From gene towards selective biomass valorization: bacterial β-etherases with catalytic activity on lignin-like polymers

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.

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.

Effect of time series on the degradation of lignin by Trametes gibbosa: Products and pathways

Lignin is the third most abundant organic resource in nature. The utilization of white-rot fungi for wood degradation effectively circumvents environmental pollution associated with chemical treatments, facilitating the benign decomposition of lignin. Trametes gibbosa is a typical white-rot fungus with rapid growth and strong wood decomposition ability. The lignin content decreased from 23.62 mg/mL to 17.05 mg/mL, which decreased by 27 % in 30 days. The activity of manganese peroxidase increased steadily by 9.44 times. The activities of laccase and lignin peroxidase had the same trend of change and reached peaks of 49.88 U/L and 10.43 U/L on the 25th day, respectively. The change in H2O2 content in vivo was opposite to its trend. For FTIR and GC-MS analysis, the fungi attacked the side chain structure of lignin phenyl propane polymer and benzene ring to crack into low molecular weight aromatic compounds. The side chains of low molecular weight aromatic compounds are oxidized, and long-chain carboxylic acids are formed. Additionally, the absorption peak in the vibration region of the benzene ring skeleton became complex, and the structure of the benzene rings changed. In the beginning, fungal growth was inhibited. Fungal autophagy was aggravated. The metal cation binding proteins of fungi were active, and the genes related to detoxification metabolism were upregulated. The newly produced compounds are related to xenobiotic metabolism. The degradation peak focused on the redox process, and the biological function was enriched in the regulation of macromolecular metabolism, lignin metabolism, and oxidoreductase activity acting on diphenols and related substances as donors. Notably, genes encoding key degradation enzymes, including lcc3, lcc4, phenol-2-monooxygenase, 3-hydroxybenzoate-6-hydroxylase, oxalate decarboxylase, and acetyl-CoA oxidase were significantly upregulated. On the 30th day, the N-glycan biosynthesis pathway was significantly enriched in glycan biosynthesis and metabolism. Weighted correlation network analysis was performed. A total of 1452 genes were clustered in the coral1 module, which were most related to lignin degradation. The genes were significantly enriched in oxidoreductase activity, peptidase activity, cell response to stimulation, signal transduction, lignin metabolism, and phenylpropane metabolism, while the rest were concentrated in glucose metabolism. In this study, the lignin degradation process and products were revealed by T. gibbosa. The molecular mechanism of lignin degradation in different stages was explored. The selection of an efficient utilization time of lignin will help to increase the degradation rate of lignin. This study provides a theoretical basis for the biofuel and biochemical production of lignin. SYNOPSIS: Trametes gibbosa degrades lignin in a pollution-free way, improving the utilization of carbon resources in an environmentally friendly spontaneous cycle. The products are the new way towards sustainable development and low-carbon technology.

Benzenoid Aromatics from Renewable Resources

In this Review, all known chemical methods for the conversion of renewable resources into benzenoid aromatics are summarized. The raw materials that were taken into consideration are CO2; lignocellulose and its constituents cellulose, hemicellulose, and lignin; carbohydrates, mostly glucose, fructose, and xylose; chitin; fats and oils; terpenes; and materials that are easily obtained via fermentation, such as biogas, bioethanol, acetone, and many more. There are roughly two directions. One much used method is catalytic fast pyrolysis carried out at high temperatures (between 300 and 700 °C depending on the raw material), which leads to the formation of biochar; gases, such as CO, CO2, H2, and CH4; and an oil which is a mixture of hydrocarbons, mostly aromatics. The carbon selectivities of this method can be reasonably high when defined small molecules such as methanol or hexane are used but are rather low when highly oxygenated compounds such as lignocellulose are used. The other direction is largely based on the multistep conversion of platform chemicals obtained from lignocellulose, cellulose, or sugars and a limited number of fats and terpenes. Much research has focused on furan compounds such as furfural, 5-hydroxymethylfurfural, and 5-chloromethylfurfural. The conversion of lignocellulose to xylene via 5-chloromethylfurfural and dimethylfuran has led to the construction of two large-scale plants, one of which has been operational since 2023.

Kraft Lignin Decomposition by Forest Soil Bacterium Pseudomonas kribbensis CHA-19

Identification of the biochemical metabolic pathway for lignin decomposition and the responsible degradative enzymes is needed for the effective biotechnological valorization of lignin to renewable chemical products. In this study, we investigated the decomposition of kraft lignin by the soil bacterium Pseudomonas kribbensis CHA-19, a strain that can utilize kraft lignin and its main degradation metabolite, vanillic acid, as growth substrates. Gel permeation chromatography revealed that CHA-19 decomposed polymeric lignin and degraded dehydrodivanillin (a representative lignin model compound); however, the degradative enzyme(s) and mechanism were not identified. Quantitative polymerase chain reaction with mRNAs from CHA-19 cells induced in the presence of lignin showed that the putative genes coding for two laccase-like multicopper oxidases (LMCOs) and three dye-decolorizing peroxidases (DyPs) were upregulated by 2.0- to 7.9-fold compared with glucose-induced cells, which indicates possible cooperation with multiple enzymes for lignin decomposition. Computational homology analysis of the protein sequences of LMCOs and DyPs also predicted their roles in lignin decomposition. Based on the above data, CHA-19 appears to initiate oxidative lignin decomposition using multifunctional LMCOs and DyPs, producing smaller metabolites such as vanillic acid, which is further degraded via ortho- and meta-ring cleavage pathways. This study not only helps to better understand the role of bacteria in lignin decomposition and thus in terrestrial ecosystems, but also expands the biocatalytic toolbox with new bacterial cells and their degradative enzymes for lignin valorization.

