A Putative Lignin Copper Oxidase from Trichoderma reesei

Genome and secretome insights: unravelling the lignocellulolytic potential of Myceliophthora verrucosa for enhanced hydrolysis of lignocellulosic biomass

Lignocellulolytic enzymes from a novel Myceliophthora verrucosa (5DR) strain was found to potentiate the efficacy of benchmark cellulase during saccharification of acid/alkali treated bagasse by ~ 2.24 fold, indicating it to be an important source of auxiliary enzymes. The De-novo sequencing and analysis of M. verrucosa genome (31.7 Mb) revealed to encode for 7989 putative genes, representing a wide array of CAZymes (366) with a high proportions of auxiliary activity (AA) genes (76). The LC/MS QTOF based secretome analysis of M. verrucosa showed high abundance of glycosyl hydrolases and AA proteins with cellobiose dehydrogenase (CDH) (AA8), being the most prominent auxiliary protein. A gene coding for lytic polysaccharide monooxygenase (LPMO) was expressed in Pichia pastoris and CDH produced by M. verrucosa culture on rice straw based solidified medium were purified and characterized. The mass spectrometry of LPMO catalyzed hydrolytic products of avicel showed the release of both C1/C4 oxidized products, indicating it to be type-3. The lignocellulolytic cocktail comprising of in-house cellulase produced by Aspergillus allahabadii strain spiked with LPMO & CDH exhibited enhanced and better hydrolysis of mild alkali deacetylated (MAD) and unwashed acid pretreated rice straw slurry (UWAP), when compared to Cellic CTec3 at high substrate loading rate.

In Vitro Fermentation of Beechwood Lignin-Carbohydrate Complexes Provides Evidence for Utilization by Gut Bacteria

Lignin-carbohydrate complexes (LCCs) are emerging as a new and natural product with pharmacological and nutraceutical potential. It is uncertain, however, whether LCCs have a positive effect on the microbiota of the gut based on the current evidence. Here, the LCC extracted from beechwood (BW-LCC) was used as a substrate for in vitro fermentation. The lignin in BW-LCC consisted of guaiacyl (G) and syringyl (S) units, which are mainly linked by β-O-4 bonds. After 24 h of in vitro fermentation, the pH had evidently declined. The concentrations of acetic acid and propionic acid, the two main short-chain fatty acids (SCFAs), were significantly higher than in the control group (CK). In addition, BW-LCC altered the microbial diversity and composition of gut microbes, including a reduction in the relative abundance of Firmicutes and an increase in the relative abundance of Proteobacteria and Bacteroidetes. The relative abundance of Escherichia coli-Shigella and Bacteroides were the most variable at the genus level. The genes of carbohydrate-active enzymes (CAZymes) also changed significantly with the fermentation and were related to the changes in microbes. Notably, the auxiliary actives (AAs), especially AA1, AA2, and AA3_2, play important roles in lignin degradation and were significantly enriched and concentrated in Proteobacteria. From this study, we are able to provide new perspectives on how gut microbes utilize LCC.

Copper radical oxidases: galactose oxidase, glyoxal oxidase, and beyond!

The copper radical oxidases (CROs) are an evolutionary and functionally diverse group of enzymes established by the historically significant galactose 6-oxidase and glyoxal oxidase from fungi. Inducted in 2013, CROs now constitute Auxiliary Activity Family 5 (AA5) in the Carbohydrate-Active Enzymes (CAZy) classification. CROs catalyse the two-electron oxidation of their substrates using oxygen as the final electron acceptor and are particularly distinguished by a cross-linked tyrosine-cysteine co-factor that is integral to radical stabilization. Recently, there has been a significant increase in the biochemically and structurally characterized CROs, which has revealed an expanded natural diversity of catalytic activities in the family. This review provides a brief historical introduction to CRO biochemistry and structural biology as a foundation for an update on current advances in CRO enzymology, biotechnology, and biology across kingdoms of life.

