Molecular characterization of a family 5 glycoside hydrolase suggests an induced-fit enzymatic mechanism

Structural insights into substrate recognition of tri-modular xyloglucanase from Aspergillus oryzae

Xeg5A from Aspergillus oryzae belongs to glycoside hydrolase family 5 subfamily 4. This enzyme has been characterized as a xyloglucan-specific endo-β-1,4-glucanase (xyloglucanase) that cleaves the main chain of xyloglucan at both unbranched and xylosylated glucosyl residues in an endo-processive mode of action. X-ray crystallography revealed that Xeg5A is a tri-modular enzyme composed of a catalytic, an Ig-like, and a C-terminal CBM46-like domains. Xeg5A structures complexed with branched xyloglucan oligosaccharides at subsite -4 to +4 showed that the recognition of xyloglucan side-chain moieties is important for Xeg5A activity. The crystal structure also provided structural insights into the role of the CBM46-like domain in contributing to regiospecificity and, possibly, processivity.

Biochemical characterization of a bilfunctional endoglucanase/glucomannanase derived from mountain soil

Metagenomics is increasingly recognized as a vital technique for exploring uncultured microorganisms, with one key application being the discovery of novel enzymes for industrial use. This study identified an endoglucanase gene from soil metagenome, termed ZFEG1801, which was expressed in E. coli BL21, purified, and characterized for its biochemical properties. The 72.8 kDa recombinant protein exhibited hydrolytic activity against sodium carboxymethyl cellulose (CMC) and konjac glucomannan (KG), with activities of 12.1 U/mg and 42.1 U/mg, respectively. The enzyme displayed optimal activity at pH 5 for CMC and pH 6 for KG, with broad pH stability ranging from 5 to 9. The optimal temperature was 40 °C, and it remained thermally stable between 20 and 40 °C, retaining over 60% of its activity. The enzyme activity remained stable in the presence of most metal ions; however, CMCase activity was inhibited by Cu2+, while glucomannanase activity was inhibited by Mn2+, Fe3+, and Ca2+. The catalytic efficiency towards both substrates was reduced by addition of SDS, DMSO, ethanol, isopropanol and acetonitrile. The Vmax and Km of the purified recombinant enzyme were 106.4 μmol/L/min and 4.9 mg/mL for CMC, and 833.3 μmol/L/min and 11.1 mg/mL for KG, respectively. The dual catalytic properties of ZFEG1801, broad pH stability and resistance to additives, demonstrate its potential for use in various biomass degradation processes.

Selective utilization of medicinal polysaccharides by human gut Bacteroides and Parabacteroides species

Human gut Bacteroides and Parabacteroides species play crucial roles in human health and are known for their capacity to utilize diverse polysaccharides. Understanding how these bacteria utilize medicinal polysaccharides is foundational for developing polysaccharides-based prebiotics and drugs. Here, we systematically mapped the utilization profiles of 20 different medicinal polysaccharides by 28 human gut Bacteroides and Parabacteroides species. The growth profiles exhibited substantial variation across different bacterial species and medicinal polysaccharides. Ginseng polysaccharides promoted the growth of multiple Bacteroides and Parabacteroides species; in contrast, Dendrobium polysaccharides selectively promoted the growth of Bacteroides uniformis. This distinct utilization profile was associated with genomic variation in carbohydrate-active enzymes, rather than monosaccharides composition variation among medicinal polysaccharides. Through comparative transcriptomics and genetical manipulation, we validated that the polysaccharide utilization locus PUL34_Bu enabled Bacteroides uniformis to utilize Dendrobium polysaccharides (i.e. glucomannan). In addition, we found that the GH26 enzyme in PUL34_Bu allowed Bacteroides uniformis to utilize multiple plant-derived mannan. Overall, our results revealed the selective utilization of medicinal polysaccharide by Bacteroides and Parabacteroides species and provided insights into the use of polysaccharides in engineering the human gut microbiome.