Development of a rapid assay for β-etherase activity using a novel chromogenic substrate

Biocatalytic processes play a crucial role in the valorization of lignin; therefore, methods enabling the monitoring of enzymes such as β-etherases, capable of breaking β-O-4 aryl-ether bonds, are of significant biotechnological interest. A novel method for quantifying β-etherase activity was developed based on the β-ester bond formation between a chromophore and acetovainillone. The chromogenic substrate β-(ρ-nitrophenoxy)-α-acetovanillone (PNPAV), was chemically synthesized. Kintetic monitoring of ρ-nitrophenolate release at 410 nm over 10 min, using recombinant LigF from Sphingobium sp SYK-6, LigF-AB and LigE-AB from Althererytrobacter sp B11, yielded enzimatic activities of 404. 3 mU/mg, 72 mU/mg, and 50 mU/mg, respectively. This method is applicable in a pH range of 7.0-9.0, with a sensitivity of up to 50 ng of enzyme, exhibiting no interference with lipolytic, glycolytic, proteolytic, and oxidoreductase enzymes.

Cloning, expression, and biochemical characterization of β-etherase LigF from Altererythrobacter sp. B11

Lignin, a complex heteropolymer present in plant cell walls, is now recognized as a valuable renewable resource with potential applications in various industries. The lignin biorefinery concept, which aims to convert lignin into value-added products, has gained significant attention in recent years. β-etherases, enzymes that selectively cleave β-O-4 aryl ether bonds in lignin, have shown promise in lignin depolymerization. In this study, the β-etherase LigF from Altererythrobacter sp. B11 was cloned, expressed, purified, and biochemically characterized. The LigF-AB11 enzyme exhibited optimal activity at 32 °C and pH 8.5 when catalyzing the substrate PNP-AV. The enzyme displayed mesophilic behavior and demonstrated higher activity at moderate temperatures. Stability analysis revealed that LigF-AB11 was not thermostable, with a complete loss of activity at 60 °C within an hour. Moreover, LigF-AB11 exhibited excellent pH stability, retaining over 50 % of its activity after 1 h under pH conditions ranging from 3.0 to 11.0. Metal ions and surface impregnation agents were found to affect the enzyme's activity, highlighting the importance of considering these factors in enzymatic processes for lignin depolymerization. This study provides valuable insights into the biochemical properties of LigF-AB11 and contributes to the development of efficient enzymatic processes for lignin biorefineries. Further optimization and understanding of β-etherases will facilitate their practical application in the valorization of lignin.

Catalytic and molecular properties of alkaliphilic and thermotolerant β-etherase from Altererythrobacter sp. B11

Phenylpropanone monomers, including guaiacyl hydroxypropanone, are important precursors for the synthesis of various chemicals. The monomers are obtained in a three-step cascade reaction catalyzed by a group of enzymes in the β-etherase system that cleaves the β-O-4 bond, the major bond in lignin. In this study, one of the β-etherase of the glutathione-S-transferase superfamily, AbLigF2, was discovered in genus Altererythrobacter, and the recombinant etherase was characterized. The enzyme showed maximal activity at 45 °C, maintained 30% of its activity after 2 h at 50 °C, and was the most thermostable among the previously reported enzymes. Moreover, N13, S14, and S115, located near the thiol group of glutathione, had a significant effect on the maximum reaction rate of enzyme activity. This study suggests that AbLigF2 has the potential to serve as a thermostable enzyme for lignin utilization and provides insights into its catalytic mechanism.

Enzymatic bioconversion process of lignin: mechanisms, reactions and kinetics

Lignin is a wasted renewable source of biomass-derived value-added chemicals. However, due to its material resistance to degradation, it remains highly underutilized. In order to develop new, catalysed and more environment friendly reaction processes for lignin valorization, science has turned a selective concentrated attention to microbial enzymes. This present work looks at the enzymes involved with the main reference focus on the different elementary mechanisms of action/conversion rate kinetics. Pathways, like with laccases/peroxidases, employ radicals, which more readily result in polymerization than de-polymerization. The β-etherase system interaction of proteins targets β-O-4 ether covalent bond, which targets lower molecular weight product species. Enzymatic activity is influenced by a wide variety of different factors which need to be considered in order to obtain the best functionality and synthesis yields.

Depolymerization and conversion of lignin to value-added bioproducts by microbial and enzymatic catalysis

Lignin, the most abundant renewable aromatic compound in nature, is an excellent feedstock for value-added bioproducts manufacturing; while the intrinsic heterogeneity and recalcitrance of which hindered the efficient lignin biorefinery and utilization. Compared with chemical processing, bioprocessing with microbial and enzymatic catalysis is a clean and efficient method for lignin depolymerization and conversion. Generally, lignin bioprocessing involves lignin decomposition to lignin-based aromatics via extracellular microbial enzymes and further converted to value-added bioproducts through microbial metabolism. In the review, the most recent advances in degradation and conversion of lignin to value-added bioproducts catalyzed by microbes and enzymes were summarized. The lignin-degrading microorganisms of white-rot fungi, brown-rot fungi, soft-rot fungi, and bacteria under aerobic and anaerobic conditions were comparatively analyzed. The catalytic metabolism of the microbial lignin-degrading enzymes of laccase, lignin peroxidase, manganese peroxidase, biphenyl bond cleavage enzyme, versatile peroxidase, and β-etherize was discussed. The microbial metabolic process of H-lignin, G-lignin, S-lignin based derivatives, protocatechuic acid, and catechol was reviewed. Lignin was depolymerized to lignin-derived aromatic compounds by the secreted enzymes of fungi and bacteria, and the aromatics were converted to value-added compounds through microbial catalysis and metabolic engineering. The review also proposes new insights for future work to overcome the recalcitrance of lignin and convert it to value-added bioproducts by microbial and enzymatic catalysis.

