was improved. The intermolecular forces of lignin in water measured by an atomic force microscope showed a significant decrease from -1.46 to 0.46 mN/m, suggesting an efficient increase in lignin hydrophilicity, which promoted lignin compatibility with sunscreen. We converted industrial lignin into colloidal balls, which improved compatibility and dispersion in the cream and more than tripled the sun protection factor compared to the direct addition of industrial lignin.

Cardiometabolic disease risk in gorillas is associated with altered gut microbial metabolism

Cardiometabolic disease is the leading cause of death in zoo apes; yet its etiology remains unknown. Here, we investigated compositional and functional microbial markers in fecal samples from 57 gorillas across U.S. zoos, 20 of which are diagnosed with cardiovascular disease, in contrast with 17 individuals from European zoos and 19 wild gorillas from Central Africa. Results show that zoo-housed gorillas in the U.S. exhibit the most diverse gut microbiomes and markers of increased protein and carbohydrate fermentation, at the expense of microbial metabolic traits associated with plant cell-wall degradation. Machine learning models identified unique microbial traits in U.S. gorillas with cardiometabolic distress; including reduced metabolism of sulfur-containing amino acids and hexoses, increased abundance of potential enteric pathogens, and low fecal butyrate and propionate production. These findings show that cardiometabolic disease in gorillas is potentially associated with altered gut microbial function, influenced by zoo-specific diets and environments.

Biohydrogen production from lignocellulosic hydrolysate: Unveiling the synergistic impact of substrate concentration and furfural inhibition

Lignocellulosic biomass offers substantial potential as an ideal feedstock for dark fermentative hydrogen production due to its sustainability and cost-effectiveness. The current study examined the influence of furfural on fermentative hydrogen production using lignocellulosic hydrolysate in the presence of furfural. Synthetic lignocellulosic hydrolysate, consisting primarily of 76% xylose, 10% glucose, 9% arabinose, and a mixture of other sugars such as galactose and mannose (85% pentose sugars and 15% hexose sugars), was employed as the substrate. Various substrate concentrations ranging from 2 to 32 g/L were tested, along with furfural concentrations of 0, 1, and 2 g/L. The investigation aimed to assess the effects of initial substrate concentration, initial furfural concentration, furfural-to-biomass ratio (F/B), and furfural-to-substrate ratio (F/S) on biohydrogen production yields. The maximum specific substrate utilization rates at different substrate concentrations were effectively characterized using Haldane's substrate inhibition model. Among the tested concentrations, the 16 g/L emerged as the optimal substrate concentration. The initial furfural concentration was identified as the most significant parameter impacting biohydrogen production, with complete inhibition observed at a furfural concentration of 2 g/L. Higher F/S ratios at substrate concentrations ranging from 2 to 16 g/L resulted in reduced maximum specific hydrogen production rates (MSHPR) and hydrogen yields. Substrate inhibition was observed at 24 g/L and 32 g/L. Lactate was the predominant metabolite in all batches containing 2-g/L furfural, as well as in batches with 1-g/L furfural and substrate concentrations of 24 and 32 g/L. Furfural at a concentration of 1 g/L was not inhibitory in any of the batches. Overall, the mixed cultures in this study could efficiently produce hydrogen from lignocellulosic hydrolysates and degrade furfural, providing new insights into fermentative hydrogen-producing bacteria with furfural tolerance.

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.

The Antioxidant Properties, Metabolism, Application and Mechanism of Ferulic Acid in Medicine, Food, Cosmetics, Livestock and Poultry

Ferulic acid is a ubiquitous ingredient in cereals, vegetables, fruits and Chinese herbal medicines. Due to the ferulic phenolic nucleus coupled to an extended side chain, it readily forms a resonant-stable phenoxy radical, which explains its potent antioxidant potential. In addition, it also plays an important role in anti-cancer, pro-angiogenesis, anti-thrombosis, neuroprotection, food preservation, anti-aging, and improving the antioxidant performance of livestock and poultry. This review provides a comprehensive summary of the structure, mechanism of antioxidation, application status, molecular mechanism of pharmacological activity, existing problems, and application prospects of ferulic acid and its derivatives. The aim is to establish a theoretical foundation for the utilization of ferulic acid in medicine, food, cosmetics, livestock, and poultry.

