Carbohydrate-binding modules: fine-tuning polysaccharide recognition

Impact of loosenins on the enzymatic preparation of cellulose nanocrystals

Whereas the enzymatic deconstruction of lignocellulosic materials is well established, comparatively few studies investigate the application of enzymes in bio-based material manufacturing. In this study, we demonstrate the potential of an ancestral endoglucanase from Bacillus subtilis (LFCA_EG) together with a loosenin from the white-rot fungus Phanerochaete carnosa (PcaLOOL12) to produce cellulose nanocrystals (CNC) with smaller size and higher yield than CNCs prepared using LFCA_EG alone. Moreover, CNCs prepared using both LFCA_EG and PcaLOOL12 retained the chemical purity, crystallinity, and thermal stability of previously described enzymatically prepared CNCs, and could be used to exfoliate graphite to generate low resistance, graphene-based conductive inks. Accordingly, this study highlights the potential of loosenins such as PcaLOOL12 to not only enhance the enzymatic deconstruction of lignocellulose but also the preparation of value-added cellulosic materials.

Teredinibacter turnerae secretome highlights key enzymes for plant cell wall degradation

Carbohydrate-active enzymes (CAZymes) are crucial in the sustainable production of fuels and raw materials from recalcitrant plant cell wall polysaccharides (PCWPs). Teredinibacter turnerae, a symbiont of wood-boring shipworms, is a prolific degrader of plant biomass, largely due to the extensive CAZyme repertoire in its genome. To identify key enzymes involved in PCWP utilization, we analyzed the secretomes of T. turnerae E7MBN strain grown on sucrose, major PCWPs (cellulose, xylan, and pectin), and residual rice hull biomass using mass spectrometry-based proteomics. Our results show that T. turnerae E7MBN exhibits minimal enzyme secretion across various carbon sources, where secretomes mostly display similar functional profiles. Enzymatic complexity varied with the substrate, with cellulose-grown secretome being the most complex and comprising the majority of secreted CAZymes. These CAZymes contain domains that primarily target cellulose, hemicellulose, or pectin, notably including multicatalytic enzymes that are consistently found in the secretome and are likely central to biomass degradation. In contrast, the xylan-grown secretome displayed a more specific response, secreting only a single bifunctional hemicellulase, E7_MBN_00081, also identified as a core component of the bacteria's enzymatic repertoire. Meanwhile, the pectin-grown secretome consists of multiple tonB-dependent receptors, which, along with isomerases, are considered common secretome constituents. E7MBN also demonstrated the capability to utilize rice hull biomass, predominantly secreting proteins previously identified under cellulose. Protein-protein interaction network analysis further revealed functional associations between CAZymes and several uncharacterized proteins, which include CBM-containing redox enzymes and a putative xylan-acting protein, thus offering new insights into their potential role in lignocellulose degradation. Overall, our work contributes to our understanding of enzymatic strategies employed by T. turnerae for PCWP deconstruction and highlights its potential as a promising source of CAZymes for sustainable biomass conversion.

Synergy between processive cellulases in Ruminoccocus albus

Endoglucanases (EGs), cellobiohydrolases (CBHs), and β-glucosidases are essential components in enzymatic degradation of cellulose. We analyzed the glycosyl hydrolases from families GH5 and GH48 from Ruminococcus albus 8 (RalCel5G and RalCel48A). Both enzymes feature a catalytic motif and a carbohydrate binding domain from family 37 (CBM37). RalCel5G also exhibited a second CBM37 with lower similarity. As a result, RalCel5G showed higher binding affinity toward insoluble substrates and broader recognition capacity. Kinetic characterization using different cellulosic substrates and reaction product analysis confirmed RalCel5G as a processive EG while RalCel48A is a CBH. Interestingly, we found a synergistic effect on their activity at a low EG to CBH ratio, despite the processive activity of RalCel5G. Furthermore, the lignocellulose degradation capacity was improved by supplementing the cellulases with hemicellulase RalXyn10A. These results provide valuable information about the interaction between processive EG and conventional CBH, necessary for the rational design of enzyme cocktails for optimized biomass processing.

Metagenomics Insights into the Role of Microbial Communities in Mycotoxin Accumulation During Maize Ripening and Storage

Mycotoxins are among the primary factors compromising food quality and safety. To investigate mycotoxin contamination, microbial diversity, and functional profiles in maize across distinct geographic regions, this study analyzed samples from Xuanwei, Fuyuan, and Zhanyi. Mycotoxin concentrations were quantified through standardized assays, while microbial community structures were characterized using metagenomics sequencing. Metabolic pathways, functional genes, and enzymatic activities were systematically annotated with the KEGG, eggNOG, and CAZy databases. The results demonstrated an absence of detectable aflatoxin (AF) levels. Deoxynivalenol (DON) concentrations varied significantly among experimental cohorts, although all values remained within regulatory thresholds. Zearalenone (ZEN) contamination exceeded permissible limits by 40%. The metagenomic profiling identified 85 phyla, 1219 classes, 277 orders, 590 families, 1171 genera, and 2130 species of microorganisms, including six mycotoxigenic fungal species. The abundance and diversity of microorganisms were similar among different treatment groups. Among 32,333 annotated KEGG pathways, primary metabolic processes predominated (43.99%), while glycoside hydrolases (GH) and glycosyltransferases (GT) constituted 76.67% of the 40,202 carbohydrate-active enzymes. These empirical findings establish a scientific framework for optimizing agronomic practices, harvest scheduling, and post-harvest management in maize cultivation.

Functional diversification of dietary plant small molecules by the gut microbiome

Plants are composed of diverse secondary metabolites (PSMs), which are widely associated with human health. Whether and how the gut microbiome mediates such impacts of PSMs is poorly understood. Here, we show that discrete dietary and medicinal phenolic glycosides, abundant health-associated PSMs, are utilized by distinct members of the human gut microbiome. Within the Bacteroides, the predominant gram-negative bacteria of the Western human gut, we reveal a specialized multi-enzyme system dedicated to the processing of distinct glycosides based on structural differences in phenolic moieties. This Bacteroides metabolic system liberates chemically distinct aglycones with diverse biological functions, such as colonization resistance against the gut pathogen Clostridioides difficile via anti-microbial activation of polydatin to the stilbene resveratrol and intestinal homeostasis via activation of salicin to the immunoregulatory aglycone saligenin. Together, our results demonstrate generation of biological diversity of phenolic aglycone "effector" functions by a distinct gut-microbiome-encoded PSM-processing system.

Exposed tryptophan residues in the chitin-binding domain of ChiA74 chitinase are important for chitin-binding and antifungal activity

The chitin-binding domain (CBD) of chitinases is crucial for substrate-binding, antibacterial, and antifungal activities. Here, we constructed various mutants to investigate the role of the exposed aromatic residues of the CBD of chitinase ChiA74 from Bacillus thuringiensis. One mutant lacked the CBD, three had mutations in surface aromatic residues (W591, W626, W645), and one harbored a mutation in the hydrophobic core (W612). Compared to ChiA74, a significant decrease (∼ 40 %) in chitin and colloidal chitin binding and a negligible (∼ 6 %) decrease in cellulose binding were observed with the CBD mutant. The tryptophan mutants exhibited reduced binding to α-chitin, colloidal chitin, and cellulose, except for ChiA74W612, for which binding to cellulose remained unchanged. ChiA74 showed the highest enzymatic activity (29.429 ± 1.728 U mg-1), whereas ChiA74W645A exhibited the lowest activity (1.203 U mg-1). All mutants demonstrated a significant reduction (∼ 30 %) in antifungal activity against Fusarium oxysporum compared to ChiA74. The significance of this work lies in the data presented here, indicating that the exposed aromatic residues are crucial for substrate binding and antifungal efficacy. This creates opportunities for engineering synthetic enzymes or constructing chimeric chitinases with enhanced performance.

Secretome analysis of the chitinolytic machinery of Chitiniphilus shinanonensis and its implication in chitooligosaccharide production

Chitin's robust structure poses significant challenges for degradation, necessitating the study of microbial processes in chitin-rich environments. We assessed the chitinolytic bacterium Chitiniphilus shinanonensis DSM 23277T (SAY3T) for converting chitin biomass into valuable saccharides using various substrates (chitin flakes, α-chitin, and β-chitin) in shake flask cultures. The bacterium successfully grew on all substrates, achieving complete degradation, although chitin flakes required more time. Maximum growth was observed on β-chitin, followed by α-chitin and chitin flakes. Scanning electron microscopy confirmed bacterial colonization and potential hydrolytic activity on chitin flakes. Proteomic analysis via nanoLC-MS/MS identified 32 chitin-degrading enzymes distributed across secretome, periplasmic, and intracellular fractions, with a notable expression of glycoside hydrolases (families 18, 19, and 20), carbohydrate esterases (family 4), and auxiliary activity proteins (family 10). Among the family 18 chitinases, ChiM, ChiI, and ChiL were significantly upregulated on all chitinous substrates compared to glucose. The chitin-active-secretome exhibited optimal activity at pH 8.0 and 45 °C in 50 mM Tris-HCl. Moreover, the chitin-active-secretome effectively degraded chitin flakes, α-chitin, and β-chitin into chitobiose and GlcNAc, with β-chitin yielding the highest chitobiose levels. The diverse chitin-degrading enzymes of C. shinanonensis efficiently utilize recalcitrant chitin as a carbon and energy source, underscoring its industrial potential for chitin degradation.