Enhanced biocatalytic degradation of lignin using combinations of lignin-degrading enzymes and accessory enzymes

Combinations of lignin-oxidizing enzymes and accessory enzymes show enhanced activity for product formation from polymeric lignin.

Complete genome reveals genetic repertoire and potential metabolic strategies involved in lignin degradation by environmental ligninolytic Klebsiella variicola P1CD1

Lignin is a recalcitrant macromolecule formed by three alcohols (monolignols) predominantly connected by β-aryl ether linkages and is one of the most abundant organic macromolecules in the biosphere. However, the role played by environmental bacteria in lignin degradation is still not entirely understood. In this study, we identified an environmental Klebsiella strain isolated from sediment collected from an altitudinal region in a unique Brazilian biome called Caatinga. This organism can also grow in the presence of kraft lignin as a sole source of carbon and aromatic compounds. We performed whole-genome sequencing and conducted an extensive genome-based metabolic reconstruction to reveal the potential mechanisms used by the bacterium Klebsiella variicola P1CD1 for lignin utilization as a carbon source. We identified 262 genes associated with lignin-modifying enzymes (LMEs) and lignin-degrading auxiliary enzymes (LDAs) required for lignin and aromatic compound degradation. The presence of one DyP (Dye-decolorizing Peroxidase) gene suggests the ability of P1CD1 strain to access phenolic and nonphenolic structures of lignin molecules, resulting in the production of catechol and protocatechuate (via vanillin or syringate) along the peripheral pathways of lignin degradation. K. variicola P1CD1 uses aldehyde-alcohol dehydrogenase to perform direct conversion of vanillin to protocatechol. The upper funneling pathways are linked to the central pathways of the protocatechuate/catechol catabolic branches via β-ketoadipate pathways, connecting the more abundant catabolized aromatic compounds with essential cellular functions, such as energy cellular and biomass production (i.e., via acetyl-CoA formation). The combination of phenotypic and genomic approaches revealed the potential dissimilatory and assimilatory ability of K. variicola P1CD1 to perform base-catalyzed lignin degradation, acting on high- and low-molecular-weight lignin fragments. These findings will be relevant for developing metabolic models to predict the ligninolytic mechanism used by environmental bacteria and shedding light on the flux of carbon in the soil.

Efficient Conversion of Pine Wood Lignin to Phenol

Obtaining chemical building blocks from biomass is attractive for meeting sustainability targets. Herein, an effective approach was developed to convert the lignin part of woody biomass into phenol, which is a valuable base chemical. Monomeric alkylmethoxyphenols were obtained from pinewood, rich in guaiacol-type lignin, through Pt/C-catalyzed reductive depolymerization. In a second step, an optimized MoP/SiO2 catalyst was used to selectively remove methoxy groups in these lignin monomers to generate 4-alkylphenols, which were then dealkylated by zeolite-catalyzed transalkylation to a benzene stream. The overall yield of phenol based on the initial lignin content in pinewood was 9.6 mol %.

Phenolic cross-links: building and de-constructing the plant cell wall

Covering: Up to 2019Phenolic cross-links and phenolic inter-unit linkages result from the oxidative coupling of two hydroxycinnamates or two molecules of tyrosine. Free dimers of hydroxycinnamates, lignans, play important roles in plant defence. Cross-linking of bound phenolics in the plant cell wall affects cell expansion, wall strength, digestibility, degradability, and pathogen resistance. Cross-links mediated by phenolic substituents are particularly important as they confer strength to the wall via the formation of new covalent bonds, and by excluding water from it. Four biopolymer classes are known to be involved in the formation of phenolic cross-links: lignins, extensins, glucuronoarabinoxylans, and side-chains of rhamnogalacturonan-I. Lignins and extensins are ubiquitous in streptophytes whereas aromatic substituents on xylan and pectic side-chains are commonly assumed to be particular features of Poales sensu lato and core Caryophyllales, respectively. Cross-linking of phenolic moieties proceeds via radical formation, is catalyzed by peroxidases and laccases, and involves monolignols, tyrosine in extensins, and ferulate esters on xylan and pectin. Ferulate substituents, on xylan in particular, are thought to be nucleation points for lignin polymerization and are, therefore, of paramount importance to wall architecture in grasses and for the development of technology for wall disassembly, e.g. for the use of grass biomass for production of 2^nd generation biofuels. This review summarizes current knowledge on the intra- and extracellular acylation of polysaccharides, and inter- and intra-molecular cross-linking of different constituents. Enzyme mediated lignan in vitro synthesis for pharmaceutical uses are covered as are industrial exploitation of mutant and transgenic approaches to control cell wall cross-linking.

