Lignocellulose biomass raw materials have a high value in energy conversion. Recently, there has been growing interest in using microorganisms to secret a series of enzymes for converting low-cost biomass into high-value products such as biofuels. We previously isolated a strain of Penicillium oxalicun 5-18 with promising lignocellulose-degrading capability. However, the mechanisms of lignocellulosic degradation of this fungus on various substrates are still unclear. In this study, we performed transcriptome-wide profiling and comparative analysis of strain 5-18 cultivated in liquid media with glucose (Glu), xylan (Xyl) or wheat bran (WB) as sole carbon source. In comparison to Glu culture, the number of differentially expressed genes (DEGs) induced by WB and Xyl was 4134 and 1484, respectively, with 1176 and 868 genes upregulated. Identified DEGs were enriched in many of the same pathways in both comparison groups (WB vs. Glu and Xly vs. Glu). Specially, 118 and 82 CAZyme coding genes were highly upregulated in WB and Xyl cultures, respectively. Some specific pathways including (Hemi)cellulose metabolic processes were enriched in both comparison groups. The high upregulation of these genes also confirmed the ability of strain 5-18 to degrade lignocellulose. Co-expression and co-upregulated of genes encoding CE and AA CAZy families, as well as other (hemi)cellulase revealed a complex degradation strategy in this strain. Our findings provide new insights into critical genes, key pathways and enzyme arsenal involved in the biomass degradation of P. oxalicum 5-18.

Wood-rotting fungi play an important role in the global carbon cycle because they are the only known organisms that digest wood, the largest carbon stock in nature. In the present study, we used linear discriminant analysis and random forest (RF) machine learning algorithms to predict white- or brown-rot decay modes from the numbers of genes encoding Carbohydrate-Active enZymes with over 98% accuracy. Unlike other algorithms, RF identified specific genes involved in cellulose and lignin degradation, including auxiliary activities (AAs) family 9 lytic polysaccharide monooxygenases, glycoside hydrolase family 7 cellobiohydrolases, and AA family 2 peroxidases, as critical factors. This study sheds light on the complex interplay between genetic information and decay modes and underscores the potential of RF for comparative genomics studies of wood-rotting fungi.
OBJECTIVE: Wood-rotting fungi are categorized as either white- or brown-rot modes based on the coloration of decomposed wood. The process of classification can be influenced by human biases. The random forest machine learning algorithm effectively distinguishes between white- and brown-rot fungi based on the presence of Carbohydrate-Active enZyme genes. These findings not only aid in the classification of wood-rotting fungi but also facilitate the identification of the enzymes responsible for degrading woody biomass.

Interactions between proteins and glycans are critical to various biological processes. With databases of carbohydrate-interacting proteins and increasing amounts of structural data, the three-sided right-handed β-helix (RHBH) has emerged as a significant structural fold for glycan interactions. In this review, we provide an overview of the sequence, mechanistic, and structural features that enable the RHBH to interact with glycans. The RHBH is a prevalent fold that exists in eukaryotes, prokaryotes, and viruses associated with adhesin and carbohydrate-active enzyme (CAZyme) functions. An evolutionary trajectory analysis on structurally characterized RHBH-containing proteins shows that they likely evolved from carbohydrate-binding proteins with their carbohydrate-degrading activities evolving later. By examining three polysaccharide lyase and three glycoside hydrolase structures, we provide a detailed view of the modes of glycan binding in RHBH proteins. The 3-dimensional shape of the RHBH creates an electrostatically and spatially favorable glycan binding surface that allows for extensive hydrogen bonding interactions, leading to favorable and stable glycan binding. The RHBH is observed to be an adaptable domain capable of being modified with loop insertions and charge inversions to accommodate heterogeneous and flexible glycans and diverse reaction mechanisms. Understanding this prevalent protein fold can advance our knowledge of glycan binding in biological systems and help guide the efficient design and utilization of RHBH-containing proteins in glycobiology research.