Dataset from a human-in-the-loop approach to identify functionally important protein residues from literature

We present a novel system that leverages curators in the loop to develop a dataset and model for detecting structure features and functional annotations at residue-level from standard publication text. Our approach involves the integration of data from multiple resources, including PDBe, EuropePMC, PubMedCentral, and PubMed, combined with annotation guidelines from UniProt, and LitSuggest and HuggingFace models as tools in the annotation process. A team of seven annotators manually curated ten articles for named entities, which we utilized to train a starting PubmedBert model from HuggingFace. Using a human-in-the-loop annotation system, we iteratively developed the best model with commendable performance metrics of 0.90 for precision, 0.92 for recall, and 0.91 for F1-measure. Our proposed system showcases a successful synergy of machine learning techniques and human expertise in curating a dataset for residue-level functional annotations and protein structure features. The results demonstrate the potential for broader applications in protein research, bridging the gap between advanced machine learning models and the indispensable insights of domain experts.

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.

A systematic analysis of marine lysogens and proviruses

Viruses are ubiquitous in the oceans, exhibiting high abundance and diversity. Here, we systematically analyze existing genomic sequences of marine prokaryotes to compile a Marine Prokaryotic Genome Dataset (MPGD, consisting of over 12,000 bacterial and archaeal genomes) and a Marine Temperate Viral Genome Dataset (MTVGD). At least 40% of the MPGD genomes contain one or more proviral sequences, indicating that they are lysogens. The MTVGD includes over 12,900 viral contigs or putative proviruses, clustered into 10,897 viral genera. We show that lysogens and proviruses are abundant in marine ecosystems, particularly in the deep sea, and marine lysogens differ from non-lysogens in multiple genomic features and growth properties. We reveal several virus-host interaction networks of potential ecological relevance, and identify proviruses that appear to be able to infect (or to be transferred between) different bacterial classes and phyla. Auxiliary metabolic genes in the MTVGD are enriched in functions related to carbohydrate metabolism. Finally, we experimentally demonstrate the impact of a prophage on the transcriptome of a representative marine Shewanella bacterium. Our work contributes to a better understanding of the ecology of marine prokaryotes and their viruses.

Feasibility insights into the application of Paenibacillus pabuli E1 in animal feed to eliminate non-starch polysaccharides

The goal of the research was to find alternative protein sources for animal farming that are efficient and cost-effective. The researchers focused on distillers dried grains with solubles (DDGS), a co-product of bioethanol production that is rich in protein but limited in its use as a feed ingredient due to its high non-starch polysaccharides (NSPs) content, particularly for monogastric animals. The analysis of the Paenibacillus pabuli E1 genome revealed the presence of 372 genes related to Carbohydrate-Active enzymes (CAZymes), with 98 of them associated with NSPs degrading enzymes that target cellulose, hemicellulose, and pectin. Additionally, although lignin is not an NSP, two lignin-degrading enzymes were also examined because the presence of lignin alongside NSPs can hinder the catalytic effect of enzymes on NSPs. To confirm the catalytic ability of the degrading enzymes, an in vitro enzyme activity assay was conducted. The results demonstrated that the endoglucanase activity reached 5.37 U/mL, while beta-glucosidase activity was 4.60 U/mL. The filter paper experiments did not detect any reducing sugars. The xylanase and beta-xylosidase activities were measured at 11.05 and 4.16 U/mL, respectively. Furthermore, the pectate lyase and pectin lyase activities were found to be 8.19 and 2.43 U/mL, respectively. The activities of laccase and MnP were determined as 1.87 and 4.30 U/mL, respectively. The researchers also investigated the effect of P. pabuli E1 on the degradation of NSPs through the solid-state fermentation of DDGS. After 240 h of fermentation, the results showed degradation rates of 11.86% for hemicellulose, 11.53% for cellulose, and 8.78% for lignin. Moreover, the crude protein (CP) content of DDGS increased from 26.59% to 30.59%. In conclusion, this study demonstrated that P. pabuli E1 possesses various potential NSPs degrading enzymes that can effectively eliminate NSPs in feed. This process improves the quality and availability of the feed, which is important for animal farming as it seeks alternative protein sources to replace traditional nutrients.