Targets for the diagnosis of Acanthamoeba eye infections include four cyst wall proteins and the mannose-binding domain of the trophozoite mannose-binding protein

Acanthamoebae, which are free-living amoebae, cause corneal inflammation (keratitis) and blindness, if not quickly diagnosed and effectively treated. The walls of Acanthamoeba cysts contain cellulose and have two layers connected by conical ostioles. Cysts are identified by in vivo confocal microscopy of the eye or calcofluor-white- or Giemsa-labeling of corneal scrapings, both of which demand great expertise. Trophozoites, which use a mannose-binding protein to adhere to keratinocytes, are identified in eye cultures that delay diagnosis and treatment. We recently used structural and experimental methods to characterize cellulose-binding domains of Luke and Leo lectins, which are abundant in the inner layer and ostioles. However, no antibodies have been made to these lectins or to a Jonah lectin and a laccase, which are abundant in the outer layer. Here, confocal microscopy of rabbit antibodies (rAbs) to recombinant Luke, Leo, Jonah, and laccase supported localizations of GFP-tagged proteins in walls of transfected Acanthamoebae. rAbs efficiently detected calcofluor white-labeled cysts of 10 of the 11 Acanthamoeba isolates tested, including six T4 genotypes that cause most cases of keratitis. Further, laccase shed into the medium during encystation was detected by an enzyme-linked immunoassay. Structural and experimental methods identified the mannose-binding domain (ManBD) of the Acanthamoeba mannose-binding protein, while rAbs to the ManBD efficiently detected DAPI-labeled trophozoites from all 11 Acanthamoeba isolates tested. We conclude that antibodies to four cyst wall proteins and the ManBD efficiently identify Acanthamoeba cysts and trophozoites, respectively.IMPORTANCEFree-living amoeba in the soil or water cause Acanthamoeba keratitis, which is diagnosed by identification of unlabeled cysts by in vivo confocal microscopy of the eye or calcofluor-white (CFW) labeled cysts by fluorescence microscopy of corneal scrapings. Alternatively, Acanthamoeba infections are diagnosed by the identification of trophozoites in eye cultures. Here, we showed that rabbit antibodies (rAbs) to four abundant cyst wall proteins (Jonah, Luke, Leo, and laccase) each efficiently identify CFW-labeled cysts of 10 of the 11 Acanthamoeba isolates tested. Further, laccase released into the medium by encysting Acanthamoebae was detected by an enzyme-linked immunoassay. We also showed that rAbs to the mannose-binding domain (ManBD) of the Acanthamoeba mannose-binding protein, which mediates adherence of trophozoites to keratinocytes, efficiently identify DAPI-labeled trophozoites of all 11 Acanthamoeba isolates tested. In summary, four wall proteins and the ManBD appear to be excellent targets for the diagnosis of Acanthamoeba cysts and trophozoites, respectively.

Chitin-binding mechanism of a CBM73 module derived from a lytic polysaccharide monooxygenase from Vibrio campbellii

A lytic polysaccharide monooxygenase from Vibrio campbellii (VhLPMO10A) consists of four functional domains including an N-terminal AA10 catalytic domain (CatD) and a C-terminal CBM73 carbohydrate-binding domain. Phylogenetic analysis of CBM73s from AA10 LPMO and GH18/GH19 chitinases revealed that CBM73 from VhLPMO10A (VhCBM73) belongs a clade different from that of a well-studied CBM73 from Cellvibrio japonicus AA10 LPMO (CjCBM73, Madland et al., J. Biol. Chem. 297 (2021) 101084). A recombinant VhCBM73 protein did not bind chitooligosaccharides, but it almost equally bound colloidal chitins prepared from squid pen/crab shell. Mutations of Tyr437, Trp441, and Trp456 of VhCBM73 to alanine (Y437A, W441A, and W456A) revealed that the effects were most intensive in Y437A, moderate in W441A, but insignificant in W456A. We concluded that a single chitin chain more hydrated interact with the binding path spanning from Tyr437 to Trp441 of VhCBM73, while multiple chitin chains (chitin surface) interact with a wider binding surface of CjCBM73. VhCBM73 and CjCBM73 may have differently evolved to acquire different binding strategies for enhancing the LPMO function.

Marine algal polysaccharides for drug delivery applications: A review

In recent decades, there has been a growing interest in the use of polysaccharides that exhibit biological activity for a wide range of innovative applications. This is due to their nontoxicity, biodegradability, biocompatibility, and therapeutic properties. The diverse properties of polysaccharides derived from marine algae make them a promising strategy for the construction of drug delivery systems (DDSs). Marine algal polysaccharides can be utilized in regenerative medicine and gene delivery to facilitate the controlled release of therapeutic substances, which is a critical stage in the fight against severe diseases. Algal polysaccharide-based nanoparticles, microspheres, hydrogels, patches, and films are among the numerous controllable and sustained anti-inflammatory and anticancer DDSs that can be used due to the biological activities of these algal polymers. This review paper summarizes the advantages and applications of marine algal polysaccharides in DDSs (such as nanoparticles, microspheres, hydrogels, patches and films) as well as recent advances in drug delivery technologies, thereby providing valuable information for future research on drug delivery-based algal polysaccharides.

Chitinases are important virulence factors in Vibrio for degrading the chitin-rich barrier of shrimp

Vibrio-induced diseases pose a significant threat to shrimp aquaculture. While the mechanisms underlying Vibrio penetration of shrimp shells and the gastrointestinal tract remain unclear, this study implicates chitinases as critical virulence factors. Despite their inability to utilize chitin or shrimp shells as sole carbon and nitrogen sources, three major shrimp pathogens-V. alginolyticus, V. harveyi, and V. parahaemolyticus-thrive on chitin-supplemented media and efficiently degrade shrimp shells. Ten extracellular chitinases were identified and two clades, ChiA and ChiD, are conserved among three Vibrio, underscoring their critical role in chitin degradation by Vibrio. Furthermore, one or two copies of evolutionarily conserved ChtBD3 are identified, facilitating targeting chitin-rich structures as virulence factors. All chitinase genes rapidly respond to shrimp shell or colloidal chitin, particularly Vpchi90, which exhibited a 33,340.8-fold increase in expression, correlating with enhanced chitinase activity. To further investigate their functional role, rVaChi89 (ChiD) and rVpChi90 (ChiA) was successfully heterologous expressed in Bacillus subtilis, achieving yields of 0.58 and 0.91 U/mL, respectively. In vitro assay confirmed their ability to degrade shrimp shells into GlcNAc and chitooligomers, further supporting their role in host invasion. This study highlights Vibrio chitinases as critical virulence factors and potential drug targets, with implications for chitin waste recycling.

The Origin, Properties, Structure, Catalytic Mechanism, and Applications of Fucoidan-Degrading Enzymes

Fucoidanase is a class of enzymes capable of hydrolyzing fucoidan, a complex sulfated polysaccharide found mainly in marine brown algae and some marine invertebrates. Fucoidan (FUC) has a wide range of potential health benefits and therapeutic effects, including antitumor, immunomodulatory, antiviral, and hypoglycemic activities. Fucoidanase can hydrolyze high-molecular-weight fucoidan into medium- and low-molecular-weight fucoidan. The low-molecular-weight fucoidan not only has good solubility, low viscosity, and high absorption rate but also retains the original biological activities of fucoidan. Fucoidanase has received much attention in recent years. This paper reviews the taxonomic origin, structure, enzymatic properties, and applications of fucoidanase to provide a reference for the study of fucoidanase.

The Impact of Chitinase Binding Domain Truncation on the Properties of CaChi18B from Chitinilyticum aquatile CSC-1

The chitinase binding domain (ChBD) plays a crucial role in the properties of enzymes. To assess its impact, we cloned a truncated mutant of the chitinase gene CaChi18B from the novel chitinase-producing facultative anaerobic bacterium Chitinilyticum aquatile CSC-1, designated as CaChi18B_ΔChBDs. The recombinant chitinase was successfully expressed and purified, exhibiting a specific activity of 3.48 U/mg on colloidal chitin, with optimal conditions at 45 °C and pH 6.0, and retaining over 80% activity at temperatures up to 40 °C. Kinetic analysis revealed that the Km value was 1.159 mg mL-1 and the Vmax was 10.37 μM min-1 mg-1. Compared to CaChi18B_ΔChBD1, which has only the first ChBD truncated at the N-terminus, CaChi18B_ΔChBDs exhibited minor changes in the optimal temperature and pH, while the Km and Vmax values increased significantly. CaChi18B_ΔChBDs exhibited tolerance to various metal ions, with K+ and NH4+ enhancing activity, while Cu2+ significantly inhibited it. Most organic reagents had minimal impact, except for formic acid, which severely reduced activity. The primary hydrolysis product in the initial phase was GlcNAc, contrasting with (GlcNAc)2 for CaChi18B_ΔChBD1. These findings indicated that the ChBD influences the enzyme's Km, Vmax, and product distribution, enhancing our understanding of ChBD's roles and advancing chitin utilization.

