Nanostructural Analysis of Enzymatic and Non-enzymatic Brown Rot Fungal Deconstruction of the Lignocellulose Cell Wall†

Effect of alkali treatment and fungal degradation on the nanostructure and cellulose arrangement in Scots pine cell walls - A neutron and X-ray scattering study

Research on new conservation treatments for historical wood requires considerable amounts of appropriate wood material, which is hard to acquire. Thus, we produced biologically and chemically degraded model wood that could be used as a representative material in future research on consolidating agents. Using chemical composition determinations, we found that fungal decay targeted mainly polysaccharides, while alkaline treatment mostly reduced hemicelluloses and lignin content. X-ray and neutron scattering showed that all decayed samples had increased disorder in microfibril alignment and larger elementary fibril cross-sections, and alkaline-treated samples had much larger elementary fibril spacing compared to those decayed by fungi. These nanoscale and chemical differences correlate with physical property changes. For example, decreased cellulose crystallinity and increased disorder of the microfibrils in degraded cell walls likely contribute to the lower elastic moduli measured for these cell walls. The obtained data improves understanding of how degradation alters wood structures and properties across length scales and will be valuable for future studies focusing on archeological wood. Moreover, it leads to the conclusion that it is more appropriate to develop treatments that consider not only spatial variability and degree of wood degradation but also the corresponding molecular and nanoscale changes in the cell walls.

SANS investigation of fungal loosenins reveal substrate dependent impacts of protein 1 action on inter-fibril distance and packing order of cellulosic substrates

BACKGROUND

Microbial expansin-related proteins include fungal loosenins, which have been previously shown to disrupt cellulose networks and enhance the enzymatic conversion of cellulosic substrates. Despite showing beneficial impacts to cellulose processing, detailed characterization of cellulosic materials after loosenin treatment is lacking. In this study, small-angle neutron scattering (SANS) was used to investigate the effects of three recombinantly produced loosenins that originate from Phanerochaete carnosa, PcaLOOL7, PcaLOOL9, and PcaLOOL12, on the organization of holocellulose preparations from Eucalyptus and Spruce wood samples.

RESULTS

Whereas the SANS analysis of Spruce holocellulose revealed an increase in interfibril spacing of neighboring cellulose microfibrils following treatment with PcaLOOL12 and to a lesser extent PcaLOOL7, the analysis of Eucalyptus holocellulose revealed a reduction in packing number following treatment with PcaLOOL12 and to a lesser extent PcaLOOL9. Parallel SEC-SAXS characterization of PcaLOOL7, PcaLOOL9, and PcaLOOL12 indicated the proteins likely function as monomers; moreover, all appear to retain a flexible disordered N-terminus and folded C-terminal region. The comparatively high impact of PcaLOOL12 motivated its NMR structural characterization, revealing a double-psi b-barrel (DPBB) domain surrounded by three alpha-helices - the largest nestled against the DPBB core and the other two part of loops extending from the core.

CONCLUSIONS

The SANS analysis of PcaLOOL action on holocellulose samples confirms their ability to disrupt cellulose fiber networks and suggests a progression from reducing microfibril packing to increasing interfibril distance. The most impactful PcaLOOL, PcaLOOL12, was previously observed to be the most highly expressed loosenin in P. carnosa. Its structural characterization herein reveals its stabilization through two disulfide linkages, and an extended N-terminal region distal to a negatively charged and surface accessible polysaccharide binding groove.

Unlocking the distinctive enzymatic functions of the early plant biomass deconstructive genes in a brown rot fungus by cell-free protein expression

Saprotrophic fungi that cause brown rot of woody biomass evolved a distinctive mechanism that relies on reactive oxygen species (ROS) to kick-start lignocellulosic polymers' deconstruction. These ROS agents are generated at incipient decay stages through a series of redox relays that shuttle electrons from fungus's central metabolism to extracellular Fenton chemistry. A list of genes has been suggested encoding the enzyme catalysts of the redox processes involved in ROS's function. However, navigating the functions of the encoded enzymes has been challenging due to the lack of a rapid method for protein synthesis. Here, we employed cell-free expression system to synthesize four redox or degradative enzymes, which were identified, by transcriptomic data, as conserved players of the ROS oxidation phase across brown rot fungal species. All four enzymes were successfully expressed and showed activities that enable confident assignment of function, namely, benzoquinone reductase (BQR), ferric reductase, α-L-arabinofuranosidase (ABF), and heme-thiolate peroxidase (HTP). Detailed analysis of their catalytic features within the context of brown rot environments allowed us to interpret their roles during ROS-driven wood decomposition. Specifically, we validated the functions of BQR as the driver redox enzyme of Fenton cycles and reconstructed its interactions with the co-occurring HTP or laccase and ABF. Taken together, this research demonstrated that the cell-free expression platform is adequate for synthesizing functional fungal enzymes and provided an alternative route for the rapid characterization of fungal proteins, escalating our understanding of the distinctive biocatalyst system for plant biomass conversion.IMPORTANCEBrown rot fungi are efficient wood decomposers in nature, and their unique degradative systems harbor untapped catalysts pursued by the biorefinery and bioremediation industries. While the use of "omics" platforms has recently uncovered the key "oxidative-hydrolytic" mechanisms that allow these fungi to attack lignocellulose, individual protein characterization is lagging behind due to the lack of a robust method for rapid synthesis of crucial fungal enzymes. This work delves into the studies of biochemical functions of brown rot enzymes using a rapid, cell-free expression platform, which allowed the successful depictions of enzymes' catalytic features, their interactions with Fenton chemistry, and their roles played during the incipient stage of brown rot when fungus sets off the reactive oxygen species for oxidative degradation. We expect this research could illuminate cell-free protein expression system's use to fulfill the increasing need for functional studies of fungal enzymes, advancing the discoveries of novel biomass-converting catalysts.