Biochemical and structural characterisation of a family GH5 cellulase from endosymbiont of shipworm P. megotara

BACKGROUND

Cellulases play a key role in the enzymatic conversion of plant cell-wall polysaccharides into simple and economically relevant sugars. Thus, the discovery of novel cellulases from exotic biological niches is of great interest as they may present properties that are valuable in the biorefining of lignocellulosic biomass.

RESULTS

We have characterized a glycoside hydrolase 5 (GH5) domain of a bi-catalytic GH5-GH6 multi-domain enzyme from the unusual gill endosymbiont Teredinibacter waterburyi of the wood-digesting shipworm Psiloteredo megotara. The catalytic GH5 domain, was cloned and recombinantly produced with or without a C-terminal family 10 carbohydrate-binding module (CBM). Both variants showed hydrolytic endo-activity on soluble substrates such as β-glucan, carboxymethylcellulose and konjac glucomannan, respectively. However, low activity was observed towards the crystalline form of cellulose. Interestingly, when co-incubated with a cellulose-active LPMO, a clear synergy was observed that boosted the overall hydrolysis of crystalline cellulose. The crystal structure of the GH5 catalytic domain was solved to 1.0 Å resolution and revealed a substrate binding cleft extension containing a putative + 3 subsite, which is uncommon in this enzyme family. The enzyme was active in a wide range of pH, temperatures and showed high tolerance for NaCl.

CONCLUSIONS

This study provides significant knowledge in the discovery of new enzymes from shipworm gill endosymbionts and sheds new light on biochemical and structural characterization of cellulolytic cellulase. Study demonstrated a boost in the hydrolytic activity of cellulase on crystalline cellulose when co-incubated with cellulose-active LPMO. These findings will be relevant for the development of future enzyme cocktails that may be useful for the biotechnological conversion of lignocellulose.

Structural and functional insights of the catalytic GH5 and Calx-β domains from the metagenome-derived endoglucanase CelE2

Cellulose is the most abundant natural polymer on Earth, representing an attractive feedstock for bioproducts and biofuel production. Cellulases promote the depolymerization of cellulose, generating short oligosaccharides and glucose, which are useful in biotechnological applications. Among the classical cellulases, those from glycoside hydrolase family 5 (GH5) are one of the most abundant in Nature, displaying several modular architectures with other accessory domains attached to its catalytic core, such as carbohydrate-binding modules (CBMs), Ig-like, FN3-like, and Calx-β domains, which can influence the enzyme activity. The metagenome-derived endoglucanase CelE2 has in its modular architecture an N-terminal domain belonging to the GH5 family and a C-terminal domain with a high identity to the Calx-β domain. In this study, the GH5 and the Calx-β domains were subcloned and heterologously expressed in E. coli, to evaluate the structural and functional properties of the individualized domains of CelE2. Thermostability analysis by circular dichroism (CD) revealed a decrease in the denaturation temperature values around 4.6 °C for the catalytic domain (CelE2_1-381) compared to CelE2 full-length. The CD analyses revealed that the Calx-β domain (CelE2_382-477) was unfolded, suggesting that this domain requires to be attached to the catalytic core to become structurally stable. The three-dimensional structure of the catalytic domain CelE2_1-381 was determined at 2.1 Å resolution, showing a typical (α/β)₈-barrel fold and a narrow active site compared to other cellulases from the same family. The biochemical characterization showed that the deletion of the Calx-β domain increased more than 3-fold the activity of the catalytic domain CelE2_1-381 towards the insoluble substrate Avicel. The main functional properties of CelE2, such as substrate specificity, optimal pH and temperature, thermal stability, and activation by CaCl_2, were not altered after the deletion of the accessory domain. Furthermore, the Small Angle X-ray Scattering (SAXS) analyses showed that the addition of CaCl₂ was beneficial CelE2_1-381 protein solvency. This work contributed to fundamental concepts about the structure and function of cellulases, which are useful in applications involving lignocellulosic materials degradation into food and feedstuffs and biofuel production.