Database Mining for Novel Bacterial β-Etherases, Glutathione-Dependent Lignin-Degrading Enzymes

Lignin is the most abundant aromatic polymer in nature and a promising renewable source for the provision of aromatic platform chemicals and biofuels. β-Etherases are enzymes with a promising potential for application in lignin depolymerization due to their selectivity in the cleavage of β-O-4 aryl ether bonds. However, only a very limited number of these enzymes have been described and characterized so far. Using peptide pattern recognition (PPR) as well as phylogenetic analyses, 96 putatively novel β-etherases have been identified, some even originating from bacteria outside the order Sphingomonadales A set of 13 diverse enzymes was selected for biochemical characterization, and β-etherase activity was confirmed for all of them. Some enzymes displayed up to 3-fold higher activity than previously known β-etherases. Moreover, conserved sequence motifs specific for either LigE- or LigF-type enzymes were deduced from multiple-sequence alignments and the PPR-derived peptides. In combination with structural information available for the β-etherases LigE and LigF, insight into the potential structural and/or functional role of conserved residues within these sequence motifs is provided. Phylogenetic analyses further suggest the presence of additional bacterial enzymes with potential β-etherase activity outside the classical LigE- and LigF-type enzymes as well as the recently described heterodimeric β-etherases.IMPORTANCE The use of biomass as a renewable source and replacement for crude oil for the provision of chemicals and fuels is of major importance for current and future societies. Lignin, the most abundant aromatic polymer in nature, holds promise as a renewable starting material for the generation of required aromatic structures. However, a controlled and selective lignin depolymerization to yield desired aromatic structures is a very challenging task. In this regard, bacterial β-etherases are especially interesting, as they are able to cleave the most abundant bond type in lignin with high selectivity. With this study, we significantly expanded the toolbox of available β-etherases for application in lignin depolymerization and discovered more active as well as diverse enzymes than previously known. Moreover, the identification of further β-etherases by sequence database mining in the future will be facilitated considerably through our deduced etherase-specific sequence motifs.

Biomimetic Reductive Cleavage of Keto Aryl Ether Bonds by Small-Molecule Thiols

The nucleophilic and reductive properties of thiolates and thiols make them ideal candidates as redox mediators via the thiol/disulfide couple. One mechanism for biological lignin depolymerization entails reduction of keto aryl ether bonds by an S_N 2 mechanism with the thiol redox mediator glutathione. In this study, mimicking this chemistry in a simple protein- and metal-free process, several small organic thiols are surveyed for their ability to cleave aryl keto ethers that model the β-O-4 linkages found in partially oxidized lignin. In polar aprotic solvents, β-mercaptoethanol and dithiothreitol yielded up to 100 % formation of phenol and acetophenone products from 2-phenoxyacetophenone, but not from its reduced alcohol congener. The effects of reaction conditions and of substituents on the aryl rings and the keto ether linkage are assessed. These results, together with activation barriers computed by quantum chemical simulations and direct observation of the expected intermediate thioether, point to an S_N 2 mechanism. This study confirms that small organic thiols can reductively break down lignin-relevant keto aryl ether linkages.

Activation of lignin by selective oxidation: An emerging strategy for boosting lignin depolymerization to aromatics

Lignin is the most abundant, renewable aromatic resource on earth and holds great potential for the production of value-added chemicals. The efficient valorization of lignin requires to deal with several formidable challenges, especially to prevent it from re-condensation reactions during its depolymerization. Recently, a strategy involving the activation of lignin side chains by selective oxidation of the benzylic alcohol in β-O-4 linkages to facilitate lignin degradation to aromatic monomers has become very popular. This strategy provides great advantages for lignin selective degradation to high yields of aromatics under mild conditions, but requires an additional pre-oxidation step. The purpose of this review is to provide the latest cutting-edge innovations of this novel approach. Various catalytic systems, including those using chemo-catalytic methods, physio-chemo catalytic methods, and/or bio-catalytic methods, for the oxidative activation of lignin side chains are summarized. By analyzing the current situation of lignin depolymerization, certain promising directions are emphasized.

Bioethanol production from waste lignocelluloses: A review on microbial degradation potential

Tremendous explosion of population has led to about 200% increment of total energy consumptions in last twenty-five years. Apart from conventional fossil fuel as limited energy source, alternative non-conventional sources are being explored worldwide to cater the energy requirement. Lignocellulosic biomass conversion for biofuel production is an important alternative energy source due to its abundance in nature and creating less harmful impacts on the environment in comparison to the coal or petroleum-based sources. However, lignocellulose biopolymer, the building block of plants, is a recalcitrant substance and difficult to break into desirable products. Commonly used chemical and physical methods for pretreating the substrate are having several limitations. Whereas, utilizing microbial potential to hydrolyse the biomass is an interesting area of research. Because of the complexity of substrate, several enzymes are required that can act synergistically to hydrolyse the biopolymer producing components like bioethanol or other energy substances. Exploring a range of microorganisms, like bacteria, fungi, yeast etc. that utilizes lignocelluloses for their energy through enzymatic breaking down the biomass, is one of the options. Scientists are working upon designing organisms through genetic engineering tools to integrate desired enzymes into a single organism (like bacterial cell). Studies on designer cellulosomes and bacteria consortia development relating consolidated bioprocessing are exciting to overcome the issue of appropriate lignocellulose digestions. This review encompasses up to date information on recent developments for effective microbial degradation processes of lignocelluloses for improved utilization to produce biofuel (bioethanol in particular) from the most plentiful substances of our planet.