Whole genome structural predictions reveal hidden diversity in putative oxidative enzymes of the lignocellulose-degrading ascomycete Parascedosporium putredinis NO1

IMPORTANCE

An annotated reference genome has revealed P. putredinis NO1 as a useful resource for the identification of new lignocellulose-degrading enzymes for biorefining of woody plant biomass. Utilizing a "structure-omics"-based searching strategy, we identified new potentially lignocellulose-active sequences that would have been missed by traditional sequence searching methods. These new identifications, alongside the discovery of novel enzymatic functions from this underexplored lineage with the recent discovery of a new phenol oxidase that cleaves the main structural β-O-4 linkage in lignin from P. putredinis NO1, highlight the underexplored and poorly represented family Microascaceae as a particularly interesting candidate worthy of further exploration toward the valorization of high value biorenewable products.

Interaction of oxalate with β-glucan: Implications for the fungal extracellular matrix, and metabolite transport

β-glucan is the major component of the extracellular matrix (ECM) of many fungi, including wood degrading fungi. Many of these species also secrete oxalate into the ECM. Our research demonstrates that β-glucan forms a novel, previously unreported, hydrogel at room temperature with oxalate. Oxalate was found to alter the rheometric properties of the β-glucan hydrogels, and modeling showed that β-glucan hydrogen bonds with oxalate in a non-covalent matrix. Change of oxalate concentration also impacted the diffusion of a high-molecular-weight protein through the gels. This finding has relevance to the diffusion of extracellular enzymes into substrates and helps to explain why some types of wood-decay fungi rely on non-enzymatic degradation schemes for carbon cycling. Further, this research has potential impact on the diffusion of metabolites in association with pathogenic/biomedical fungi.

First Description of Non-Enzymatic Radical-Generating Mechanisms Adopted by Fomitiporia mediterranea: An Unexplored Pathway of the White Rot Agent of the Esca Complex of Diseases

Fomitiporia mediterranea (Fmed) is the primary Basidiomycota species causing white rot in European vineyards affected by the Esca complex of diseases (ECD). In the last few years, an increasing number of studies have highlighted the importance of reconsidering the role of Fmed in ECD etiology, justifying an increase in research interest related to Fmed's biomolecular pathogenetic mechanisms. In the context of the current re-evaluation of the binary distinction (brown vs. white rot) between biomolecular decay pathways induced by Basidiomycota species, our research aims to investigate the potential for non-enzymatic mechanisms adopted by Fmed, which is typically described as a white rot fungus. Our results demonstrate how, in liquid culture reproducing nutrient restriction conditions often found in wood, Fmed can produce low molecular weight compounds, the hallmark of the non-enzymatic "chelator-mediated Fenton" (CMF) reaction, originally described for brown rot fungi. CMF reactions can redox cycle with ferric iron, generating hydrogen peroxide and ferrous iron, necessary reactants leading to hydroxyl radical (^•OH) production. These observations led to the conclusion that a non-enzymatic radical-generating CMF-like mechanism may be utilized by Fmed, potentially together with an enzymatic pool, to contribute to degrading wood constituents; moreover, indicating significant variability between strains.