Genetic Determinants of Fiber-Associated Traits in Flax Identified by Omics Data Integration

In this paper, we explore potential genetic factors in control of flax phenotypes associated with fiber by mining a collection of 306 flax accessions from the Federal Research Centre of the Bast Fiber Crops, Torzhok, Russia. In total, 11 traits were assessed in the course of 3 successive years. A genome-wide association study was performed for each phenotype independently using six different single-locus models implemented in the GAPIT3 R package. Moreover, we applied a multivariate linear mixed model implemented in the GEMMA package to account for trait correlations and potential pleiotropic effects of polymorphisms. The analyses revealed a number of genomic variants associated with different fiber traits, implying the complex and polygenic control. All stable variants demonstrate a statistically significant allelic effect across all 3 years of the experiment. We tested the validity of the predicted variants using gene expression data available for the flax fiber studies. The results shed new light on the processes and pathways associated with the complex fiber traits, while the pinpointed candidate genes may be further used for marker-assisted selection.

Unique properties of a Dictyostelium discoideum carbohydrate-binding module expand our understanding of CBM-ligand interactions

Deciphering how enzymes interact, modify, and recognize carbohydrates has long been a topic of interest in academic, pharmaceutical, and industrial research. Carbohydrate-binding modules (CBMs) are noncatalytic globular protein domains attached to carbohydrate-active enzymes that strengthen enzyme affinity to substrates and increase enzymatic efficiency via targeting and proximity effects. CBMs are considered auspicious for various biotechnological purposes in textile, food, and feed industries, representing valuable tools in basic science research and biomedicine. Here, we present the first crystallographic structure of a CBM8 family member (CBM8), DdCBM8, from the slime mold Dictyostelium discoideum, which was identified attached to an endo-β-1,4-glucanase (glycoside hydrolase family 9). We show that the planar carbohydrate-binding site of DdCBM8, composed of aromatic residues, is similar to type A CBMs that are specific for crystalline (multichain) polysaccharides. Accordingly, pull-down assays indicated that DdCBM8 was able to bind insoluble forms of cellulose. However, affinity gel electrophoresis demonstrated that DdCBM8 also bound to soluble (single chain) polysaccharides, especially glucomannan, similar to type B CBMs, although it had no apparent affinity for oligosaccharides. Therefore, the structural characteristics and broad specificity of DdCBM8 represent exceptions to the canonical CBM classification. In addition, mutational analysis identified specific amino acid residues involved in ligand recognition, which are conserved throughout the CBM8 family. This advancement in the structural and functional characterization of CBMs contributes to our understanding of carbohydrate-active enzymes and protein–carbohydrate interactions, pushing forward protein engineering strategies and enhancing the potential biotechnological applications of glycoside hydrolase accessory modules.

Thermophiles and carbohydrate-active enzymes (CAZymes) in biofilm microbial consortia that decompose lignocellulosic plant litters at high temperatures

The SKY hot spring is a unique site filled with a thick layer of plant litter. With the advancement of next-generation sequencing, it is now possible to mine many new biocatalyst sequences. In this study, we aimed to (i) identify the metataxonomic of prokaryotes and eukaryotes in microbial mats using 16S and 18S rRNA markers, (ii) and explore carbohydrate degrading enzymes (CAZymes) that have a high potential for future applications. Green microbial mat, predominantly photosynthetic bacteria, was attached to submerged or floating leaves litter. At the spring head, the sediment mixture consisted of plant debris, predominantly brownish-reddish gelatinous microbial mat, pale tan biofilm, and grey-white filament biofilm. The population in the spring head had a higher percentage of archaea and hyperthermophiles than the green mat. Concurrently, we cataloged nearly 10,000 sequences of CAZymes in both green and brown biofilms using the shotgun metagenomic sequencing approach. These sequences include β-glucosidase, cellulase, xylanase, α-N-arabinofuranosidase, α-l-arabinofuranosidase, and other CAZymes. In conclusion, this work elucidated that SKY is a unique hot spring due to its rich lignocellulosic material, often absent in other hot springs. The data collected from this study serves as a repository of new thermostable macromolecules, in particular families of glycoside hydrolases.