Antigenotoxic Activity of Polyphenolic Composition BP-C2 in Mouse Germ Cells In Vivo

In vivo antigenotoxic activity of BP-C2 composition (at doses of 60, 80, and 120 mg/kg) based on polyphenolic compounds derived from hydrolyzed lignin was evaluated in mouse germ cells. The BP-C2 composition dose-dependently reduced the aneugenic activity of topoisomerase II inhibitor etoposide in mouse oocytes without affecting the clastogenic activity of the genotoxicant. In mouse testicular cells, the BP-C2 composition reduced the DNA-damaging activity of the pro-oxidant genotoxicant dioxidine, but not etoposide. The cytoprotective activity of BP-C2 composition was revealed in relation to etoposide-induced cytotoxicity.

Machine learning-aided engineering of a cytochrome P450 for optimal bioconversion of lignin fragments

Using machine learning, molecular dynamics simulations, and density functional theory calculations we gain insight into the selectivity patterns of substrate activation by the cytochromes P450. In nature, the reactions catalyzed by the P450s lead to the biodegradation of xenobiotics, but recent work has shown that fungi utilize P450s for the activation of lignin fragments, such as monomer and dimer units. These fragments often are the building blocks of valuable materials, including drug molecules and fragrances, hence a highly selective biocatalyst that can produce these compounds in good yield with high selectivity would be an important step in biotechnology. In this work a detailed computational study is reported on two reaction channels of two P450 isozymes, namely the O-deethylation of guaethol by CYP255A and the O-demethylation versus aromatic hydroxylation of p-anisic acid by CYP199A4. The studies show that the second-coordination sphere plays a major role in substrate binding and positioning, heme access, and in the selectivity patterns. Moreover, the local environment affects the kinetics of the reaction through lowering or raising barrier heights. Furthermore, we predict a site-selective mutation for highly specific reaction channels for CYP199A4.

Microaeration promotes volatile siloxanes conversion to methane and simpler monomeric products

The ubiquitous use of volatile siloxanes in a myriad of product formulations has led to a widespread distribution of these persistent contaminants in both natural ecosystems and wastewater treatment plants. Microbial degradation under microaerobic conditions is a promising approach to mitigate D4 and D5 siloxanes while recovering energy in wastewater treatment plants. This study examined D4/D5 siloxanes biodegradation under both anaerobic and microaerobic conditions ( [Formula: see text]  = 0, 1, 3 %) using wastewater sludge. Results show that the use of microaeration in an otherwise strictly anaerobic environment significantly enhances siloxane conversion to methane. 16S rRNA gene sequencing identified potential degraders, including Clostridium lituseburense, Clostridium bifermentans and Synergistales species. Furthermore, chemical analysis suggested a stepwise siloxane conversion preceding methanogenesis under microaerobic conditions. This study demonstrates the feasibility of microaerobic siloxane biodegradation, laying groundwork for scalable removal technologies in wastewater treatment plants, ultimately highlighting the importance of using bio-based approaches in tackling persistent pollutants.

Advancements and Perspectives toward Lignin Valorization via O-Demethylation

Lignin represents the largest aromatic carbon resource in plants, holding significant promise as a renewable feedstock for bioaromatics and other cyclic hydrocarbons in the context of the circular bioeconomy. However, the methoxy groups of aryl methyl ethers, abundantly found in technical lignins and lignin-derived chemicals, limit their pertinent chemical reactivity and broader applicability. Unlocking the phenolic hydroxyl functionality through O-demethylation (ODM) has emerged as a valuable approach to mitigate this need and enables further applications. In this review, we provide a comprehensive summary of the progress in the valorization of technical lignin and lignin-derived chemicals via ODM, both catalytic and non-catalytic reactions. Furthermore, a detailed analysis of the properties and potential applications of the O-demethylated products is presented, accompanied by a systematic overview of available ODM reactions. This review primarily focuses on enhancing the phenolic hydroxyl content in lignin-derived species through ODM, showcasing its potential in the catalytic funneling of lignin and value-added applications. A comprehensive synopsis and future outlook are included in the concluding section of this review.