Whole-cell cascade for the preparation of enantiopure β-O-4 aryl ether compounds with glutathione recycling

Bacterial β-etherases and glutathione lyases are glutathione-dependent enzymes that catalyze the selective cleavage of β-O-4 aryl ether bonds found in lignin. Their glutathione (GSH) dependence is regarded as major limitation for their application in the production of aromatics from lignin polymer and oligomers, as stoichiometric glutathione amounts are required. Thus, recycling of the GSH cofactor by a NAD(P)H-dependent glutathione reductase was proposed previously. Herein, the use of a whole-cell catalyst was studied for efficient β-O-4 aryl ether bond cleavage with intracellular GSH supply and recycling. After optimization of the whole-cell catalyst as well as reaction conditions, up to 5 mM lignin model substrate 2,6-methoxyphenoxy-α-veratrylglycerone (2,6-MP-VG) were efficiently converted into 2,6-methoxyphenol (2,6-MP) and veratryl glycerone (VG) without addition of external GSH. Unexpectedly, no glucose supply was required for glutathione recycling within the cells up to this substrate concentration. To demonstrate the applicability of this whole-cell approach, a whole-cell cascade combining a stereoselective β-etherase (either LigE from Sphingobium sp. SYK-6 or LigF-NA from Novosphingobium aromaticivorans) and a glutathione lyase (LigG-TD from Thiobacillus denitrificans) was employed in the kinetic resolution of racemic 2,6-MP-VG. This way, enantiopure (S)- and (R)-2,6-MP-VG were obtained on semi-preparative scale without the need for external GSH supply.

A heterodimeric glutathione S-transferase that stereospecifically breaks lignin's β(R)-aryl ether bond reveals the diversity of bacterial β-etherases

Lignin is a heterogeneous polymer of aromatic subunits that is a major component of lignocellulosic plant biomass. Understanding how microorganisms deconstruct lignin is important for understanding the global carbon cycle and could aid in developing systems for processing plant biomass into valuable commodities. Sphingomonad bacteria use stereospecific glutathione S-transferases (GSTs) called β-etherases to cleave the β-aryl ether (β-O-4) bond, the most common bond between aromatic subunits in lignin. Previously characterized bacterial β-etherases are homodimers that fall into two distinct GST subclasses: LigE homologues, which cleave the β(R) stereoisomer of the bond, and LigF homologues, which cleave the β(S) stereoisomer. Here, we report on a heterodimeric β-etherase (BaeAB) from the sphingomonad Novosphingobium aromaticivorans that stereospecifically cleaves the β(R)-aryl ether bond of the di-aromatic compound β-(2-methoxyphenoxy)-γ-hydroxypropiovanillone (MPHPV). BaeAB's subunits are phylogenetically distinct from each other and from other β-etherases, although they are evolutionarily related to LigF, despite the fact that BaeAB and LigF cleave different β-aryl ether bond stereoisomers. We identify amino acid residues in BaeAB's BaeA subunit important for substrate binding and catalysis, including an asparagine that is proposed to activate the GSH cofactor. We also show that BaeAB homologues from other sphingomonads can cleave β(R)-MPHPV and that they may be as common in bacteria as LigE homologues. Our results suggest that the ability to cleave the β-aryl ether bond arose independently at least twice in GSTs and that BaeAB homologues may be important for cleaving the β(R)-aryl ether bonds of lignin-derived oligomers in nature.

From beech wood to itaconic acid: case study on biorefinery process integration

Renewable raw materials in sustainable biorefinery processes pose new challenges to the manufacturing routes of platform chemicals. Beside the investigations of individual unit operations, the research on process chains, leading from plant biomass to the final products like lactic acid, succinic acid, and itaconic acid is increasing. This article presents a complete process chain from wooden biomass to the platform chemical itaconic acid. The process starts with the mechanical pretreatment of beech wood, which subsequently is subjected to chemo-catalytic biomass fractionation (OrganoCat) into three phases, which comprise cellulose pulp, aqueous hydrolyzed hemicellulose, and organic lignin solutions. Lignin is transferred to further chemical valorization. The aqueous phase containing oxalic acid as well as hemi-cellulosic sugars is treated by nanofiltration to recycle the acid catalyst back to the chemo-catalytic pretreatment and to concentrate the sugar hydrolysate. In a parallel step, the cellulose pulp is enzymatically hydrolyzed to yield glucose, which-together with the pentose-rich stream-can be used as a carbon source in the fermentation. The fermentation of the sugar fraction into itaconic acid can either be performed with the established fungi Aspergillus terreus or with Ustilago maydis. Both fermentation concepts were realized and evaluated. For purification, (in situ) filtration, (in situ) extraction, and crystallization were investigated. The presented comprehensive examination and discussion of the itaconate synthesis process-as a case study-demonstrates the impact of realistic process conditions on product yield, choice of whole cell catalyst, chemocatalysts and organic solvent system, operation mode, and, finally, the selection of a downstream concept.

Enzyme biotechnology in degradation and modification of plant cell wall polymers

Lignocelluloses are abundant raw materials for production of fuels, chemicals and materials. The purpose of this paper is to review the enzyme-types and enzyme-technologies studied and applied in the processing of the lignocelluloses into different products. The enzymes here are mostly glycoside hydrolases, esterases and different redox enzymes. Enzymatic hydrolysis of lignocellulosic polysaccharides to platform sugars has been widely studied leading to development of advanced commercial products for this purpose. Restricted hydrolysis or oxidation of cellulosic fibers have been applied in processing of pulps to paper products, nanocelluloses and textile fibers. Oxidation, transglycosylation and derivatization have been utilized in functionalization of fibers, cellulosic surfaces and polysaccharides. Enzymatic polymerization, depolymerization and grafting methods are being developed for lignin valorization.