Carbohydrate binding modules (CBMs) are independent non-catalytic domains widely found in carbohydrate-active enzymes (CAZymes), and they play an essential role in the substrate binding process of CAZymes by guiding the appended catalytic modules to the target substrates. Owing to their precise recognition and selective affinity for different substrates, CBMs have received increasing research attention over the past few decades. To date, CBMs from different origins have formed a large number of families that show a variety of substrate types, structural features, and ligand recognition mechanisms. Moreover, through the modification of specific sites of CBMs and the fusion of heterologous CBMs with catalytic domains, improved enzymatic properties and catalytic patterns of numerous CAZymes have been achieved. Based on cutting-edge technologies in computational biology, gene editing, and protein engineering, CBMs as auxiliary components have become portable and efficient tools for the evolution and application of CAZymes. With the aim to provide a theoretical reference for the functional research, rational design, and targeted utilization of novel CBMs in the future, we systematically reviewed the function-related characteristics and potentials of CAZyme-derived CBMs in this review, including substrate recognition and binding mechanisms, non-catalytic contributions to enzyme performances, module modifications, and innovative applications in various fields.

Carbohydrate-active enzymes (CAZymes) are responsible for the biosynthesis, modification and degradation of all glycans in Nature. Advances in genomic and metagenomic methodologies, in conjunction with lower cost gene synthesis, have provided access to a steady stream of new CAZymes with both well-established and novel mechanisms. At the same time, increasing access to cryo-EM has resulted in exciting new structures, particularly of transmembrane glycosyltransferases of various sorts. This improved understanding has resulted in widespread progress in applications of CAZymes across diverse fields, including therapeutics, organ transplantation, foods, and biofuels. Herein, we highlight a few of the many important advances that have recently been made in the understanding and applications of CAZymes.

BACKGROUND: Microbial expansins (EXLXs) are non-lytic proteins homologous to plant expansins involved in plant cell wall formation. Due to their non-lytic cell wall loosening properties and potential to disaggregate cellulosic structures, there is considerable interest in exploring the ability of microbial expansins (EXLX) to assist the processing of cellulosic biomass for broader biotechnological applications. Herein, EXLXs with different modular structure and from diverse phylogenetic origin were compared in terms of ability to bind cellulosic, xylosic, and chitinous substrates, to structurally modify cellulosic fibrils, and to boost enzymatic deconstruction of hardwood pulp.
RESULTS: Five heterogeneously produced EXLXs (Clavibacter michiganensis; CmiEXLX2, Dickeya aquatica; DaqEXLX1, Xanthomonas sacchari; XsaEXLX1, Nothophytophthora sp.; NspEXLX1 and Phytophthora cactorum; PcaEXLX1) were shown to bind xylan and hardwood pulp at pH 5.5 and CmiEXLX2 (harboring a family-2 carbohydrate-binding module) also bound well to crystalline cellulose. Small-angle X-ray scattering revealed a 20-25% increase in interfibrillar distance between neighboring cellulose microfibrils following treatment with CmiEXLX2, DaqEXLX1, or NspEXLX1. Correspondingly, combining xylanase with CmiEXLX2 and DaqEXLX1 increased product yield from hardwood pulp by ~ 25%, while supplementing the TrAA9A LPMO from Trichoderma reesei with CmiEXLX2, DaqEXLX1, and NspEXLX1 increased total product yield by over 35%.
CONCLUSIONS: This direct comparison of diverse EXLXs revealed consistent impacts on interfibrillar spacing of cellulose microfibers and performance of carbohydrate-active enzymes predicted to act on fiber surfaces. These findings uncover new possibilities to employ EXLXs in the creation of value-added materials from cellulosic biomass.