The etherase system of Novosphingobium sp. MBES04 functions as a sensor of lignin fragments through phenylpropanone production to induce specific transcriptional responses

The MBES04 strain of Novosphingobium accumulates phenylpropanone monomers as end-products of the etherase system, which specifically and reductively cleaves the β-O-4 ether bond (a major bond in lignin molecules). However, it does not utilise phenylpropanone monomers as an energy source. Here, we studied the response to the lignin-related perturbation to clarify the physiological significance of its etherase system. Transcriptome analysis revealed two gene clusters, each consisting of four tandemly linked genes, specifically induced by a lignin preparation extracted from hardwood (Eucalyptus globulus) and a β-O-4-type lignin model biaryl compound, but not by vanillin. The most strongly induced gene was a 2,4'-dihydroxyacetophenone dioxygenase-like protein, which leads to energy production through oxidative degradation. The other cluster was related to multidrug resistance. The former cluster was transcriptionally regulated by a common promoter, where a phenylpropanone monomer acted as one of the effectors responsible for gene induction. These results indicate that the physiological significance of the etherase system of the strain lies in its function as a sensor for lignin fragments. This may be a survival strategy to detect nutrients and gain tolerance to recalcitrant toxic compounds, while the strain preferentially utilises easily degradable aromatic compounds with lower energy demands for catabolism.

Fine root decomposition in forest ecosystems: an ecological perspective

Fine root decomposition is a physio-biochemical activity that is critical to the global carbon cycle (C) in forest ecosystems. It is crucial to investigate the mechanisms and factors that control fine root decomposition in forest ecosystems to understand their system-level carbon balance. This process can be influenced by several abiotic (e.g., mean annual temperature, mean annual precipitation, site elevation, stand age, salinity, soil pH) and biotic (e.g., microorganism, substrate quality) variables. Comparing decomposition rates within sites reveals positive impacts of nitrogen and phosphorus concentrations and negative effects of lignin concentration. Nevertheless, estimating the actual fine root breakdown is difficult due to inadequate methods, anthropogenic activities, and the impact of climate change. Herein, we propose that how fine root substrate and soil physiochemical characteristics interact with soil microorganisms to influence fine root decomposition. This review summarized the elements that influence this process, as well as the research methods used to investigate it. There is also need to study the influence of annual and seasonal changes affecting fine root decomposition. This cumulative evidence will provide information on temporal and spatial dynamics of forest ecosystems, and will determine how logging and reforestation affect fine root decomposition.

Impact of lignin constituents on the bacterial community and polycyclic aromatic hydrocarbon co-metabolism in an agricultural soil

Lignin is a complex biopolymer comprising phenolic monomers with different degrees of methoxylation and may potentially enhance the degradation of soil pollutants such as polycyclic aromatic hydrocarbons (PAHs) through co-metabolism. However, the contribution of lignin constituents, including phenolic and methoxy subunits, to PAH biodegradation remains unclear. Here, p-hydroxybenzoate (pHBA), vanillate and methanol were selected to simulate phenolic units and methoxy groups of lignin. Soil microcosms receiving these compounds were established to evaluate their regulation on the bacterial community and PAH co-metabolism. There were different effects of different components on the biodegradation of a four-ring PAH, benzo(a)anthracene (BaA), as characterized using an isotopic tracer. Only vanillate significantly stimulated BaA mineralization to CO2, with pHBA and methanol leading to no appreciable change in the allocation of BaA in soil compartments. The lignin constituents had differential impacts on the soil bacterial community, with substantial enrichment of methylotrophs occurring in methanol-supplemented microcosms. Both vanillate and pHBA selected several aromatic degraders. Vanillate caused additional enrichment of methylotrophs, suggesting structure-dependent stimulation of bacterial functional guilds by lignin monomers. Compared with its constituents, lignin produced more extensive responses in terms of bacterial diversity and composition and the fate of BaA. However, it was difficult to link BaA co-metabolism to any specific bacterial taxa in the presence of lignin or its subunits. The results indicate that the co-metabolism effects of lignin may not be directly associated with phenolic or methoxy metabolism but with its regulation of the soil microbiome.

Oxidation-driven lignin removal by Agaricus bisporus from wheat straw-based compost at industrial scale

Fungi are main lignin degraders and the edible white button mushroom, Agaricus bisporus, inhabits lignocellulose-rich environments. Previous research hinted at delignification when A. bisporus colonized pre-composted wheat straw-based substrate in an industrial setting, assumed to aid subsequent release of monosaccharides from (hemi-)cellulose to form fruiting bodies. Yet, structural changes and specific quantification of lignin throughout A. bisporus mycelial growth remain largely unresolved. To elucidate A. bisporus routes of delignification, at six timepoints throughout mycelial growth (15 days), substrate was collected, fractionated, and analyzed by quantitative pyrolysis-GC-MS, 2D-HSQC NMR, and SEC. Lignin decrease was highest between day 6 and day 10 and reached in total 42 % (w/w). The substantial delignification was accompanied by extensive structural changes of residual lignin, including increased syringyl to guaiacyl (S/G) ratios, accumulated oxidized moieties, and depleted intact interunit linkages. Hydroxypropiovanillone and hydroxypropiosyringone (HPV/S) subunits accumulated, which are indicative for β-|O-4' ether cleavage and imply a laccase-driven ligninolysis. We provide compelling evidence that A. bisporus is capable of extensive lignin removal, have obtained insights into mechanisms at play and susceptibilities of various substructures, thus we were contributing to understanding fungal lignin conversion.