Genomic and proteomic analysis of lignin degrading and polyhydroxyalkanoate accumulating β-proteobacterium Pandoraea sp. ISTKB

BACKGROUND

Lignin is a major component of plant biomass and is recalcitrant to degradation due to its complex and heterogeneous aromatic structure. The biomass-based research mainly focuses on polysaccharides component of biomass and lignin is discarded as waste with very limited usage. The sustainability and success of plant polysaccharide-based biorefinery can be possible if lignin is utilized in improved ways and with minimal waste generation. Discovering new microbial strains and understanding their enzyme system for lignin degradation are necessary for its conversion into fuel and chemicals. The Pandoraea sp. ISTKB was previously characterized for lignin degradation and successfully applied for pretreatment of sugarcane bagasse and polyhydroxyalkanoate (PHA) production. In this study, genomic analysis and proteomics on aromatic polymer kraft lignin and vanillic acid are performed to find the important enzymes for polymer utilization.

RESULTS

Genomic analysis of Pandoraea sp. ISTKB revealed the presence of strong lignin degradation machinery and identified various candidate genes responsible for lignin degradation and PHA production. We also applied label-free quantitative proteomic approach to identify the expression profile on monoaromatic compound vanillic acid (VA) and polyaromatic kraft lignin (KL). Genomic and proteomic analysis simultaneously discovered Dyp-type peroxidase, peroxidases, glycolate oxidase, aldehyde oxidase, GMC oxidoreductase, laccases, quinone oxidoreductase, dioxygenases, monooxygenases, glutathione-dependent etherases, dehydrogenases, reductases, and methyltransferases and various other recently reported enzyme systems such as superoxide dismutases or catalase-peroxidase for lignin degradation. A strong stress response and detoxification mechanism was discovered. The two important gene clusters for lignin degradation and three PHA polymerase spanning gene clusters were identified and all the clusters were functionally active on KL-VA.

CONCLUSIONS

The unusual aerobic '-CoA'-mediated degradation pathway of phenylacetate and benzoate (reported only in 16 and 4-5% of total sequenced bacterial genomes), peroxidase-accessory enzyme system, and fenton chemistry based are the major pathways observed for lignin degradation. Both ortho and meta ring cleavage pathways for aromatic compound degradation were observed in expression profile. Genomic and proteomic approaches provided validation to this strain's robust machinery for the metabolism of recalcitrant compounds and PHA production and provide an opportunity to target important enzymes for lignin valorization in future.

Microbial β-etherases and glutathione lyases for lignin valorisation in biorefineries: current state and future perspectives

Lignin is the major aromatic biopolymer in nature, and it is considered a valuable feedstock for the future supply of aromatics. Hence, its valorisation in biorefineries is of high importance, and various chemical and enzymatic approaches for lignin depolymerisation have been reported. Among the enzymes known to act on lignin, β-etherases offer the possibility for a selective cleavage of the β-O-4 aryl ether bonds present in lignin. These enzymes, together with glutathione lyases, catalyse a reductive, glutathione-dependent ether bond cleavage displaying high stereospecificity. β-Etherases and glutathione lyases both belong to the superfamily of glutathione transferases, and several structures have been solved recently. Additionally, different approaches for their application in lignin valorisation have been reported in the last years. This review gives an overview on the current knowledge on β-etherases and glutathione lyases, their biochemical and structural features, and critically discusses their potential for application in biorefineries.

Bacterial Catabolism of β-Hydroxypropiovanillone and β-Hydroxypropiosyringone Produced in the Reductive Cleavage of Arylglycerol-β-Aryl Ether in Lignin

Sphingobium sp. strain SYK-6 converts four stereoisomers of arylglycerol-β-guaiacyl ether into achiral β-hydroxypropiovanillone (HPV) via three stereospecific reaction steps. Here, we determined the HPV catabolic pathway and characterized the HPV catabolic genes involved in the first two steps of the pathway. In SYK-6 cells, HPV was oxidized to vanilloyl acetic acid (VAA) via vanilloyl acetaldehyde (VAL). The resulting VAA was further converted into vanillate through the activation of VAA by coenzyme A. A syringyl-type HPV analog, β-hydroxypropiosyringone (HPS), was also catabolized via the same pathway. SLG_12830 (hpvZ), which belongs to the glucose-methanol-choline oxidoreductase family, was isolated as the HPV-converting enzyme gene. An hpvZ mutant completely lost the ability to convert HPV and HPS, indicating that hpvZ is essential for the conversion of both the substrates. HpvZ produced in Escherichia coli oxidized both HPV and HPS and other 3-phenyl-1-propanol derivatives. HpvZ localized to both the cytoplasm and membrane of SYK-6 and used ubiquinone derivatives as electron acceptors. Thirteen gene products of the 23 aldehyde dehydrogenase (ALDH) genes in SYK-6 were able to oxidize VAL into VAA. Mutant analyses suggested that multiple ALDH genes, including SLG_20400, contribute to the conversion of VAL. We examined whether the genes encoding feruloyl-CoA synthetase (ferA) and feruloyl-CoA hydratase/lyase (ferB and ferB2) are involved in the conversion of VAA. Only FerA exhibited activity toward VAA; however, disruption of ferA did not affect VAA conversion. These results indicate that another enzyme system is involved in VAA conversion.IMPORTANCE Cleavage of the β-aryl ether linkage is the most essential process in lignin biodegradation. Although the bacterial β-aryl ether cleavage pathway and catabolic genes have been well documented, there have been no reports regarding the catabolism of HPV or HPS, the products of cleavage of β-aryl ether compounds. HPV and HPS have also been found to be obtained from lignin by chemoselective catalytic oxidation by 2,3-dichloro-5,6-dicyano-1,4-benzoquinone/tert-butyl nitrite/O₂, followed by cleavage of the β-aryl ether with zinc. Therefore, value-added chemicals are expected to be produced from these compounds. In this study, we determined the SYK-6 catabolic pathways for HPV and HPS and identified the catabolic genes involved in the first two steps of the pathways. Since SYK-6 catabolizes HPV through 2-pyrone-4,6-dicarboxylate, which is a building block for functional polymers, characterization of HPV catabolism is important not only for understanding the bacterial lignin catabolic system but also for lignin utilization.