Fungal cellulases: protein engineering and post-translational modifications

Enzymatic degradation of lignocelluloses into fermentable sugars to produce biofuels and other biomaterials is critical for environmentally sustainable development and energy resource supply. However, there are problems in enzymatic cellulose hydrolysis, such as the complex cellulase composition, low degradation efficiency, high production cost, and post-translational modifications (PTMs), all of which are closely related to specific characteristics of cellulases that remain unclear. These problems hinder the practical application of cellulases. Due to the rapid development of computer technology in recent years, computer-aided protein engineering is being widely used, which also brings new opportunities for the development of cellulases. Especially in recent years, a large number of studies have reported on the application of computer-aided protein engineering in the development of cellulases; however, these articles have not been systematically reviewed. This article focused on the aspect of protein engineering and PTMs of fungal cellulases. In this manuscript, the latest literatures and the distribution of potential sites of cellulases for engineering have been systematically summarized, which provide reference for further improvement of cellulase properties. KEY POINTS: •Rational design based on virtual mutagenesis can improve cellulase properties. •Modifying protein side chains and glycans helps obtain superior cellulases. •N-terminal glutamine-pyroglutamate conversion stabilizes fungal cellulases.

Structural and biochemical insights into the substrate-binding mechanism of a glycoside hydrolase family 12 β-1,3-1,4-glucanase from Chaetomium sp

β-1,3-1,4-Glucanases are a type of hydrolytic enzymes capable of catalyzing the strict cleavage of β-1,4 glycosidic bonds adjacent to β-1,3 linkages in β-D-glucans and have exhibited great potential in food and feed industrials. In this study, a novel glycoside hydrolase (GH) family 12 β-1,3-1,4-glucanase (CtGlu12A) from the thermophilic fungus Chaetomium sp. CQ31 was identified and biochemically characterized. CtGlu12A was most active at pH 7.5 and 65 °C, respectively, and exhibited a high specific activity of 999.9 U mg^-1 towards lichenin. It maintained more than 80% of its initial activity in a wide pH range of 5.0-11.0, and up to 60 °C after incubation at 55 °C for 60 min. Moreover, the crystal structures of CtGlu12A with gentiobiose and tetrasccharide were resolved. CtGlu12A had a β-jellyroll fold, and performed retaining mechanism with two glutamic acids severing as the catalytic residues. In the complex structure, cellobiose molecule showed two binding modes, occupying subsites -2 to -1 and subsites + 1 to + 2, respectively. The concave cleft made mixed β-1,3-1,4-glucan substrates maintain a bent conformation to fit into the active site. Overall, this study is not only helpful for the understanding of the substrate-binding model and catalytic mechanism of GH 12 β-1,3-1,4-glucanases, but also provides a basis for further enzymatic engineering of β-1,3-1,4-glucanases.

ANALYSIS OF CARBOHYDRATES AND GLYCOCONJUGATES BY MATRIX-ASSISTED LASER DESORPTION/IONIZATION MASS SPECTROMETRY: AN UPDATE FOR 2015-2016

This review is the ninth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2016. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented over 30 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show no sign of deminishing. © 2020 Wiley Periodicals, Inc.