Systematic Approach to Parametrization of Disaccharides for the Martini 3 Coarse-Grained Force Field

Sugars are ubiquitous in biology; they occur in all kingdoms of life. Despite their prevalence, they have often been somewhat neglected in studies of structure-dynamics-function relationships of macromolecules to which they are attached, with the exception of nucleic acids. This is largely due to the inherent difficulties of not only studying the conformational dynamics of sugars using experimental methods but indeed also resolving their static structures. Molecular dynamics (MD) simulations offer a route to the prediction of conformational ensembles and the time-dependent behavior of sugars and glycosylated macromolecules. However, at the all-atom level of detail, MD simulations are often too computationally demanding to allow a systematic investigation of molecular interactions in systems of interest. To overcome this, large scale simulations of complex biological systems have profited from advances in coarse-grained (CG) simulations. Perhaps the most widely used CG force field for biomolecular simulations is Martini. Here, we present a parameter set for glucose- and mannose-based disaccharides for Martini 3. The generation of the CG parameters from atomistic trajectories is automated as fully as possible, and where not possible, we provide details of the protocol used for manual intervention.

Comprehensive cDNA cloning and putative feature analysis of endogenous cellulases possessed by the Pacific oyster, Crassostrea gigas

Previous studies have examined the cellulase activity of Crassostrea gigas (Pacific oyster) and suggested its potential utilization of terrestrial lignocellulose. However, no studies have been conducted to comprehensively assess its endogenous cellulases. Therefore, our objective was to identify the cellulases present in C. gigas through transcriptome and genomic analyses. The results showed that there are 10 cellulase orthologs, seven of which are endogenous. Phylogenetic analysis revealed that two of these cellulases belong to the glycoside hydrolase family (GHF) 5, four to GHF9, and one to GHF45. An alignment of the amino acid sequences suggested the presence of at least endo-β-1,4-glucanase. Therefore, C. gigas is likely capable of decomposing lignocellulose into glucose. This finding supports the fact that C. gigas, a globally commercial bivalve species, thrives in environments that lack phytoplankton, such as mangroves.

Structural and functional snapshots of a broad-specificity endoglucanase from Thermogutta terrifontis for biomass saccharification

Multifunctionality, processivity, and thermostability are critical for the cost-effective enzymatic saccharification of non-food plant biomass polymers such as β-glucans, celluloses, and xylans to generate biofuels and other valuable products. We present molecular insights into a processive multifunctional endo-1,3-1,4-β-d-glucanase (Tt_End5A) from the hyperthermophilic bacterium Thermogutta terrifontis. Tt_End5A demonstrated activities against a broad spectrum of β-polysaccharides, including barley glucan, lichenan, carboxymethyl cellulose, regenerated amorphous cellulose (RAC), Avicel, xylan, laminarin, mannan, curdlan, xanthan, and various chromogenic substrates at pH 7 and temperatures ranging from 70 to 80°C. The enzyme exhibited a high level of processivity on RAC and retained over 90% activity at 80°C for an extended period, indicating exceptional thermal stability. The 1.20 Å crystal structure of the Tt_End5A catalytic domain revealed an archetypal glycoside hydrolase family 5 (GH5) catalytic TIM-(β/α)8-barrel, supplemented with additional β-strands, elongated α-helices, and a rare cis-non-Pro (His481-cis-Ala482) peptide. A large central cleft was observed in the 3D structure, which is likely related to the enzyme's multifunctionality and processivity. The catalytic domain is preceded by a novel N-terminal multivalent carbohydrate-binding module (CBM) that enhances the enzymatic degradation of insoluble polysaccharides. Mutagenesis studies, ligand interaction analyses, and the structurally conserved positions of E329 and E448 in Tt_End5A suggest that these residues function as the proton donor and nucleophile in the catalytic mechanism. Owing to its multifunctionality and processivity, Tt_End5A can reduce the need for multiple saccharification enzymes to generate fermentable sugars from plant biomass for bioethanol production. Additionally, it holds promise for applications in the pharmaceutical, feed, and food industries.

Deciphering the structural and biochemical aspects of xylosidase from Pseudopedobacter saltans

Xylose, a key constituent of the heterogeneous hemicellulose polymer, occurs in lignocellulosic biomass and forms xylan polymers through β-1,4 glycosidic linkages. The β-1,4-xylosidase enzyme was isolated from Pseudopedobacter saltans (PsGH43) to find an effective enzyme with enhanced activity to depolymerize xylo-oligosaccharides. β-1,4-xylosidase belongs to the GH431 family as classified in the Carbohydrate-Active Enzyme Database (CAZy). PsGH432 was found to be active only on xylose-based substrate, 4NPX3, with maximum activity occurring at a pH 7 and 30 °C (Km 1.96 ± 0.2 mM and Vmax 0.43 mM/min). The study also confirms the influence of Ca2+ ions on enzymatic activity and thermal stability. Subsequently, native PsGH43 was crystallized at optimum conditions and the structure was determined at 2.5 Å resolution. Crystallographic analysis revealed an asymmetric unit containing eight monomers and 16 calcium ions wherein a tetramer constituted the functional unit. Each monomer exhibits a characteristic GH43 N-terminal β-propeller fold that serves as a catalytic domain accommodating one calcium ion in the centre, while the C-terminal β-sandwich fold associated with the CBM64 family preserves another calcium ion. Our study reveals a novel tetrameric arrangement of β-1,4-xylosidase which unravels its functional indispensability. This study opens newer avenues to engineer a potential enzyme for biofuel and bioethanol industry.

Exploring the competitive inhibition of α-glucosidase by citrus pectin enzymatic hydrolysate and its mechanism: An integrated experimental and simulation approach

The endo-polygalacturonase D (PgaD) from Aspergillus niger JL15 was recombinantly expressed in Escherichia coli BL21, exhibiting an optimal activity at 55 °C and pH 4.0. Hydrolysis products of citrus pectin by recombinant PgaD included galacturonic acid (GalA), digalacturonic acid (GalA2), trigalacturonic acid (GalA3), and tetragalacturonic acid (GalA4). The hydrolysates exhibited significant antioxidant capacity and dose-dependent competitive inhibition of α-glucosidase. GalA2 and GalA3 acted as competitive inhibitors of α-glucosidase, with inhibition constant of 0.0589 mmol.L-1 and 0.6732 mmol.L-1, respectively. Molecular dynamics (MD) simulations revealed that both GalA2 and GalA3 penetrated the catalytic pocket of α-glucosidase and formed stable hydrogen bonds with key catalytic residues D352 and D215. The binding free energies of GalA2-α-glucosidase and GalA3-α-glucosidase complexes were - 10.3 ± 0.6 kcal·mol-1 and -10.8 ± 0.7 kcal·mol-1, respectively. These findings might offer new ideas for the development of α-glucosidase inhibitors sourced from citrus pectin, as well as enhance utilization of the renewable plant polysaccharide resources.

JRSeek: Artificial Intelligence Meets Jelly Roll Fold Classification in Viruses

The jelly roll (JR) fold is the most common structural motif found in the capsid and nucleocapsid of viruses. Its pervasiveness across many different viral families motives developing a tool to predict its presence from a sequence. In the current work, logistic regression (LR) models trained on six different large language model (LLM) embeddings exhibited over 95% accuracy in differentiating JR from non-JR sequences. The dataset used for training and testing included sequences from single JR viruses, non-JR viruses, and non-virus immunoglobulin-like β-sandwich (IGLBS) proteins which closely resemble the JR fold in structure. The high accuracy is particularly remarkable given the low sequence similarity across viral families and the balanced nature of the dataset. Also, the accuracy of the models was independent of LLM embeddings, suggesting that peak accuracy for predicting viral JR folds hinges more on the data quality and quantity rather than on the specific mathematical models used. Given that many viral capsid and nucleocapsid structures have yet to be resolved, using sequence-based LLMs is a promising strategy that can readily be applied to available data. Principal Component Analysis of the Bert-U100 embeddings demonstrates that most IGLBS sequences and a subset of JR and non-JR sequences are distinguishable even before the application of the LR model, but the LR model is necessary to differentiate a subset of more ambiguous sequences. When applied to double JR folds, the Bert-U100 model was able to assign the JR motif for some viral families, providing evidence for the model's generalizability. However, for other families, this generalizability was not observed, motivating a future need to develop other models informed by double JR folds. Lastly, the Bert-U100 model was also able to predict whether sequences from a dataset of unclassified viruses produce the JR fold. Two examples are given and the JR predictions are corroborated by AlphaFold3. Altogether, this work demonstrates that JR folds can, in principle, be predicted from their sequences.