Selective Cleavage of Lignin β-O-4 Aryl Ether Bond by β-Etherase of the White-Rot Fungus Dichomitus squalens

Production of value-added compounds from a renewable aromatic polymer, lignin, has proven to be challenging. Chemical procedures, involving harsh reaction conditions, are costly and often result in nonselective degradation of lignin linkages. Therefore, enzymatic catalysis with selective cleavage of lignin bonds provides a sustainable option for lignin valorization. In this study, we describe the first functionally characterized fungal intracellular β-etherase from the wood-degrading white-rot basidiomycete Dichomitus squalens. This enzyme, Ds-GST1, from the glutathione-S-transferase superfamily selectively cleaved the β-O-4 aryl ether bond of a dimeric lignin model compound in a glutathione-dependent reaction. Ds-GST1 also demonstrated activity on polymeric synthetic lignin fractions, shown by a decrease in molecular weight distribution of the laccase-oxidized guaiacyl dehydrogenation polymer. In addition to a possible role of Ds-GST1 in intracellular catabolism of lignin-derived aromatic compounds, the cleavage of the most abundant linkages in lignin under mild reaction conditions makes this biocatalyst an attractive green alternative in biotechnological applications.

Bacterial catabolism of lignin-derived aromatics: New findings in a recent decade: Update on bacterial lignin catabolism

Lignin is the most abundant phenolic polymer; thus, its decomposition by microorganisms is fundamental to carbon cycling on earth. Lignin breakdown is initiated by depolymerization catalysed by extracellular oxidoreductases secreted by white-rot basidiomycetous fungi. On the other hand, bacteria play a predominant role in the mineralization of lignin-derived heterogeneous low-molecular-weight aromatic compounds. The outline of bacterial catabolic pathways for lignin-derived bi- and monoaryls are typically composed of the following sequential steps: (i) funnelling of a wide variety of lignin-derived aromatics into vanillate and syringate, (ii) O demethylation of vanillate and syringate to form catecholic derivatives and (iii) aromatic ring-cleavage of the catecholic derivatives to produce tricarboxylic acid cycle intermediates. Knowledge regarding bacterial catabolic systems for lignin-derived aromatic compounds is not only important for understanding the terrestrial carbon cycle but also valuable for promoting the shift to a low-carbon economy via biological lignin valorisation. This review summarizes recent progress in bacterial catabolic systems for lignin-derived aromatic compounds, including newly identified catabolic pathways and genes for decomposition of lignin-derived biaryls, transcriptional regulation and substrate uptake systems. Recent omics approaches on catabolism of lignin-derived aromatic compounds are also described.

Dissolving Lignin in Water through Enzymatic Sulfation with Aryl Sulfotransferase

We introduce the concept of using site-specific sulfation of various lignins for increasing their aqueous solubility and thereby their processability. Using p-nitrophenylsulfate as a sulfate source and an aryl sulfotransferase enzyme as catalyst, lignins are easily sulfated at ambient conditions. We demonstrate the specific sulfation of phenolic hydroxyl groups on five different lignins: Indulin AT (Kraft softwood), Protobind 1000 (mixed wheat straw/Sarkanda grass soda) and three organosolv lignins. The reaction proceeds smoothly and the increase in solubility is visible to the naked eye. We then examine the reaction kinetics, and show that these are easily monitored qualitatively and quantitatively using UV/Vis spectroscopy. The UV/Vis results are validated with ³¹ P NMR spectroscopy of the lignin phenol groups after derivatization with phosphorylation reagent II. In general, the results are more significant with organosolv lignins, as Kraft and soda lignins are produced from aqueous lignocellulose extraction processes.

Enzymatic Specific Production and Chemical Functionalization of Phenylpropanone Platform Monomers from Lignin

Enzymatic catalysis is an ecofriendly strategy for the production of high-value low-molecular-weight aromatic compounds from lignin. Although well-definable aromatic monomers have been obtained from synthetic lignin-model dimers, enzymatic-selective synthesis of platform monomers from natural lignin has not been accomplished. In this study, we successfully achieved highly specific synthesis of aromatic monomers with a phenylpropane structure directly from natural lignin using a cascade reaction of β-O-4-cleaving bacterial enzymes in one pot. Guaiacylhydroxylpropanone (GHP) and the GHP/syringylhydroxylpropanone (SHP) mixture are exclusive monomers from lignin isolated from softwood (Cryptomeria japonica) and hardwood (Eucalyptus globulus). The intermediate products in the enzymatic reactions show the capacity to accommodate highly heterologous substrates at the substrate-binding sites of the enzymes. To demonstrate the applicability of GHP as a platform chemical for bio-based industries, we chemically generate value-added GHP derivatives for bio-based polymers. Together with these chemical conversions for the valorization of lignin-derived phenylpropanone monomers, the specific and enzymatic production of the monomers directly from natural lignin is expected to provide a new stream in "white biotechnology" for sustainable biorefineries.