Identification and characterization of a novel glucomannanase from Paenibacillus polymyxa

Konjac glucomannan oligosaccharide has attracted much attention due to its broad biological activities. Specific glucomannan degrading enzymes are effective tools for the production of oligosaccharides from konjac glucomannan. However, there are still few reports of commercial enzymes that can specifically degrade konjac glucomannan. The gene ppgluB encoding a glucomannanase consisting of 553 amino acids (61.5 kDa) from Paenibacillus polymyxa 3-3 was cloned and heterologous expressed in Escherichia coli BL21 (DE3). The recombinant PpGluB showed high specificity for the degradation of konjac glucomannan. Moreover, the hydrolytic products of PpGluB degrade konjac glucomannan were a series of oligosaccharides with degrees of polymerisation of 2-12. Furthermore, the biochemical properties indicated that PpGluB is the optimal active at 45 to 55 °C and pH 5.0-6.0, and shows highly pH stability over a very broad pH range. The present characteristics indicated that PpGluB is a potential tool to be used to produce oligosaccharides from konjac glucomannan.

Carbohydrate Binding Modules: Diversity of Domain Architecture in Amylases and Cellulases From Filamentous Microorganisms

Enzymatic degradation of abundant renewable polysaccharides such as cellulose and starch is a field that has the attention of both the industrial and scientific community. Most of the polysaccharide degrading enzymes are classified into several glycoside hydrolase families. They are often organized in a modular manner which includes a catalytic domain connected to one or more carbohydrate-binding modules. The carbohydrate-binding modules (CBM) have been shown to increase the proximity of the enzyme to its substrate, especially for insoluble substrates. Therefore, these modules are considered to enhance enzymatic hydrolysis. These properties have played an important role in many biotechnological applications with the aim to improve the efficiency of polysaccharide degradation. The domain organization of glycoside hydrolases (GHs) equipped with one or more CBM does vary within organisms. This review comprehensively highlights the presence of CBM as ancillary modules and explores the diversity of GHs carrying one or more of these modules that actively act either on cellulose or starch. Special emphasis is given to the cellulase and amylase distribution within the filamentous microorganisms from the genera of Streptomyces and Aspergillus that are well known to have a great capacity for secreting a wide range of these polysaccharide degrading enzyme. The potential of the CBM and other ancillary domains for the design of improved polysaccharide decomposing enzymes is discussed.

High-resolution structure of a modular hyperthermostable endo-β-1,4-mannanase from Thermotoga petrophila: The ancillary immunoglobulin-like module is a thermostabilizing domain

The endo-β-1,4-mannanase from the hyperthermostable bacterium Thermotoga petrophila (TpMan) is an enzyme that catalyzes the hydrolysis of mannan and heteromannan polysaccharides. Of the three domains that comprise TpMan, the N-terminal GH5 catalytic domain and the C-terminal carbohydrate-binding domain are connected through a central ancillary domain of unknown structure and function. In this study, we report the partial crystal structure of the TpMan at 1.45 Å resolution, so far, the first modular hyperthermostable endo-β-1,4-mannanase structure determined. The structure exhibits two domains, a (β/α)₈-barrel GH5 catalytic domain connected via a linker to the central domain with an immunoglobulin-like β-sandwich fold formed of seven β-strands. Functional analysis showed that whereas the immunoglobulin-like domain does not have the carbohydrate-binding function, it stacks on the GH5 catalytic domain acting as a thermostabilizing domain and allowing operation at hyperthermophilic conditions. The carbohydrate-binding domain is absent in the crystal structure most likely due to its high flexibility around the immunoglobulin-like domain which may act also as a pivot. These results represent new structural and functional information useful on biotechnological applications for biofuel and food industries.

Extent and Origins of Functional Diversity in a Subfamily of Glycoside Hydrolases