Unbiased picture of the ligand docking process for the hevein protein-oligosaccharide complex

The ligand-docking behavior of hevein, the major latex protein from the rubber tree Hevea brasiliensis (Euphorbiaceae), has been investigated by the unguided molecular dynamics (MD) simulation method. An oligosaccharide molecule, initially placed in an arbitrary position, was allowed to move around hevein for a prolonged simulation time, on the order of microseconds, with the expectation of spontaneous ligand docking of the oligosaccharide molecule to the binding site of hevein. In the binary solution system consisting of a hevein molecule and a chito-trisaccharide (GlcNAc3) molecule, three out of the six separate simulation runs successfully reproduced the complex structure of the observed binding from. It appeared that the surface topology formed by two aromatic side chains of the hevein molecule played a role in orienting the GlcNAc3 molecule in the correct direction. We also performed MD simulations of the ternary solution system containing a cello-hexasaccharide (Glc6) molecule in addition to hevein and a chito-hexasaccharide (GlcNAc6) molecule. Formation of hevein-GlcNAc6 complex structures was exclusively observed, while the Glc6 molecule remained in the solvent phase throughout the simulations. Obviously, the acetamide groups of GlcNAc play a role in detecting the binding site and its vicinity on the protein surface.

Genome-Wide Identification and Analysis of Carbohydrate-Binding Modules in Colletotrichum graminicola

Colletotrichum graminicola is the causative agent of both maize stem rot and leaf blight, which are among the most damaging diseases affecting maize. Carbohydrate-binding modules (CBMs) are protein domains that lack catalytic activity and are commonly found alongside carbohydrate-hydrolyzing enzymes in fungi. A comprehensive examination of the C. graminicola TZ-3 genome resulted in the identification of 83 C. graminicola CBM (CgCBM) genes, which are characterized by distinct gene structures and protein motifs. Subcellular localization analysis revealed that the majority of CgCBM proteins were localized in the extracellular space. Investigation of the promoter regions of CgCBM genes uncovered a variety of responsive elements associated with plant hormones, including abscisic acid and methyl jasmonate response elements, as well as various stress-related response elements for drought, cold, defense, and other stress factors. Gene ontology analysis identified the primary functions of CgCBM genes as being linked to polysaccharide metabolism processes. Furthermore, the 83 CgCBM genes exhibited varying responses at different time points during C. graminicola infection, indicating their contribution to the fungus-maize interaction and their potential roles in the fungal pathogenic process. This study provides essential insights into CgCBMs, establishing a crucial foundation for further exploration of their functions in the mechanisms of fungal pathogenicity.

The Lipocone Superfamily: A Unifying Theme In Metabolism Of Lipids, Peptidoglycan And Exopolysaccharides, Inter-Organismal Conflicts And Immunity

Wnt proteins are critical signaling molecules in developmental processes across animals. Despite intense study, their evolutionary roots have remained enigmatic. Using sensitive sequence analysis and structure modeling, we establish that the Wnts are part of a vast assemblage of domains, the Lipocone superfamily, defined here for the first time. It includes previously studied enzymatic domains like the phosphatidylserine synthases (PTDSS1/2) and the TelC toxin domain from Streptococcus intermedius , the enigmatic VanZ proteins, the animal Serum Amyloid A (SAA) and a further host of uncharacterized proteins in a total of 30 families. Though the metazoan Wnts are catalytically inactive, we present evidence for a conserved active site across this superfamily, versions of which are consistently predicted to operate on head groups of either phospholipids or polyisoprenoid lipids, catalyzing transesterification and phosphate-containing head group severance reactions. We argue that this superfamily originated as membrane proteins, with one branch (including Wnt and SAA) evolving into soluble versions. By comprehensively analyzing contextual information networks derived from comparative genomics, we establish that they act in varied functional contexts, including regulation of membrane lipid composition, extracellular polysaccharide biosynthesis, and biogenesis of bacterial outer-membrane components, like lipopolysaccharides. On multiple occasions, members of this superfamily, including the bacterial progenitors of Wnt and SAA, have been recruited as effectors in biological conflicts spanning inter-organismal interactions and anti-viral immunity in both prokaryotes and eukaryotes. These findings establish a unifying theme in lipid biochemistry, explain the origins of Wnt signaling and provide new leads regarding immunity across the tree of life.

Carbohydrate Deacetylase Unique to Gut Microbe Bacteroides Reveals Atypical Structure

Bacteroides are often the most abundant, commensal species in the gut microbiome of industrialized human populations. One of the most commonly detected species is Bacteroides ovatus. It has been linked to benefits like the suppression of intestinal inflammation but is also correlated with some autoimmune disorders, for example irritable bowel disorder (IBD). Bacterial cell surface carbohydrates, like capsular polysaccharides (CPS), may play a role in modulating these varied host interactions. Recent studies have begun to explore the diversity of CPS loci in Bacteroides; however, there is still much unknown. Here, we present structural and functional characterization of a putative polysaccharide deacetylase from Bacteroides ovatus (BoPDA) encoded in a CPS biosynthetic locus. We solved four high resolution crystal structures (1.36-1.56 Å) of the enzyme bound to divalent cations Co2+, Ni2+, Cu2+, or Zn2+ and performed carbohydrate binding and deacetylase activity assays. Structural analysis of BoPDA revealed an atypical domain architecture that is unique to this enzyme, with a carbohydrate esterase 4 (CE4) superfamily catalytic domain inserted into a carbohydrate binding module (CBM). Additionally, BoPDA lacks the canonical CE4 His-His-Asp metal binding motif and our structures show it utilizes a noncanonical His-Asp dyad to bind metal ions. BoPDA is the first protein involved in CPS biosynthesis from B. ovatus to be characterized, furthering our understanding of significant biosynthetic processes in this medically relevant gut microbe.

Important ecophysiological roles of Nocardiopsis in lignocellulose degradation during aerobic compost with humic acid addition

Improving lignocellulose degradation and organic matter conversion in agricultural and livestock wastes remains a great challenge. Here, the contribution of humic acid (HA) to lignocellulose degradation was investigated, focusing on the abundance of key microbial species and carbohydrate-active enzymes during aerobic composting. The results demonstrated that the addition of HA not only increased the complexity of the microbial network, but also enhanced the positive interaction between microorganism. The abundance of phylum Actinobacteria related to lignin degradation was significantly increased, especially genus Nocardiopsis (50.97 %), and Nocardiopsis was significantly positively correlated with HA and humus (HS) (p < 0.05). Additionally, the abundance of GH (43.45%) and AA (5.88%) enzymes and the activation of metabolic pathways of AA, carbohydrates and energy were significantly increased (p < 0.05). Remarkably, the quantity of lignocellulose-degrading genes and carbohydrate-active enzymes experienced a marked boost (p < 0.05), with the peak abundance observed in Nocardiopsis. The structural equation model revealed that the addition of HA boosted the abundance of Nocardiopsis, which in turn amplified lignocellulose degradation by up-regulating lignocellulose degradation genes and enhancing carbohydrase activity, and facilitating the conversion of HA and FA. The lignocellulose degradation experiment verified that Nocardiopsis alba exhibited good ability in the degradation of cellulose and hemicellulose. These findings provided a novel perspective on the mechanisms underlying lignocellulose degradation, and broaden the understanding of the ecophysiological role of Nocardiopsis in composting system.

Three intertwining effects guide the mode of action of chitin deacetylase de- and N-acetylation reactions

Chitosans are promising multi-functional biomolecules for various applications whose performance is dependent on three key structural parameters, including the pattern of acetylation (PA). To date, chitin deacetylases (CDAs) are the only tool to control the PA of chitosan polymers via their specific mode of action during de- or N-acetylation. For a start, this review summarizes the current state of research on the classification of carbohydrate esterase 4 enzymes, the features in sequence and structure of CDAs, and the different PAs produced by different CDAs during de- or N-acetylation. In the main part, we introduce three effects that guide the mode of action of these enzymes: the already established subsite capping effect, the subsite occupation effect, and the subsite preference effect. We show how their interplay controls the PA of CDA products and describe their molecular basis. For one thing, this review aims to equip the reader with the knowledge to understand and analyze CDAs - including a guide for in silico and in vitro analyses. But more importantly, we intend to reform and extend the model explaining their mode of action on chitosans to facilitate a deeper understanding of these important enzymes for biology and biotechnology.

A modular enzyme with combined hemicellulose-removing and LPMO activity increases cellulose accessibility in softwood

Because of the association with other complex polysaccharides, extracting and utilizing cellulose from lignocellulosic materials requires the combined action of a broad range of carbohydrate-active enzymes, including multiple glycoside hydrolases (GHs) and lytic polysaccharide monooxygenases (LPMOs). The interplay between these enzymes and the way in which Nature orchestrates their co-existence and combined action are topics of great scientific and industrial interest. To gain more insight into these issues, we have studied the lignocellulose-degrading abilities of an enzyme from Caldibacillus cellulovorans (CcLPMO10-Man5), comprising an LPMO domain, a GH5 mannanase domain and two family 3 carbohydrate-binding modules (CBM3). Using a natural softwood substrate, we show that this enzyme promotes cellulase activity, i.e., saccharification of cellulose, both by removing mannan covering the cellulose and by oxidatively breaking up the cellulose structure. Synergy with CcLPMO10-Man5 was most pronounced for two tested cellobiohydrolases, whereas effects were smaller for a tested endoglucanase, which is in line with the notion that cellobiohydrolases and LPMOs attack the same crystalline regions of the cellulose, whereas endoglucanases attack semi-crystalline and amorphous regions. Importantly, the LPMO domain of CcLPMO10-Man5 is incapable of accessing the softwood cellulose in absence of the mannanase domain. Considering that LPMOs not bound to a substrate are sensitive to autocatalytic inactivation, this intramolecular synergy provides a perfect rationale for the evolution of modular enzymes such as CcLPMO10-Man5. The intramolecular coupling of the LPMO with a mannanase and two CBMs ensures that the LPMO is directed to areas where mannans are removed and cellulose thus becomes available.