Mussel-inspired laccase-mediated polydopamine graft onto bamboo fibers and its improvement effect on poly(3-hydroxybutyrate) based biocomposite

Bamboo fiber (BF) reinforced polyhydroxybutyrate (PHB) has become popular in developing an eco-friendly and sustainable biocomposite, while the weak interfacial compatibility between them is a major problem to overcome. This work, inspired by mussel super adhesion, creates a facile, highly efficient, and environmentally friendly solution based on in situ laccase-catalysed dopamine polymerization under a naturally acidic environment. The result indicates that a stabilized polydopamine coating is successfully grafted onto the lignin of BF, and it also enhances the thermal stability of the BF and biocomposite. Furthermore, modification of BF via laccase-catalysed polydopamine is superior to the conventional method of polydopamine under alkaline condition, and has outstanding advantages in terms of BF integrity protection. The optimal composition of biocomposite with BF treated by polydopamine under 1 U/ml concentration of laccase shows improvement in the impact strength, tensile strength, tensile modulus, bending strength, and modulus of elastic by 33.85 %, 9.27 %, 31.74 %, 11.76 %, and 12.92 %, respectively, compared to the unmodified counterpart. This work provides an insightful understanding of the mechanism and benefits of laccase-catalysed polydopamine modification of BF in a natural environment. It contributes to the efficient and environmentally friendly utilization of polydopamine for fabricating high-performance lignocellulosic fiber reinforced biocomposites.

Identification of a Phylogenetically Divergent Vanillate O-Demethylase from Rhodococcus ruber R1 Supporting Growth on Meta-Methoxylated Aromatic Acids

Rieske-type two-component vanillate O-demethylases (VanODs) catalyze conversion of the lignin-derived monomer vanillate into protocatechuate in several bacterial species. Currently, VanODs have received attention because of the demand of effective lignin valorization technologies, since these enzymes own the potential to catalyze methoxy group demethylation of distinct lignin monomers. In this work, we identified a phylogenetically divergent VanOD from Rhodococcus ruber R1, only distantly related to previously described homologues and whose presence, along with a 3-hydroxybenzoate/gentisate pathway, correlated with the ability to grow on other meta-methoxylated aromatics, such as 3-methoxybenzoate and 5-methoxysalicylate. The complementation of catabolic abilities by heterologous expression in a host strain unable to grow on vanillate, and subsequent resting cell assays, suggest that the vanAB genes of R1 strain encode a proficient VanOD acting on different vanillate-like substrates; and also revealed that a methoxy group in the meta position and a carboxylic acid moiety in the aromatic ring are key for substrate recognition. Phylogenetic analysis of the oxygenase subunit of bacterial VanODs revealed three divergent groups constituted by homologues found in Proteobacteria (Type I), Actinobacteria (Type II), or Proteobacteria/Actinobacteria (Type III) in which the R1 VanOD is placed. These results suggest that VanOD from R1 strain, and its type III homologues, expand the range of methoxylated aromatics used as substrates by bacteria.

Properties, Physiological Functions and Involvement of Basidiomycetous Alcohol Oxidase in Wood Degradation

Extensive research efforts have been devoted to describing yeast alcohol oxidase (AO) and its promoter region, which is vastly applied in studies of heterologous gene expression. However, little is known about basidiomycetous AO and its physiological role in wood degradation. This review describes several alcohol oxidases from both white and brown rot fungi, highlighting their physicochemical and kinetic properties. Moreover, the review presents a detailed analysis of available AO-encoding gene promoter regions in basidiomycetous fungi with a discussion of the manipulations of culture conditions in relation to the modification of alcohol oxidase gene expression and changes in enzyme production. The analysis of reactions catalyzed by lignin-modifying enzymes (LME) and certain lignin auxiliary enzymes (LDA) elucidated the possible involvement of alcohol oxidase in the degradation of derivatives of this polymer. Combined data on lignin degradation pathways suggest that basidiomycetous AO is important in secondary reactions during lignin decomposition by wood degrading fungi. With numerous alcoholic substrates, the enzyme is probably engaged in a variety of catalytic reactions leading to the detoxification of compounds produced in lignin degradation processes and their utilization as a carbon source by fungal mycelium.