Cellulose is the most abundant renewable bioresources on earth, and the biodegradation and utilization of cellulose would contribute to the sustainable development of global environment. Sporocytophaga species are common aerobic cellulose-degrading bacteria in soil, which can adhere to the surface of cellulose matrix and motile by gliding. In this study, a differential transcriptome analysis of Sporocytophaga sp. CX11 was performed and a total of 4,217 differentially expressed genes (DEGs) were identified. Gene Ontology enrichment results showed that there are three GO categories related to cellulose degradation function among the annotated DEGs. A total of 177 DEGs were identified as genes encoding carbohydrate-active enzymes (CAZymes), among which 54 significantly upregulated CAZymes were mainly cellulases, hemicellulases, pectinases, etc. 39 DEGs were screened to associate with gliding function. In order to explore unannotated genes potentially related to cellulose metabolism, cluster analysis was performed using the Short-Time Series Expression Miner algorithm (STEM). 281 unannotated genes were predicted to be associated with the initial-middle stage of cellulose degradation and 289 unannotated genes might function in the middle-last stage of cellulose degradation. Sporocytophaga sp. CX11 could produce extracellular endo-xylanase, endo-glucanase, FPase and β-glucosidase, respectively, according to different carbon source conditions. Altogether, this study provides valuable insights into the transcriptome information of Sporocytophaga sp. CX11, which would be useful to explore its application in biodegradation and utilization of cellulose resources.

Teredinibacter turnerae is a cultivable cellulolytic Gammaproeteobacterium (Cellvibrionaceae) that commonly occurs as an intracellular endosymbiont in the gills of wood-eating bivalves of the family Teredinidae (shipworms). The genome of T. turnerae encodes a broad range of enzymes that deconstruct cellulose, hemicellulose, and pectin and contribute to lignocellulose digestion in the shipworm gut. However, the mechanism by which symbiont-made enzymes are secreted by T. turnerae and subsequently transported to the site of lignocellulose digestion in the shipworm gut is incompletely understood. Here, we show that T. turnerae cultures grown on carboxymethyl cellulose (CMC) produce outer membrane vesicles (OMVs) that contain a variety of proteins identified by LC-MS/MS as carbohydrate-active enzymes with predicted activities against cellulose, hemicellulose, and pectin. Reducing sugar assays and zymography confirm that these OMVs retain cellulolytic activity, as evidenced by hydrolysis of CMC. Additionally, these OMVs were enriched with TonB-dependent receptors, which are essential to carbohydrate and iron acquisition by free-living bacteria. These observations suggest potential roles for OMVs in lignocellulose utilization by T. turnerae in the free-living state, in enzyme transport and host interaction during symbiotic association, and in commercial applications such as lignocellulosic biomass conversion.

[This corrects the article DOI: 10.3389/fmicb.2023.1294854.].

Suillus bovinus is a wild edible ectomycorrhizal fungus with important economic and ecological value, which often forms an ectomycorrhiza with pine trees. We know little about the mechanisms associated with the metabolism and symbiosis of S. bovinus and its effects on the nutritional value. In this study, the whole-genome sequencing of S. bovinus was performed using Illumina, HiFi, and Hi-C technologies, and the sequencing data were subjected to genome assembly, gene prediction, and functional annotation to obtain a high-quality chromosome-level genome of S. bovinus. The final assembly of the S. bovinus genome includes 12 chromosomes, with a total length of 43.03 Mb, a GC content of 46.58%, and a contig N50 size of 3.78 Mb. A total of 11,199 coding protein sequences were predicted from genome annotation. The S. bovinus genome contains a large number of small secreted proteins (SSPs) and genes that encode enzymes related to carbohydrates, as well as genes related to terpenoids, auxin, and lipochitooligosaccharides. These genes may contribute to symbiotic processes. The whole-genome sequencing and genetic information provide a theoretical basis for a deeper understanding of the mechanism of the mycorrhizal symbiosis of S. bovinus and can serve as a reference for comparative genomics of ectomycorrhizal fungi.