Host-intestinal microbiota interactions in Edwardsiella piscicida-induced lethal enteritis in big-belly seahorses: Novel insights into the role of Carbohydrate-Active enzymes and host transcriptional responses

Edwardsiella piscicida-induced lethal enteritis is a major threat to the sustainable development of seahorse aquaculture. The roles of Carbohydrate-Active enzymes (CAZymes) in interactions between the pathogen and the host are poorly understood. In this study, we found that 22 key CAZymes encoded by E. piscicida might involve in the coordination of five key stages of infection. Specifically, during the motility, adherence, and invasion stages, 10 CAZymes, including CE4, PL8, and CBM48, may significantly increase the activities of Lipid metabolism-associated pathways of the intestinal microbiota (P < 0.01), facilitating pathogen invasion of the host intestinal epithelium. During the replication stage, 11 CAZymes, including GH20, GT4, and GH3, may significantly increase activities of pathways associated with Carbohydrate metabolism (P < 0.01) to promote replication and proliferation of the pathogen. And for avoiding host defenses, GH2 and GH1 may enhance activities of both Carbohydrate and Amino acid metabolic pathways (P < 0.01), facilitating infection and immune evasion. Conjoint analysis showed that E. piscicida might mainly rely on Carbohydrate metabolism for infection, while the host might activate Amino acid metabolic pathways for self-defense. In addition, expressions of 10 key genes, Aldh9a1b, Aoc1, Tpi1b, PCK1, Ldha, Me1, Gla, Cel.2, Ugdh, and Mao, were significantly altered (P < 0.01) and may be used for characterizing host responses to E. piscicida infection. Activities of both Glycolysis/Gluconeogenesis and Tryptophan metabolism were found oppositely changed (P < 0.01) between pathogen and host, respectively, representing the primary focuses of the competition. Overall, this study provides new insights into E. piscicida-mediated intestinal enteritis in fish for the first time from the perspective of CAZymes, as well as a theoretical reference for the prevention and control of these diseases in the aquaculture of seahorses and other fish.

A novel CBM serving as a module for efficiently decomposing xanthan by modifying the processivity of hydrolase

The inefficient decomposition of polysaccharides, particularly branched polysaccharides limits their large-scale industrial applications. Further understanding and modification of glycoside hydrolases (GHs) processivity is expected to overcome this limitation. Here, a novel xanthan-binding CBM (MiXBM), which was supposed to alter the processivity of GHs, was systematically characterized. Phylogeny and structure analyses indicated that MiXBM is closely related to putative polysaccharide side chain-binding modules. Quantitative binding assays further revealed that MiXBM probably has a high affinity for xanthan side chain via a variable loop site. Moreover, catalytic performance demonstrated that xanthanase chimeras containing MiXBM promote highly efficient hydrolysis of xanthan because of improved substrate accessibility. Notably, MiXBM was observed to enhance the processivity of xanthanase, owing to its high substrate affinity to the repeating unit xanthan. Furthermore, sequential hydrolysis of xanthan by xanthanases with varying processivity resulted in significantly increased hydrolytic efficiency and focused oligoxanthans array. These results expand understanding of CBM-substrate recognition and shed light on efficient degradation of other regularly branched polysaccharides using modified GHs.

Engineering Adhesion of the Probiotic Strain Escherichia coli Nissle to the Fungal Pathogen Candida albicans

Engineering live biotherapeutic products against fungal pathogens such as Candida albicans has been suggested as a means to tackle the increasing threat of fungal infections and the development of resistance to classical antifungal treatments. One important challenge in the design of live therapeutics is to control their localization inside the human body. The specific binding capability to target organisms or tissues would greatly increase their effectiveness by increasing the local concentration of effector molecules at the site of infection. In this study, we utilized surface display of carbohydrate binding domains to enable the probiotic E. coli Nissle 1917 to adhere specifically to the pathogenic yeast Candida albicans. Binding was quantified using a newly developed method based on the automated analysis of microscopic images. In addition to a rationally selected chitin binding domain, a synthetic peptide of identical length but distinct sequence also conferred binding. Efficient binding was specific to fungal hyphae, the invasive form of C. albicans, while the yeast form, as well as abiotic cellulose and PET particles, was only weakly recognized.

Thermobifida fusca Cel6B moves bidirectionally while processively degrading cellulose

BACKGROUND

Cellulose, an abundant biopolymer, has great potential to be utilized as a renewable fuel feedstock through its enzymatic degradation into soluble sugars followed by sugar fermentation into liquid biofuels. However, crystalline cellulose is highly resistant to hydrolysis, thus industrial-scale production of cellulosic biofuels has been cost-prohibitive to date. Mechanistic studies of enzymes that break down cellulose, called cellulases, are necessary to improve and adapt such biocatalysts for implementation in biofuel production processes. Thermobifida fusca Cel6B (TfCel6B) is a promising candidate for industrial use due to its thermostability and insensitivity to pH changes. However, mechanistic studies probing TfCel6B hydrolytic activity have been limited to ensemble-scale measurements.

RESULTS

We utilized optical tweezers to perform single-molecule, nanometer-scale measurements of enzyme displacement during cellulose hydrolysis by TfCel6B. Records featured forward motility on the order of 0.17 nm s-1 interrupted by backward motions and long pauses. Processive run lengths were on the order of 5 nm in both forward and backward directions. Motility records also showed rapid bidirectional displacements greater than 5 nm. Single-enzyme velocity and bulk ensemble activity were assayed on multiple crystalline cellulose allomorphs revealing that the degree of crystallinity and hydrogen bonding have disparate effects on the single-molecule level compared to the bulk scale. Additionally, we isolated and monitored the catalytic domain of TfCel6B and observed a reduction in velocity compared to the full-length enzyme that includes the carbohydrate-binding module. Applied force has little impact on enzyme velocity yet it readily facilitates dissociation from cellulose. Preliminary measurements at elevated temperatures indicated enzyme velocity strongly increases with temperature.

CONCLUSIONS

The unexpected motility patterns of TfCel6B are likely due to previously unknown mechanisms of processive cellulase motility implicating irregularities in cellulose substrate ultrastructure. While TfCel6B is processive, it has low motility at room temperature. Factors that most dramatically impact enzyme velocity are temperature and the presence of its native carbohydrate-binding module and linker. In contrast, substrate ultrastructure and applied force did not greatly impact velocity. These findings motivate further study of TfCel6B for its engineering and potential implementation in industrial processes.

Discovery of a novel marine Bacteroidetes with a rich repertoire of carbohydrate-active enzymes

Members of the phylum Bacteroidetes play a key role in the marine carbon cycle through their degradation of polysaccharides via carbohydrate-active enzymes (CAZymes) and polysaccharide utilization loci (PULs). The discovery of novel CAZymes and PULs is important for our understanding of the marine carbon cycle. In this study, we isolated and identified a potential new genus of the family Catalimonadaceae, in the phylum Bacteroidetes, from the southwest Indian Ocean. Strain TK19036, the type strain of the new genus, is predicted to encode CAZymes that are relatively abundant in marine Bacteroidetes genomes. Tunicatimonas pelagia NBRC 107804T, Porifericola rhodea NBRC 107748T and Catalinimonas niigatensis NBRC 109829T, which exhibit 16 S rRNA similarities exceeding 90% with strain TK19036, and belong to the same family, were selected as reference strains. These organisms possess a highly diverse repertoire of CAZymes and PULs, which may enable them to degrade a wide range of polysaccharides, especially pectin and alginate. In addition, some secretory CAZymes in strain TK19036 and its relatives were predicted to be transported by type IX secretion system (T9SS). Further, to the best of our knowledge, we propose the first reported "hybrid" PUL targeting alginates in T. pelagia NBRC 107804T. Our findings provide new insights into the polysaccharide degradation capacity of marine Bacteroidetes, and suggest that T9SS may play a more important role in this process than previously believed.