Allyl Aryl Ether Cleavage by Blautia sp. MRG-PMF1 Cocorrinoid O-Demethylase

Coabalamin-dependent O-demethylase in Blautia sp. strain MRG-PMF1 was found to catalyze the unprecedented allyl aryl ether cleavage reaction. To expand the potential biotechnological applications, the reaction mechanism of the allyl aryl ether C-O bond cleavage, proposed to utilize the reactive Co(I) supernucleophile species, was studied further from the anaerobic whole-cell biotransformation. Various allyl naphthyl ether derivatives were reacted with Blautia sp. MRG-PMF1 O-demethylase, and stereoisomers of allyl naphthyl ethers, including prenyl and but-2-enyl naphthyl ethers, were converted to the corresponding naphthol in a stereoselective manner. The allyl aryl ether cleavage reaction was regioselective, and 2-naphthyl ethers were converted faster than the corresponding 1-naphthyl ethers. However, MRG-PMF1 cocorrinoid O-demethylase was not able to convert (2-methylallyl) naphthyl ether substrates, and the conversion of propargyl naphthyl ether was extremely slow. From the results, it was proposed that the allyl ether cleavage reaction follows the nucleophilic conjugate substitution (S_N2') mechanism. The reactivity and mechanism of the new allyl ether cleavage reaction by cobalamin-dependent O-demethylase would facilitate the application of Blautia sp. MRG-PMF1 O-demethylase in the area of green biotechnology. IMPORTANCE Biodegradation of environmental pollutants and valorization of biomaterials in a greener way is of great interest. Cobalamin-dependent O-demethylase in Blautia sp. MRG-PMF1 exclusively involves anaerobic C1 metabolism by cleaving the C-O bond of aromatic methoxy group and also produces various aryl alcohols by metabolizing allyl aryl ether compounds. Whereas methyl ether cleavage reaction is known to follow the S_N2' mechanism, the reaction pattern and mechanism of the new allyl ether cleavage reaction by cobalamin-dependent O-demethylase have never been studied. For the first time, stereoselectivity and the S_N2' mechanism of allyl aryl ether cleavage reaction by Blautia sp. MRG-PMF1 O-demethylase is reported, and the results would facilitate the application of Blautia sp. MRG-PMF1 O-demethylase in the area of green biotechnology.

Photochemical Production of Carbon Monoxide from Dissolved Organic Matter: Role of Lignin Methoxyarene Functional Groups

Carbon monoxide (CO) is the second most abundant identified product of dissolved organic matter (DOM) photodegradation after CO₂, but its formation mechanism remains unknown. Previous work showed that aqueous photodegradation of methoxy-substituted aromatics (ArOCH₃) produces CO considerably more efficiently than aromatic carbonyls. Following on this precedent, we propose that the methoxy aromatic groups of lignin act as the C source for the photochemical formation of CO from terrestrial DOM via a two-step pathway: formal hydrolytic demethylation to methanol and methanol oxidation to CO. To test the reasonableness of this mechanism, we investigated the photochemistry of eight lignin model compounds. We first observed that initial CO production rates are positively correlated with initial substrate degradation rates only for models containing at least one ArOCH₃ group, regardless of other structural features. We then confirmed that all ArOCH₃-containing substrates undergo formal hydrolytic demethylation by detecting methanol and the corresponding phenolic transformation products. Finally, we showed that hydroxyl radicals, likely oxidants to initiate methanol oxidation to CO, form during irradiation of all models. This work proposes an explicit mechanism linking ubiquitous, abundant, and easily quantifiable DOM functionalities to CO photoproduction. Our results further hint that methanol may be an abundant (yet overlooked) DOM photoproduct and a likely precursor of formaldehyde, formic acid, and CO₂ and that lignin photodegradation may represent a source of hydroxyl radicals.