Some glycoside hydrolases have broad specificity for hydrolysis of glycosidic bonds, potentially increasing their functional utility and flexibility in physiological and industrial applications. To deepen the understanding of the structural and evolutionary driving forces underlying specificity patterns in glycoside hydrolase family 5, we quantitatively screened the activity of the catalytic core domains from subfamily 4 (GH5_4) and closely related enzymes on four substrates: lichenan, xylan, mannan, and xyloglucan. Phylogenetic analysis revealed that GH5_4 consists of three major clades, and one of these clades, referred to here as clade 3, displayed average specific activities of 4.2 and 1.2 U/mg on lichenan and xylan, approximately 1 order of magnitude larger than the average for active enzymes in clades 1 and 2. Enzymes in clade 3 also more consistently met assay detection thresholds for reaction with all four substrates. We also identified a subfamily-wide positive correlation between lichenase and xylanase activities, as well as a weaker relationship between lichenase and xyloglucanase. To connect these results to structural features, we used the structure of CelE from Hungateiclostridium thermocellum (PDB 4IM4) as an example clade 3 enzyme with activities on all four substrates. Comparison of the sequence and structure of this enzyme with others throughout GH5_4 and neighboring subfamilies reveals at least two residues (H149 and W203) that are linked to strong activity across the substrates. Placing GH5_4 in context with other related subfamilies, we highlight several possibilities for the ongoing evolutionary specialization of GH5_4 enzymes.

SAXSMoW 2.0: Online calculator of the molecular weight of proteins in dilute solution from experimental SAXS data measured on a relative scale

Knowledge of molecular weight, oligomeric states, and quaternary arrangements of proteins in solution is fundamental for understanding their molecular functions and activities. We describe here a program SAXSMoW 2.0 for robust and quick determination of molecular weight and oligomeric state of proteins in dilute solution, starting from a single experimental small-angle scattering intensity curve, I(q), measured on a relative scale. The first version of this calculator has been widely used during the last decade and applied to analyze experimental SAXS data of many proteins and protein complexes. SAXSMoW 2.0 exhibits new features which allow for the direct input of experimental intensity curves and also automatic modes for quick determinations of the radius of gyration, volume, and molecular weight. The new program was extensively tested by applying it to many experimental SAXS curves downloaded from the open databases, corresponding to proteins with different shapes and molecular weights ranging from ~10 kDa up to about ~500 kDa and different shapes from globular to elongated. These tests reveal that the use of SAXSMoW 2.0 allows for determinations of molecular weights of proteins in dilute solution with a median discrepancy of about 12% for globular proteins. In case of elongated molecules, discrepancy value can be significantly higher. Our tests show discrepancies of approximately 21% for the proteins with molecular shape aspect ratios up to 18.

Biochemical characterization and low-resolution SAXS structure of two-domain endoglucanase BlCel9 from Bacillus licheniformis

Lignocellulose feedstock constitutes the most abundant carbon source in the biosphere; however, its recalcitrance remains a challenge for microbial conversion into biofuel and bioproducts. Bacillus licheniformis is a microbial mesophilic bacterium capable of secreting a large number of glycoside hydrolase (GH) enzymes, including a glycoside hydrolase from GH family 9 (BlCel9). Here, we conducted biochemical and biophysical studies of recombinant BlCel9, and its low-resolution molecular shape was retrieved from small angle X-ray scattering (SAXS) data. BlCel9 is an endoglucanase exhibiting maximum catalytic efficiency at pH 7.0 and 60 °C. Furthermore, it retains 80% of catalytic activity within a broad range of pH values (5.5-8.5) and temperatures (up to 50 °C) for extended periods of time (over 48 h). It exhibits the highest hydrolytic activity against phosphoric acid swollen cellulose (PASC), followed by bacterial cellulose (BC), filter paper (FP), and to a lesser extent carboxymethylcellulose (CMC). The HPAEC-PAD analysis of the hydrolytic products demonstrated that the end product of the enzymatic hydrolysis is primarily cellobiose, and also small amounts of glucose, cellotriose, and cellotetraose are produced. SAXS data analysis revealed that the enzyme adopts a monomeric state in solution and has a molecular mass of 65.8 kDa as estimated from SAXS data. The BlCel9 has an elongated shape composed of an N-terminal family 3 carbohydrate-binding module (CBM3c) and a C-terminal GH9 catalytic domain joined together by 20 amino acid residue long linker peptides. The domains are closely juxtaposed in an extended conformation and form a relatively rigid structure in solution, indicating that the interactions between the CBM3c and GH9 catalytic domains might play a key role in cooperative cellulose biomass recognition and hydrolysis.