Carbohydrate-binding module could integrate with ELISA and serve the simple and specific quantification of hyaluronic acid

Quantification is essential in the research and development of polysaccharides. However, achieving simplicity and specificity in polysaccharide quantification remains a challenging task. Enzyme-linked immunosorbent assay (ELISA) based on antibodies provides a straightforward and specific quantification strategy. Nevertheless, acquiring antibodies for polysaccharides is complicated. Carbohydrate-binding modules (CBMs), which can be efficiently obtained, exhibit the capability to specifically recognize and bind carbohydrates. In this study, we verified the feasibility of a CBM-based ELISA for the quantification of hyaluronic acid (HA) by replacing an antibody with a CBM. The CBM-based ELISA, which employed a HA-specific CBM, exhibited a linear detection range spanning from 10 to 100 μg/mL. Both intra-assay and inter-assay coefficients of variation remained below 15 % and recoveries ranged from 96.26 % to 98.22 %, indicating favorable precision and accuracy. The method exhibited specificity exclusively to HA, suggesting its reliance on CBM binding specificity. The effectiveness of the method in analyzing commercial products was confirmed. Additionally, a comparison with the carbazole assay revealed a highly significant correlation (r = 0.994). By integrating CBMs with ELISA, the study presented a novel and easily implementable solution for simple and specific quantification of HA while also highlighting the potential of this strategy to advance polysaccharide detection.

Biochemical and inhibitor analysis of recombinant cellobiohydrolases from Phanerochaete chrysosporium

The demand for greener energy sources necessitates the development of more efficient processes. Lignocellulosic biomass holds significant potential for biofuels production, but improvements in its enzymatic degradation are required to mitigate the susceptibility of enzymes by reaction products and pretreatment impurities. In this work, two cellobiohydrolases (CBHs) from the basidiomycete Phanerochaete chrysosporium (PcCel7C and PcCel7D) were heterologously expressed, characterized, and analyzed in the presence of their products (glucose and cellobiose) and harmful compounds commonly found in industrial processes (phenolics), as well as their adsorption to lignin and cellulose. The enzymes exhibited an optimum temperature of 55 °C and displayed a pH profile similar to the model CBHI from Trichoderma reesei (TrCel7A). Activity decreased consistently for all CBHs in the presence of cellobiose, while glucose significantly impacted the basidiomycete CBHs. Phenolic compounds with a higher content of OH groups were found to be more detrimental to the enzymes, with the location of the OH group on the phenolic ring playing a crucial role in enzyme deactivation. Molecular docking simulations predicted that the product-binding site of CBHs has the highest affinity for interaction with phenolics; however, they are unlikely to interact at this site in the presence of substrate. PcCel7C and PcCel7D exhibited poorer adsorption on cellulose compared to the TrCel7A enzyme. These findings provide insights into how the structure of CBHs influences their susceptibility to inhibitors and deactivating compounds present in saccharification reaction medium.

Characterization of a novel multifunctional glycoside hydrolase family in the metagenome-assembled genomes of horse gut

The gut microbiota is a treasure trove of carbohydrate-active enzymes (CAZymes). To explore novel and efficient CAZymes, we analyzed the 4,142 metagenome-assembled genomes (MAGs) of the horse gut microbiota and found the MAG117.bin13 genome (Bacteroides fragilis) contains the highest number of polysaccharide utilisation loci sites (PULs), indicating its high capability for carbohydrate degradation. Bioinformatics analysis indicate that the PULs region of the MAG117.bin13 genome encodes many hypothetical proteins, which are important sources for exploring novel CAZymes. Interestingly, we discovered a hypothetical protein (595 amino acids). This protein exhibits potential CAZymes activity and has a lower similarity to CAZymes, we named it BfLac2275. We purified the protein using prokaryotic expression technology and studied its enzymatic function. The hydrolysis experiment of the polysaccharide substrate showed that the BfLac2275 protein has the ability to degrade α-lactose (156.94 U/mg), maltose (92.59 U/mg), raffinose (86.81 U/mg), and hyaluronic acid (5.71 U/mg). The enzyme activity is optimal at pH 5.0 and 30 ℃, indicating that the hypothetical protein BfLac2275 is a novel and multifunctional CAZymes in the glycoside hydrolases (GHs). These properties indicate that BfLac2275 has broad application prospects in many fields such as plant polysaccharide decomposition, food industry, animal feed additives and enzyme preparations. This study not only serves as a reference for exploring novel CAZymes encoded by gut microbiota but also provides an example for further studying the functional annotation of hypothetical genes in metagenomic assembly genomes.

Structural Analysis of Mammalian Sialic Acid Esterase

Sialic acid esterase (SIAE) catalyzes the removal of O-acetyl groups from sialic acids found on cell surface glycoproteins to regulate cellular processes such as B cell receptor signalling and apoptosis. Loss-of-function mutations in SIAE are associated with several common autoimmune diseases including Crohn's, ulcerative colitis, and arthritis. To gain a better understanding of the function and regulation of this protein, we determined crystal structures of SIAE from three mammalian homologs, including an acetate bound structure. The structures reveal that the catalytic domain adopts the fold of the SGNH hydrolase superfamily. The active site is composed of a catalytic dyad, as opposed to the previously reported catalytic triad. Attempts to determine a substrate-bound structure yielded only the hydrolyzed product acetate in the active site. Rigid docking of complete substrates followed by molecular dynamics simulations revealed that the active site does not form specific interactions with substrates, rather it appears to be broadly specific to accept sialoglycans with diverse modifications. Based on the acetate bound structure, a catalytic mechanism is proposed. Structural mapping of disease mutations reveals that most are located on the surface of the enzyme and would only cause minor disruptions to the protein fold, suggesting that these mutations likely affect binding to other factors. These results improve our understanding of SIAE biology and may aid in the development of therapies for autoimmune diseases and cancer.

Structural insight into sugar-binding modes of microbial ß-amylase

ß-Amylase, which catalyses the release of ß-anomeric maltose from the non-reducing end of starch, is widely used in the food industry. Increasing its enzyme activity through protein engineering might improve the efficiency of food processing. To obtain detailed structural information to assist rationale design, here the crystal structure of Bacillus cereus β-amylase (BCB) complexed with maltose was determined by molecular replacement and refined using anisotropic temperature factors to 1.26 Å resolution with Rwork/Rfree factors of 12.4/15.7 %. The structure contains six maltose and one glucose molecules, of which two maltose and one glucose are bound at sites not previously observed in BCB structures. These three new sugar-binding sites are located on the surface and likely to be important in enhancing the degradation of raw-starch granules. In the active site of BCB, two maltose molecules are bound in tandem at subsites -2 ∼ -1 and +1 ∼ +2. Notably, the conformation of the glucose moiety bound at subsite -1 is a mixture of α-anomeric distorted 1,4B boat and 4C1 chair forms, while those at subsites -2, +1 ∼ +2 are all in the 4C1 chair forms. The O1 of the distorted α-glucose residue at subsite -1 occupies the position of the putative catalytic water, forming a hydrogen bond with OE1 of Glu367 (base catalyst), suggesting that this distorted sugar is not involved in catalysis. Together, these findings pave the way for further improving the functionality of microbial ß-amylase enzymes.

Termites and subsocial roaches inherited many bacterial-borne carbohydrate-active enzymes (CAZymes) from their common ancestor

Termites digest wood using Carbohydrate-Active Enzymes (CAZymes) produced by gut bacteria with whom they have cospeciated at geological timescales. Whether CAZymes were encoded in the genomes of their ancestor's gut bacteria and transmitted to modern termites or acquired more recently from bacteria not associated with termites is unclear. We used gut metagenomes from 195 termites and one Cryptocercus, the sister group of termites, to investigate the evolution of termite gut bacterial CAZymes. We found 420 termite-specific clusters in 81 bacterial CAZyme gene trees, including 404 clusters showing strong cophylogenetic patterns with termites. Of the 420 clusters, 131 included at least one bacterial CAZyme sequence associated with Cryptocercus or Mastotermes, the sister group of all other termites. Our results suggest many bacterial CAZymes have been encoded in the genomes of termite gut bacteria since termite origin, indicating termites rely upon many bacterial CAZymes endemic to their guts to digest wood.

Enhancement of the activity of a porphyranase by fusing a polymerization-inducing domain

Porphyra is one of the most economically valuable species of red algae, with porphyran being its primary bioactive polysaccharide. Highly active enzymes play a significant role in the research and development of porphyran. This study identified a PKD domain within a polysaccharide-binding protein, displaying an apparent molecular weight (Mw) of 20.20 kDa that is approximately twice the theoretical value, thereby suggesting the possibility of self-aggregation. By fusing it with porphyranase Por16B_Wf, a chimeric enzyme PKD-Por16B was constructed. It was confirmed that the fusion enzyme successfully assembles into an aggregation under the mediation of PKD domain, with its apparent Mw (65.13 kDa) significantly higher than theoretical Mw (46.02 kDa). The activity of PKD-Por16B was remarkably enhanced from 65.31 U/mg to 325.69 U/mg, accompanied by an improvement in enzymatic stability. Meanwhile, the hydrolysis pattern of PKD-Por16B remained unaltered in comparison to that of Por16B_Wf, indicating no significant deviation in its substrate specificity or reaction mechanism. These results suggest the feasibility of a strategy based on domain-induced aggregation to enhance enzyme activity, which is easy and economical.