Lignin Metabolism by Selected Fungi and Microbial Consortia for Plant Stimulation: Implications for Biologically Active Humus Genesis

Plant lignin is regarded as an important source for soil humic substances (HSs). Nonetheless, it remains unclear whether microbial metabolism on lignin is related to the genesis of unique HS biological activities (e.g., direct plant stimulation). Here, selected white-rot fungi (i.e., Ganoderma lucidum and Irpex lacteus) and plant litter- or mountain soil-derived microbial consortia were exploited to structurally modify lignin, followed by assessing the plant-stimulatory activity of the lignin-derived products. Parts solubilized by microbial metabolism on lignin were proven to exhibit organic moieties of phenol, carboxylic acid, and aliphatic groups and the enhancement of chromogenic features (i.e., absorbance at 450 nm), total phenolic contents, and radical-scavenging capacities with the cultivation times. In addition, high-resolution mass spectrometry revealed the shift of lignin-like molecules toward those showing either more molar oxygen-to-carbon or more hydrogen-to-carbon ratios. These results support the findings that the microbes involved, solubilize lignin by fragmentation, oxygenation, and/or benzene ring opening. This notion was also substantiated by the detection of related exoenzymes (i.e., peroxidases, copper radical oxidases, and hydrolases) in the selected fungal cultures, while the consortia treated with antibacterial agents showed that the fungal community is a sufficient condition to induce the lignin biotransformation. Major families of fungi (e.g., Nectriaceae, Hypocreaceae, and Saccharomycodaceae) and bacteria (e.g., Burkholderiaceae) were identified in the lignin-enriched cultures. All the microbially solubilized lignin products were likely to stimulate plant root elongation in the order selected white-rot fungi > microbial consortia > antibacterial agent-treated microbial consortia. Overall, this study supports the idea that microbial transformation of lignin can contribute to the formation of biologically active organic matter. IMPORTANCE Structurally stable humic substances (HSs) in soils are tightly associated with soil fertility, and it is thus important to understand how soil HSs are naturally formed. It is believed that microbial metabolism on plant matter contributes to natural humification, but detailed microbial species and their metabolisms inducing humic functionality (e.g., direct plant stimulation) need to be further investigated. Our findings clearly support that microbial metabolites of lignin could contribute to the formation of biologically active humus. This research direction appears to be meaningful not only for figuring out the natural processes, but also for confirming natural microbial resources useful for artificial humification that can be linked to the development of high-quality soil amendments.

Active-Site Engineering Switches Carbohydrate Regiospecificity in a Fungal Copper Radical Oxidase

Copper radical oxidases (CROs) from Auxiliary Activity Family 5, Subfamily 2 (AA5_2), are organic cofactor-free biocatalysts for the selective oxidation of alcohols to the corresponding aldehydes. AA5_2 CROs comprise canonical galactose-6-oxidases as well as the more recently discovered general alcohol oxidases and aryl alcohol oxidases. Guided by primary and tertiary protein structural analyses, we targeted a distinct extended loop in the active site of a Colletotrichum graminicola aryl alcohol oxidase (CgrAAO) to explore its effect on catalysis in the broader context of AA5_2. Deletion of this loop, which is bracketed by a conserved disulfide bridge, significantly reduced the inherent activity of the enzyme toward extended galacto-oligosaccharides, as anticipated from molecular modeling. Unexpectedly, kinetic and product analysis on a range of monosaccharides and disaccharides revealed that an altered carbohydrate specificity in CgrAAO-Δloop was accompanied by a complete change in regiospecificity from C-6 to C-1 oxidation, thereby generating aldonic acids. C-1 regiospecificity is unprecedented in AA5 enzymes and is classically associated with flavin-dependent carbohydrate oxidases of Auxiliary Activity Family 3. Thus, this work further highlights the catalytic adaptability of the unique mononuclear copper radical active site and provides a basis for the design of improved biocatalysts for diverse potential applications.