Decoding how a soil bacterium extracts building blocks and metabolic energy from ligninolysis provides road map for lignin valorization

Sphingobium sp. SYK-6 is a soil bacterium boasting a well-studied ligninolytic pathway and the potential for development into a microbial chassis for lignin valorization. An improved understanding of its metabolism will help researchers in the engineering of SYK-6 for the production of value-added chemicals through lignin valorization. We used ¹³C-fingerprinting, ¹³C metabolic flux analysis (¹³C-MFA), and RNA-sequencing differential expression analysis to uncover the following metabolic traits: (i) SYK-6 prefers alkaline conditions, making it an efficient host for the consolidated bioprocessing of lignin, and it also lacks the ability to metabolize sugars or organic acids; (ii) the CO₂ release (i.e., carbon loss) from the ligninolysis-based metabolism of SYK-6 is significantly greater than the CO₂ release from the sugar-based metabolism of Escherichia coli; (iii) the vanillin catabolic pathway (which is the converging point of majority of the lignin catabolic pathways) is coupled with the tetrahydrofolate-dependent C1 pathway that is essential for the biosynthesis of serine, histidine, and methionine; (iv) catabolic end products of lignin (pyruvate and oxaloacetate) must enter the tricarboxylic acid (TCA) cycle first and then use phosphoenolpyruvate carboxykinase to initiate gluconeogenesis; and (v) ¹³C-MFA together with RNA-sequencing differential expression analysis establishes the vanillin catabolic pathway as the major contributor of NAD(P)H synthesis. Therefore, the vanillin catabolic pathway is essential for SYK-6 to obtain sufficient reducing equivalents for its healthy growth; cosubstrate experiments support this finding. This unique energy feature of SYK-6 is particularly interesting because most heterotrophs rely on the transhydrogenase, the TCA cycle, and the oxidative pentose phosphate pathway to obtain NADPH.

Cascade enzymatic cleavage of the β-O-4 linkage in a lignin model compound

The optimized Lig enzymatic system reached the full bioconversion of a racemic mixture of GGE, a lignin model compound.

Combination of six enzymes of a marine Novosphingobium converts the stereoisomers of β-O-4 lignin model dimers into the respective monomers

Lignin, an aromatic polymer of phenylpropane units joined predominantly by β-O-4 linkages, is the second most abundant biomass component on Earth. Despite the continuous discharge of terrestrially produced lignin into marine environments, few studies have examined lignin degradation by marine microorganisms. Here, we screened marine isolates for β-O-4 cleavage activity and determined the genes responsible for this enzymatic activity in one positive isolate. Novosphingobium sp. strain MBES04 converted all four stereoisomers of guaiacylglycerol-β-guaiacyl ether (GGGE), a structural mimic of lignin, to guaiacylhydroxypropanone as an end metabolite in three steps involving six enzymes, including a newly identified Nu-class glutathione-S-transferase (GST). In silico searches of the strain MBES04 genome revealed that four GGGE-metabolizing GST genes were arranged in a cluster. Transcriptome analysis demonstrated that the lignin model compounds GGGE and (2-methoxyphenoxy)hydroxypropiovanillone (MPHPV) enhanced the expression of genes in involved in energy metabolism, including aromatic-monomer assimilation, and evoked defense responses typically expressed upon exposure to toxic compounds. The findings from this study provide insight into previously unidentified bacterial enzymatic systems and the physiological acclimation of microbes associated with the biological transformation of lignin-containing materials in marine environments.

From gene to biorefinery: microbial β-etherases as promising biocatalysts for lignin valorization

The set-up of biorefineries for the valorization of lignocellulosic biomass will be core in the future to reach sustainability targets. In this area, biomass-degrading enzymes are attracting significant research interest for their potential in the production of chemicals and biofuels from renewable feedstock. Glutathione-dependent β-etherases are emerging enzymes for the biocatalytic depolymerization of lignin, a heterogeneous aromatic polymer abundant in nature. They selectively catalyze the reductive cleavage of β-O-4 aryl-ether bonds which account for 45–60% of linkages present in lignin. Hence, application of β-etherases in lignin depolymerization would enable a specific lignin breakdown, selectively yielding (valuable) low-molecular-mass aromatics. Albeit β-etherases have been biochemically known for decades, only very recently novel β-etherases have been identified and thoroughly characterized for lignin valorization, expanding the enzyme toolbox for efficient β-O-4 aryl-ether bond cleavage. Given their emerging importance and potential, this mini-review discusses recent developments in the field of β-etherase biocatalysis covering all aspects from enzyme identification to biocatalytic applications with real lignin samples.

Enzymatic conversion of lignin into renewable chemicals

The aromatic heteropolymer lignin is a major component of plant cell walls, and is produced industrially from paper/pulp manufacture and cellulosic bioethanol production. Conversion of lignin into renewable chemicals is a major unsolved problem in the development of a biomass-based biorefinery. The review describes recent developments in the understanding of bacterial enzymes for lignin breakdown, such as DyP peroxidases, bacterial laccases, and beta-etherase enzymes. The use of pathway engineering methods to construct genetically modified microbes to convert lignin to renewable chemicals (e.g. vanillin, adipic acid) via fermentation is discussed, and the search for novel applications for lignin (e.g. carbon fibre).