Development of a carbohydrate-binding protein prediction algorithm using structural features of stacking aromatic rings

Carbohydrate-protein interactions play fundamental roles in numerous aspects of biological activities, and the search for new carbohydrate (CHO)-binding proteins (CBPs) has long been a research focus. In this study, through the analysis of CBP structures, we identified significant enrichment of aromatic residues in CHO-binding regions. We further summarized the structural features of these aromatic rings within the CHO-stacking region, namely "exposing" and "proximity" features, and developed a screening algorithm that can identify CHO-stacking Trp (tryptophan) residues based on these two features. Our Trp screening algorithm can achieve high accuracy in both CBP (specificity score 0.93) and CBS (Carbohydrate binding site, precision score 0.77) prediction using experimentally determined protein structures. We also applied our screening algorithm on AlphaGO pan-species predicted models and observed significant enrichment of carbohydrate-related functions in predicted CBP candidates across different species. Moreover, through carbohydrate arrays, we experimentally verified the CHO-binding ability of four candidate proteins, which further confirms the robustness of the algorithm. This study provides another perspective on proteome-wide CBP and CBS prediction. Our results not only help to reveal the structural mechanism of CHO-binding, but also provide a pan-species CBP dataset for future CHO-protein interaction exploration.

Unique Fn3-like biosensor in σI/anti-σI factors for regulatory expression of major cellulosomal scaffoldins in Pseudobacteroides cellulosolvens

Lignocellulolytic clostridia employ multiple pairs of alternative σ/anti-σ (SigI/RsgI) factors to regulate cellulosomal components for substrate-specific degradation of cellulosic biomass. The current model has proposed that RsgIs use a sensor domain to bind specific extracellular lignocellulosic components and activate cognate SigIs to initiate expression of corresponding cellulosomal enzyme genes, while expression of scaffoldins can be initiated by several different SigIs. Pseudobacteroides cellulosolvens contains the most complex known cellulosome system and the highest number of SigI-RsgI regulons yet discovered. However, the function of many RsgI sensor domains and their relationship with the various enzyme types are not fully understood. Here, we report that RsgI4 from P. cellulosolvens employs a C-terminal module that bears distant similarity to the fibronectin type III (Fn3) domain and serves as the sensor domain. Substrate-binding analysis revealed that the Fn3-like domain of RsgI4 represents a novel carbohydrate-binding module (CBM) that binds to a wide range of polysaccharide types. Structure determination further revealed that the Fn3-like domain belongs to the type B group of CBMs with a predicted concave face for substrate binding. Promoter sequence analysis of cellulosomal genes revealed that SigI4 is responsible for cellulosomal regulation of major scaffoldins rather than enzymes, consistent with the broad substrate specificity of the RsgI4 sensor domain. Notably, scaffoldins are invariably required as cellulosome components regardless of the substrate type. These findings suggest that the intricate cellulosome system of P. cellulosolvens comprises a more elaborate regulation mechanism than other bacteria and thus expands the paradigm of cellulosome regulation.

Advances in molecular enzymology of β-1,3-glucanases: A comprehensive review

β-1,3-Glucanases are essential enzymes involved in the hydrolysis of β-1,3-glucans, with significant biological and industrial relevance. These enzymes are derived from diverse sources, including bacteria, fungi, plants, and animals, each exhibiting unique substrate specificities and biochemical properties. This review provides an in-depth analysis of the natural sources and ecological roles of β-1,3-glucanases, exploring their enzymatic properties such as optimal pH, temperature, molecular weight, isoelectric points, and kinetic parameters, which are crucial for understanding their functionality and stability. Advances in molecular enzymology are discussed, focusing on gene cloning, expression in systems like Escherichia coli and Pichia pastoris, and structural-functional relationships. The reaction mechanisms and the role of non-catalytic carbohydrate-binding modules in enhancing substrate hydrolysis are examined. Industrial applications of β-1,3-glucanases are highlighted, including the production of β-1,3-glucooligosaccharides, uses in the food industry, biological control of plant pathogens, and nutritional roles. This review aims to provide a foundation for future research, improving the efficiency and robustness of β-1,3-glucanases for various industrial applications.

Identification of new targets for the diagnosis of cysts (four) and trophozoites (one) of the eye pathogen Acanthamoeba

Acanthamoebae , which are free-living amoebae, cause corneal inflammation (keratitis) and blindness, if not diagnosed and effectively treated. While trophozoites adhere to and damage the cornea, Acanthamoeba cysts, the walls of which contain cellulose and have two layers connected by conical ostioles, are the diagnostic form by microscopy of the eye or of corneal scrapings. We recently used structural and experimental methods to characterize cellulose-binding domains of Luke and Leo lectins, which are abundant in the inner layer and ostioles. However, no antibodies have been made to these lectins or to a Jonah lectin and a laccase, which are abundant in the outer layer. Here we used confocal microscopy to show that rabbit antibodies to recombinant Luke, Leo, Jonah, and laccase generally support localizations of GFP-tagged proteins in walls of transfected Acanthamoebae. Rabbit antibodies to all four wall proteins efficiently detected calcofluor white-labeled cysts of 10 of 11 Acanthamoeba isolates obtained from the ATCC, including five T4 genotypes that cause most cases of keratitis. Laccase shed into the medium during encystation was detected by an enzyme-linked immunoassay. We also used structural and experimental methods to characterize the mannose-binding domain of an Acanthamoeba mannose-binding protein and showed that rabbit antibodies to the mannose-binding domain efficiently detected trophozoites of all 11 Acanthamoeba isolates. We conclude that four wall proteins are all excellent targets for diagnosing Acanthamoeba cysts in the eye or corneal scrapings, while the mannose-binding domain is an excellent target for identifying trophozoites in cultures of corneal scrapings.

Importance

Free-living amoeba in the soil or water cause Acanthamoeba keratitis, which is diagnosed by identification of cysts by microscopy of the eye or of corneal scrapings, using calcofluor-white that unfortunately cross-reacts with fungi and plants. Alternatively, Acanthamoeba infections are diagnosed by identification of trophozoites in cultures of scrapings. Here we showed that rabbit antibodies to four abundant cyst wall proteins (Jonah, Luke, Leo, and laccase) each efficiently detect calcofluor-white-labeled cysts of 10 of 11 Acanthamoeba isolates obtained from the ATCC. Further, laccase released into the medium by encysting Acanthamoebae was detected by an enzyme-linked immunoassay. We also showed that rabbit antibodies to the mannose-binding domain of the Acanthamoeba mannose-binding protein, which mediates adherence of trophozoites to keratinocytes, efficiently identifies trophozoites of all 11 ATCC isolates. In summary, four wall proteins and the ManBD appear to be excellent targets for diagnosis of Acanthamoeba cysts and trophozoites, respectively.

Characterization and structural identification of a novel alginate-specific carbohydrate-binding module (CBM): The founding member of a new CBM family

Alginate is a commercially important polysaccharide widely distributed in brown algae. Carbohydrate-binding modules (CBMs), a class of commonly used polysaccharide-binding proteins, have greatly facilitated the investigations of polysaccharides. Few alginate-binding CBMs have been hitherto reported and structurally characterized. Herein, an unknown domain from a potential PL6 family alginate lyase in the marine bacterium Vibrio breoganii was discovered and recombinantly expressed. The obtained protein, designated VbCBM106, displayed the favorable specificity to alginate. The unique sequence and well-defined function of VbCBM106 reveal a new CBM family (CBM106). Moreover, the structure of VbCBM106 was determined at a 1.5 Å resolution by the X-ray crystallography, which shows a typical β-sandwich fold comprised of two antiparallel β-sheets. Site-directed mutagenesis assays confirmed that positively charged polar residues are crucial for the ligand binding of VbCBM106. The discovery of VbCBM106 enriches the toolbox of alginate-binding proteins, and the elucidation of critical residues would guide the future practical applications of VbCBM106.

Comparative biochemistry of PET hydrolase-carbohydrate-binding module fusion enzymes on a variety of PET substrates

Enzyme-driven recycling of PET has now become a fully developed industrial process. With the right pre-treatment, PET can be completely depolymerized within workable timeframes. This has been realized due to extensive research conducted over the past decade, resulting in a large set of engineered PET hydrolases. Among various engineering strategies to enhance PET hydrolases, fusion with binding domains has been used to tune affinity and boost activity of the enzymes. While fusion enzymes have demonstrated higher activity in many cases, these results are primarily observed under conditions that would not be economically viable at scale. Furthermore, the wide variation in PET substrates, conditions, and combinations of PET hydrolases and binding domains complicates direct comparisons. Here, we present a self-consistent and thorough analysis of two leading PET hydrolases, LCCICCG and PHL7. Both enzymes were evaluated both without and with a substrate-binding domain across a range of industrially relevant PET substrates. We demonstrate that the presence of a substrate-binding module does not significantly affect the affinity of LCCICCG and PHL7 for PET. However, significant differences exist in how the fusion enzymes act on different PET substrates and solid substrate loading, ranging from a 3-fold increase in activity to a 6-fold decrease. These findings could inform the tailoring of enzyme choice to different industrial scenarios.