Microbial rhodoquinone biosynthesis proceeds via an atypical RquA-catalyzed amino transfer from S-adenosyl-L-methionine to ubiquinone

Rhodoquinone (RQ) is a close analogue of ubiquinone (UQ) that confers diverse bacterial and eukaryotic taxa the ability to utilize fumarate as an electron acceptor in hypoxic conditions. The RquA protein, identified in a Rhodospirillum rubrum RQ-deficient mutant, has been shown to be required for RQ biosynthesis in bacteria. In this report, we demonstrate that RquA, homologous to SAM-dependent methyltransferases, is necessary and sufficient to catalyze RQ biosynthesis from UQ in vitro. Remarkably, we show that RquA uses SAM as the amino group donor in a substitution reaction that converts UQ to RQ. In contrast to known aminotransferases, RquA does not use pyridoxal 5'-phosphate (PLP) as a coenzyme, but requires the presence of Mn²⁺ as a cofactor. As these findings reveal, RquA provides an example of a non-canonical SAM-dependent enzyme that does not catalyze methyl transfer, instead it uses SAM in an atypical amino transfer mechanism.

Variations in lignin monomer contents and stable hydrogen isotope ratios in methoxy groups during the biodegradation of garden biomass

Lignin, a highly polymerized organic component of plant cells, is one of the most difficult aromatic substances to degrade. Selective biodegradation under mild conditions is a promising method, but the dynamic variations in lignin monomers during the biodegradation of lignocellulose are not fully understood. In this study, we evaluated the differences in lignin degradation under different microbial inoculation based on the lignin monomer content, monomer ratio, and stable hydrogen isotope ratio of lignin methoxy groups (δ2HLM). The weight loss during degradation and the net loss of lignocellulosic components improved dramatically with fungal inoculation. Syringyl monolignol (S-lignin), which contains two methoxy groups, was more difficult to degrade than guaiacyl (G-lignin), which contains only one methoxy group. The co-culture of Pseudomonas mandelii and Aspergillus fumigatus produced the greatest decrease in the G/S ratio, but δ2HLM values did not differ significantly among the three biodegradation experiments, although the enrichment was done within the fungal inoculation. The fluctuation of δ2HLM values during the initial phase of biodegradation may be related to the loss of pectic polysaccharides (another methoxy donor), which mainly originate from fallen leaves. Overall, the relative δ2HLM signals were preserved despite decreasing G/S ratios in the three degradation systems. Nevertheless, some details of lignin δ2HLM as a biomarker for biogeochemical cycles need to be explored further.

Unravelling Formaldehyde Metabolism in Bacteria: Road towards Synthetic Methylotrophy

Formaldehyde metabolism is prevalent in all organisms, where the accumulation of formaldehyde can be prevented through the activity of dissimilation pathways. Furthermore, formaldehyde assimilatory pathways play a fundamental role in many methylotrophs, which are microorganisms able to build biomass and obtain energy from single- and multicarbon compounds with no carbon–carbon bonds. Here, we describe how formaldehyde is formed in the environment, the mechanisms of its toxicity to the cells, and the cell’s strategies to circumvent it. While their importance is unquestionable for cell survival in formaldehyde rich environments, we present examples of how the modification of native formaldehyde dissimilation pathways in nonmethylotrophic bacteria can be applied to redirect carbon flux toward heterologous, synthetic formaldehyde assimilation pathways introduced into their metabolism. Attempts to engineer methylotrophy into nonmethylotrophic hosts have gained interest in the past decade, with only limited successes leading to the creation of autonomous synthetic methylotrophy. Here, we discuss how native formaldehyde assimilation pathways can additionally be employed as a premise to achieving synthetic methylotrophy. Lastly, we discuss how emerging knowledge on regulation of formaldehyde metabolism can contribute to creating synthetic regulatory circuits applied in metabolic engineering strategies.

Cytochromes P450 in the biocatalytic valorization of lignin

The valorization of lignin is critical to establishing sustainable biorefineries as we transition away from petroleum-derived feedstocks. Advances in lignin fractionation and depolymerization are yielding new opportunities for the biocatalytic upgrading of lignin-derived aromatic compounds (LDACs) using microbial cell factories. Given their roles in lignin metabolism and their catalytic versatility, cytochromes P450 are attractive enzymes in engineering such biocatalysts. Here we highlight P450s that catalyze aromatic O-demethylation, a rate-limiting step in the conversion of LDACs to valuable chemicals, including efforts to engineer the specificity of these enzymes and to use them in developing biocatalysts. We also discuss broader opportunities at the intersection of biochemistry, structure-guided enzyme engineering, and metabolic engineering for application of P450s in the emerging area of microbial lignin valorization.