Modulation of glucan-enzyme interactions by domain V in GTF-SI from Streptococcus mutans

Glucansucrase GTF-SI from Streptococcus mutans is a multidomain enzyme that catalyzes the synthesis of glucan polymers. Domain V locates 100 Å from the catalytic site and is required for an optimal activity. Nevertheless, the mechanism governing its functional role remains elusive. In this work, homology modeling and molecular dynamics simulations were employed to examine the effect of domain V in the structure and glucan-binding ability of GTF-SI in full and truncated enzyme models. Our results showed that domain V increases the flexibility of the α4'-loop-α4″ motif near the catalytic site resulting in a higher surface for glucan association, and modulates the orientation of a growing oligosaccharide (N=8-23) in glucan-enzyme complexes towards engaging in favorable contacts throughout the protein, whereas in the truncated model the glucan protrudes randomly from domain B towards the solvent. These results are valuable to increase understanding about the functional role of domain V in GH70 glucansucrases.

Engineering Geobacillus thermodenitrificans to introduce cellulolytic activity; expression of native and heterologous cellulase genes

Background

Consolidated bioprocessing (CBP) is a cost-effective approach for the conversion of lignocellulosic biomass to biofuels and biochemicals. The enzymatic conversion of cellulose to glucose requires the synergistic action of three types of enzymes: exoglucanases, endoglucanases and β-glucosidases. The thermophilic, hemicellulolytic Geobacillus thermodenitrificans T12 was shown to harbor desired features for CBP, although it lacks the desired endo and exoglucanases required for the conversion of cellulose. Here, we report the expression of both endoglucanase and exoglucanase encoding genes by G. thermodenitrificans T12, in an initial attempt to express cellulolytic enzymes that complement the enzymatic machinery of this strain.

Results

A metagenome screen was performed on 73 G. thermodenitrificans strains using HMM profiles of all known CAZy families that contain endo and/or exoglucanases. Two putative endoglucanases, GE39 and GE40, belonging to glucoside hydrolase family 5 (GH5) were isolated and expressed in both E. coli and G. thermodenitrificans T12. Structure modeling of GE39 revealed a folding similar to a GH5 exo-1,3-β-glucanase from S. cerevisiae. However, we determined GE39 to be a β-xylosidase having pronounced activity towards p-nitrophenyl-β-d-xylopyranoside. Structure modelling of GE40 revealed its protein architecture to be similar to a GH5 endoglucanase from B. halodurans, and its endoglucanase activity was confirmed by enzymatic activity against 2-hydroxyethylcellulose, carboxymethylcellulose and barley β-glucan. Additionally, we introduced expression constructs into T12 containing Geobacillus sp. 70PC53 endoglucanase gene celA and both endoglucanase genes (M1 and M2) from Geobacillus sp. WSUCF1. Finally, we introduced expression constructs into T12 containing the C. thermocellum exoglucanases celK and celS genes and the endoglucanase celC gene.

Conclusions

We identified a novel G. thermodenitrificans β-xylosidase (GE39) and a novel endoglucanase (GE40) using a metagenome screen based on multiple HMM profiles. We successfully expressed both genes in E. coli and functionally expressed the GE40 endoglucanase in G. thermodenitrificans T12. Additionally, the heterologous production of active CelK, a C. thermocellum derived exoglucanase, and CelA, a Geobacillus derived endoglucanase, was demonstrated with strain T12. The native hemicellulolytic activity and the heterologous cellulolytic activity described in this research provide a good basis for the further development of G. thermodenitrificans T12 as a host for consolidated bioprocessing.

Electronic supplementary material

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Molecular dynamics simulations elucidate conformational selection and induced fit mechanisms in the binding of PD-1 and PD-L1

PD-L1 binds PD-1 through a complex mechanism including both the conformational selection and induced fit pathways.