Cellulose binding and the timing of expression influence protein targeting to the double-layered cyst wall of Acanthamoeba

The cyst wall of the eye pathogen Acanthamoeba castellanii contains cellulose and has ectocyst and endocyst layers connected by conical ostioles. Cyst walls contain families of lectins that localize to the ectocyst layer (Jonah) or the endocyst layer and ostioles (Luke and Leo). How lectins and an abundant laccase bind cellulose and why proteins go to locations in the wall are not known and are the focus of the studies here. Structural predictions identified β-jelly-roll folds (BJRFs) of Luke and sets of four disulfide knots (4DKs) of Leo, each of which contains linear arrays of aromatic amino acids, also present in carbohydrate-binding modules of bacterial and plant endocellulases. Ala mutations showed that these aromatics are necessary for cellulose binding and proper localization of Luke and Leo in the Acanthamoeba cyst wall. BJRFs of Luke, 4DKs of Leo, a single β-helical fold (BHF) of Jonah, and a copper oxidase domain of the laccase each bind to glycopolymers in both layers of deproteinated cyst walls. Promoter swaps showed that ectocyst localization does not just correlate with but is caused by early encystation-specific expression, while localization in the endocyst layer and ostioles is caused by later expression. Evolutionary studies showed distinct modes of assembly of duplicated domains in Luke, Leo, and Jonah lectins and suggested Jonah BHFs originated from bacteria, Luke BJRFs share common ancestry with slime molds, while 4DKs of Leo are unique to Acanthamoeba.IMPORTANCEAcanthamoebae is the only human parasite with cellulose in its cyst wall and conical ostioles that connect its inner and outer layers. Cyst walls are important virulence factors because they make Acanthamoebae resistant to surface disinfectants, hand sanitizers, contact lens sterilizers, and antibiotics applied to the eye. The goal here was to understand better how proteins are targeted to specific locations in the cyst wall. To this end, we identified three new proteins in the outer layer of the cyst wall, which may be targets for diagnostic antibodies in corneal scrapings. We used structural predictions and mutated proteins to show linear arrays of aromatic amino acids of two unrelated wall proteins are necessary for binding cellulose and proper wall localization. We showed early expression during encystation causes proteins to localize to the outer layer, while later expression causes proteins to localize to the inner layer and the ostioles.

Hydrolysis Mechanism of Multimodular Endoglucanases with Distinctive Domain Composition in the Saccharification of Cellulosic Substrates

Two multimodular endoglucanases in glycoside hydrolase family 5, ReCel5 and ElCel5, share 73% identity and exhibit similar modular structures: family 1 carbohydrate-binding module (CBM1); catalytic domain; CBMX2; module of unknown function. However, they differed in their biochemical properties and catalytic performance. ReCel5 showed optimal activity at pH 4.0 and 70 °C, maintaining stability at 70 °C (>80% activity). Conversely, ElCel5 is optimal at pH 3.0 and 50 °C (>50% activity at 50 °C). ElCel5 excels in degrading CMC-Na (256 U/mg vs 53 U/mg of ReCel5). Five domain-truncated (TM1-TM5) and four domain-replaced (RM1-RM4) mutants of ReCel5 with the counterparts of ElCel5 were constructed, and their enzymatic properties were compared with those of the wild type. Only RM1, with ElCel5-CBM1, displayed enhanced thermostability and activity. The hydrolysis of pretreated corn stover was reduced in most TM and RM mutants. Molecular dynamics simulations revealed interdomain interactions within the multimodular endoglucanase, potentially affecting its structural stability and complex biological catalytic processes.

In vitro and ex vivo metabolism of chemically diverse fructans by bovine rumen Bifidobacterium and Lactobacillus species

BACKGROUND

Inulin and inulin-derived fructooligosaccharides (FOS) are well-known prebiotics for use in companion animals and livestock. The mechanisms by which FOS contribute to health has not been fully established. Further, the fine chemistry of fructan structures from diverse sources, such as graminan-type fructans found in cereal crops, has not been fully elucidated. New methods to study fructan structure and microbial responses to these complex carbohydrates will be key for evaluating the prebiotic potency of cereal fructans found in cattle feeds. As the rumen microbiome composition is closely associated with their metabolic traits, such as feed utilization and waste production, prebiotics and probiotics represent promising additives to shift the microbial community toward a more productive state.

RESULTS

Within this study, inulin, levan, and graminan-type fructans from winter wheat, spring wheat, and barley were used to assess the capacity of rumen-derived Bifidobacterium boum, Bifidobacterium merycicum, and Lactobacillus vitulinus to metabolize diverse fructans. Graminan-type fructans were purified and structurally characterized from the stems and kernels of each plant. All three bacterial species grew on FOS, inulin, and cereal crop fructans in pure cultures. L. vitulinus was the only species that could metabolize levan, albeit its growth was delayed. Fluorescently labelled polysaccharides (FLAPS) were used to demonstrate interactions with Gram-positive bacteria and confirm fructan metabolism at the single-cell level; these results were in agreement with the individual growth profiles of each species. The prebiotic potential of inulin was further investigated within naïve rumen microbial communities, where increased relative abundance of Bifidobacterium and Lactobacillus species occurred in a dose-dependent and temporal-related manner. This was supported by in situ analysis of rumen microbiota from cattle fed inulin. FLAPS probe derived from inulin and fluorescent in situ hybridization using taxon-specific probes confirmed that inulin interacts with Bifidobacteria and Lactobacilli at the single-cell level.

CONCLUSION

This research revealed that rumen-derived Bifidobacteria and Lactobacilli vary in their metabolism of structurally diverse fructans, and that inulin has limited prebiotic potential in the rumen. This knowledge establishes new methods for evaluating the prebiotic potential of fructans from diverse plant sources as prebiotic candidates for use in ruminants and other animals.

Investigating Cellulose Binding of Peptides Derived from Carbohydrate Binding Module 1

Carbohydrate-binding modules (CBM) have emerged as useful tools for a wide range of tasks, including the use as purification tags or for cellulose fiber modification. For this purpose, the CBM needs to be attached to a target protein leading to large constructs. We investigated if short peptides from the carbohydrate binding site of CBMs can bind in a similar way as native, full-length CBMs to nanocrystalline cellulose (NCC) or cotton linter paper. We designed our cellulose-binding peptides to be less hydrophobic and shorter than those previously reported. Starting from the binding site of Cel7A-CBM1, we incorporated the essential amino acids involved in cellulose binding into our peptides. These peptides, as well as control peptides with scrambled sequences or a lack of essential amino acids, bound to cellulose with similar affinity as CBM regardless of their secondary structure, sequence, or hydrophobicity. This unspecific mode of cellulose binding displayed by the presented peptides may be exploited to functionalize cellulose-based biomaterials by means of peptide-conjugates.

Streptomyces small laccase expressed in Aspergillus Niger as a new addition for the lignocellulose bioconversion toolbox

Laccases are multi-copper oxidases that are usually composed of three Cu-oxidase domains. Domains one and three house the copper binding sites, and the second domain is involved in forming a substrate-binding cleft. However, Streptomyces species are found to have small laccases (SLAC) that lack one of the three Cu-oxidase domains. This type of SLAC with interesting lignocellulose bioconversion activities has not been reported in Aspergillus niger. In our research, we explored the expression and engineering of the SLAC from Streptomyces leeuwenhoekii C34 in A. niger. Genes encoding two versions of the SLAC were expressed. One encoding the SLAC in its native form and a second encoding the SLAC fused to two N-terminal CBM1 domains. The latter is a configuration also known for specific yeast laccases. Both SLAC variants were functionally expressed in A. niger as shown by in vitro activity assays and proteome analysis. Laccase activity was also analyzed toward bioconversion of lignocellulosic rice straw. From this analysis it was clear that the SLAC activity improved the efficiency of saccharification of lignocellulosic biomass by cellulase enzyme cocktails.

Chemical mapping of xyloglucan distribution and cellulose crystallinity in cotton textiles reveals novel enzymatic targets to improve clothing longevity

Pilling is a form of textile mechanical damage, forming fibrous bobbles on the surface of garments, resulting in premature disposal of clothing by consumers. However, our understanding on how the structural properties of the cellulosic matrix compliment the three-dimensional shape of cotton pills remains limited. This knowledge gap has hindered the development of effective 'pillase' technologies over the past 20 years due to challenges in balancing depilling efficacy with fabric integrity preservation. Therefore, the main focus here was characterising the role of cellulose and the hemicellulose components in cotton textiles to elucidate subtle differences between the chemistry of pills and fibre regions involved in structural integrity. State-of-the-art bioimaging using carbohydrate binding modules, monoclonal antibodies, and Leica SP8 and a Nikon A1R confocal microscopes, revealed the biophysical structure of cotton pills for the first time. Identifying regions of increased crystalline cellulose in the base of anchor fibres and weaker amorphous cellulose at dislocations in their centres, enhancing our understanding of current enzyme specificity. Surprisingly, pills contained a 7-fold increase in the concentration of xyloglucan compared to the main textile. Therefore, xyloglucan offers a previously undescribed target for overcoming this benefit-to-risk paradigm, suggesting a role for xyloglucanase enzymes in future pillase systems.