X-Ray Scattering Reveals Two Mechanisms of Cellulose Microfibril Degradation by Filamentous Fungi

Mushroom-forming fungi (Agaricomycetes) employ enzymatic and nonenzymatic cellulose degradation mechanisms, the latter presumably relying on Fenton-generated radicals. The effects of the two mechanisms on the cellulose microfibrils structure remain poorly understood. We examined cellulose degradation caused by litter decomposers and wood decomposers, including brown-rot and white-rot fungi and one fungus with uncertain wood decay type, by combining small- and wide-angle X-ray scattering. We also examined the effects of commercial enzymes and Fenton-generated radicals on cellulose using the same method. We detected two main degradation or modification mechanisms. The first characterized the mechanism used by most fungi and resembled enzymatic cellulose degradation, causing simultaneous microfibril thinning and decreased crystalline cellulose. The second mechanism was detected in one brown-rot fungus and one litter decomposer and was characterized by patchy amorphogenesis of crystalline cellulose without substantial thinning of the fibers. This pattern did not resemble the effect of Fenton-generated radicals, suggesting a more complex mechanism is involved in the destruction of cellulose crystallinity by fungi. Furthermore, our results showed a mismatch between decay classifications and cellulose degradation patterns and that even within litter decomposers two degradation mechanisms were found, suggesting higher functional diversity under current ecological classifications of fungi.

IMPORTANCE Cellulose degradation by fungi plays a fundamental role in terrestrial carbon cycling, but the mechanisms by which fungi cope with the crystallinity of cellulose are not fully understood. We used X-ray scattering to analyze how fungi, a commercial enzyme mix, and a Fenton reaction-generated radical alter the crystalline structure of cellulose. Our data revealed two mechanisms involved in crystalline cellulose degradation by fungi: one that results in the thinning of the cellulose fibers, resembling the enzymatic degradation of cellulose, and one that involves amorphogenesis of crystalline cellulose by yet-unknown pathways, resulting in a patchy-like degradation pattern. These results pave the way to a deeper understanding of cellulose degradation and the development of novel ways to utilize crystalline cellulose.

Nanostructural Changes Correlated to Decay Resistance of Chemically Modified Wood Fibers

Reactive chemical modifications have been shown to impart decay resistance to wood. These modifications change hydroxyl availability, water uptake, surface energy, and the nanostructure of wood. Because fungal action occurs on the micro and nano scale, further investigation into the nanostructure may lead to better strategies to prevent fungal decay. The aim of this article is to introduce our findings using small angle neutron scattering (SANS) to probe the effects of chemical modifications on the nanostructure of wood fibers. Southern pine wood fiber samples were chemically modified to various weight percentage gains (WPG) using propylene oxide (PO), butylene oxide (BO), or acetic anhydride (AA). After modification, the samples were water leached for two weeks to remove any unreacted reagents, homopolymers or by-products and then the equilibrium moisture content (EMC) was determined. Laboratory soil-block-decay evaluations against the brown rot fungus Gloeophyllum trabeum were performed to determine weight loss and decay resistance of the modifications. To assist in understanding the mechanism behind fungal decay resistance, SANS was used to study samples that were fully immersed in deuterium oxide (D2O). These measurements revealed that modifying the fibers led to differences in the swollen wood nanostructure compared to unmodified wood fibers. Moreover, the modifications led to differences in the nanoscale features observed in samples that were exposed to brown rot fungal attack compared to unmodified wood fibers and solid wood blocks modified with alkylene oxides.

Effects of Biological and Chemical Degradation on the Properties of Scots Pine Wood-Part I: Chemical Composition and Microstructure of the Cell Wall

Research on new conservation treatment for archaeological wood requires large amounts of wooden material. For this purpose, artificial wood degradation (biological-using brown-rot fungus Coniophora puteana, and chemical-using NaOH solution) under laboratory conditions was conducted to obtain an abundance of similar samples that mimic naturally degraded wood and can serve for comparative studies. However, knowledge about its properties is necessary to use this material for further study. In this study, the chemical composition and microstructure of degraded cell walls were investigated using FT-IR, XRD, helium pycnometry and nitrogen absorption methods. The results show that biological degradation caused the loss of hemicelluloses and celluloses, including the reduction in cellulose crystallinity, and led to lignin modification, while chemical degradation mainly depleted the amount of hemicelluloses and lignin, but also affected crystalline cellulose. These changes affected the cell wall microstructure, increasing both surface area and total pore volume. However, the chemical degradation produced a greater number of mesopores of smaller size compared to fungal decomposition. Both degradation processes weakened the cell wall's mechanical strength, resulting in high shrinkage of degraded wood during air-drying. The results of the study suggest that degraded wood obtained under laboratory conditions can be a useful material for studies on new consolidants for archaeological wood.

How Do Shipworms Eat Wood? Screening Shipworm Gill Symbiont Genomes for Lignin-Modifying Enzymes

Shipworms are ecologically and economically important mollusks that feed on woody plant material (lignocellulosic biomass) in marine environments. Digestion occurs in a specialized cecum, reported to be virtually sterile and lacking resident gut microbiota. Wood-degrading CAZymes are produced both endogenously and by gill endosymbiotic bacteria, with extracellular enzymes from the latter being transported to the gut. Previous research has predominantly focused on how these animals process the cellulose component of woody plant material, neglecting the breakdown of lignin – a tough, aromatic polymer which blocks access to the holocellulose components of wood. Enzymatic or non-enzymatic modification and depolymerization of lignin has been shown to be required in other wood-degrading biological systems as a precursor to cellulose deconstruction. We investigated the genomes of five shipworm gill bacterial symbionts obtained from the Joint Genome Institute Integrated Microbial Genomes and Microbiomes Expert Review for the production of lignin-modifying enzymes, or ligninases. The genomes were searched for putative ligninases using the Joint Genome Institute’s Function Profile tool and blastp analyses. The resulting proteins were then modeled using SWISS-MODEL. Although each bacterial genome possessed at least four predicted ligninases, the percent identities and protein models were of low quality and were unreliable. Prior research demonstrates limited endogenous ability of shipworms to modify lignin at the chemical/molecular level. Similarly, our results reveal that shipworm bacterial gill-symbiont enzymes are unlikely to play a role in lignin modification during lignocellulose digestion in the shipworm gut. This suggests that our understanding of how these keystone organisms digest and process lignocellulose is incomplete, and further research into non-enzymatic and/or other unknown mechanisms for lignin modification is required.

Multi-omics analysis provides insights into lignocellulosic biomass degradation by Laetiporus sulphureus ATCC 52600

BACKGROUND

Wood-decay basidiomycetes are effective for the degradation of highly lignified and recalcitrant plant substrates. The degradation of lignocellulosic materials by brown-rot strains is carried out by carbohydrate-active enzymes and non-enzymatic Fenton mechanism. Differences in the lignocellulose catabolism among closely related brown rots are not completely understood. Here, a multi-omics approach provided a global understanding of the strategies employed by L. sulphureus ATCC 52600 for lignocellulose degradation.

RESULTS

The genome of Laetiporus sulphureus ATCC 52600 was sequenced and phylogenomic analysis supported monophyletic clades for the Order Polyporales and classification of this species within the family Laetiporaceae. Additionally, the plasticity of its metabolism was revealed in growth analysis on mono- and disaccharides, and polysaccharides such as cellulose, hemicelluloses, and polygalacturonic acid. The response of this fungus to the presence of lignocellulosic substrates was analyzed by transcriptomics and proteomics and evidenced the occurrence of an integrated oxidative-hydrolytic metabolism. The transcriptomic profile in response to a short cultivation period on sugarcane bagasse revealed 125 upregulated transcripts, which included CAZymes (redox enzymes and hemicellulases) as well as non-CAZy redox enzymes and genes related to the synthesis of low-molecular-weight compounds. The exoproteome produced in response to extended cultivation time on Avicel, and steam-exploded sugarcane bagasse, sugarcane straw, and Eucalyptus revealed 112 proteins. Contrasting with the mainly oxidative profile observed in the transcriptome, the secretomes showed a diverse hydrolytic repertoire including constitutive cellulases and hemicellulases, in addition to 19 upregulated CAZymes. The secretome induced for 7 days on sugarcane bagasse, representative of the late response, was applied in the saccharification of hydrothermally pretreated grass (sugarcane straw) and softwood (pine) by supplementing a commercial cocktail.

CONCLUSION

This study shows the singularity of L. sulphureus ATCC 52600 compared to other Polyporales brown rots, regarding the presence of cellobiohydrolase and peroxidase class II. The multi-omics analysis reinforces the oxidative-hydrolytic metabolism involved in lignocellulose deconstruction, providing insights into the overall mechanisms as well as specific proteins of each step.

Fungal Degradation of Wood: Emerging Data, New Insights and Changing Perceptions

Wood durability researchers have long described fungal decay of timber using the starkly simple terms of white, brown and soft rot, along with the less destructive mold and stain fungi. These terms have taken on an almost iconic meaning but are only based upon the outward appearance of the damaged timber. Long-term deterioration studies, as well as the emerging genetic tools, are showing the fallacy of simplifying the decay process into such broad groups. This paper briefly reviews the fundamentals of fungal decay, staining and mold processes, then uses these fundamentals as the basis for a discussion of fungal attack of wood in light of current knowledge about these processes. Biotechnological applications of decay fungi are reviewed, and an overview is presented on how fungi surmount the protective barriers that coatings provide on surfaces. Advances in biochemical analyses have, in some cases, radically altered our perceptions of how wood is degraded, and even the relationships between fungal species, while other new findings have reinforced traditional perspectives. Suggestions for future research needs in the coatings field relative to enhanced fungal and environmental protection are presented.