Large-scale analyses of glycosylation in cellulases

Glycosylation of cellulase: a novel strategy for improving cellulase

Protein glycosylation is the most complex posttranslational modification process. Most cellulases from filamentous fungi contain N-glycosylation and O-glycosylation. Here, we discuss the potential roles of glycosylation on the characteristics and function of cellulases. The use of certain cultivation, inducer, and alteration of engineering glycosylation pathway can enable the rational control of cellulase glycosylation. Glycosylation does not occur arbitrarily and may tend to modify the 3D structure of cellulases by using specially distributed glycans. Therefore, glycoengineering should be considered comprehensively along with the spatial structure of cellulases. Cellulase glycosylation may be an evolution phenomenon, which has been considered as an economical way for providing different functions from identical proteins. In addition to gene and transcription regulations, glycosylation may be another regulation on the protein expression level. Enhanced understanding of the potential regulatory role of cellulase glycosylation will enable synthetic biology approaches for the development of commercial cellulase.

A polygenic stacking classifier revealed the complicated platelet transcriptomic landscape of adult immune thrombocytopenia

Immune thrombocytopenia (ITP) is an autoimmune disease with the typical symptom of a low platelet count in blood. ITP demonstrated age and sex biases in both occurrences and prognosis, and adult ITP was mainly induced by the living environments. The current diagnosis guideline lacks the integration of molecular heterogenicity. This study recruited the largest cohort of platelet transcriptome samples. A comprehensive procedure of feature selection, feature engineering, and stacking classification was carried out to detect the ITP biomarkers using RNA sequencing (RNA-seq) transcriptomes. The 40 detected biomarkers were loaded to train the final ITP detection model, with an overall accuracy 0.974. The biomarkers suggested that ITP onset may be associated with various transcribed components, including protein-coding genes, long intergenic non-coding RNA (lincRNA) genes, and pseudogenes with apparent transcriptions. The delivered ITP detection model may also be utilized as a complementary ITP diagnosis tool. The code and the example dataset is freely available on http://www.healthinformaticslab.org/supp/resources.php

Experimental and computational studies of cellulases as bioethanol enzymes

Bioethanol industries and bioprocesses have many challenges that constantly impede commercialization of the end product. One of the bottlenecks in the bioethanol industry is the challenge of discovering highly efficient catalysts that can improve biomass conversion. The current promising bioethanol conversion catalysts are microorganism-based cellulolytic enzymes, but lack optimization for high bioethanol conversion, due to biological and other factors. A better understanding of molecular underpinnings of cellulolytic enzyme mechanisms and significant ways to improve them can accelerate the bioethanol commercial production process. In order to do this, experimental methods are the primary choice to evaluate and characterize cellulase’s properties, but they are time-consuming and expensive. A time-saving, complementary approach involves computational methods that evaluate the same properties and improves our atomistic-level understanding of enzymatic mechanism of action. Theoretical methods in many cases have proposed research routes for subsequent experimental testing and validation, reducing the overall research cost. Having a plethora of tools to evaluate cellulases and the yield of the enzymatic process will aid in planning more optimized experimental setups. Thus, there is a need to connect the computational evaluation methods with the experimental methods to overcome the bottlenecks in the bioethanol industry. This review discusses various experimental and computational methods and their use in evaluating the multiple properties of cellulases.

Whole-Genome Sequence and Comparative Analysis of Trichoderma asperellum ND-1 Reveal Its Unique Enzymatic System for Efficient Biomass Degradation

The lignocellulosic enzymes of Trichoderma asperellum have been intensely investigated toward efficient conversion of biomass into high-value chemicals/industrial products. However, lack of genome data is a remarkable hurdle for hydrolase systems studies. The secretory enzymes of newly isolated T. asperellum ND-1 during lignocellulose degradation are currently poorly known. Herein, a high-quality genomic sequence of ND-1, obtained by both Illumina HiSeq 2000 sequencing platforms and PacBio single-molecule real-time, has an assembly size of 35.75 Mb comprising 10,541 predicted genes. Secretome analysis showed that 895 proteins were detected, with 211 proteins associated with carbohydrate-active enzymes (CAZymes) responsible for biomass hydrolysis. Additionally, T. asperellum ND-1, T. atroviride IMI 206040, and T. virens Gv-298 shared 801 orthologues that were not identified in T. reesei QM6a, indicating that ND-1 may play critical roles in biological-control. In-depth analysis suggested that, compared with QM6a, the genome of ND-1 encoded a unique enzymatic system, especially hemicellulases and chitinases. Moreover, after comparative analysis of lignocellulase activities of ND-1 and other fungi, we found that ND-1 displayed higher hemicellulases (particularly xylanases) and comparable cellulases activities. Our analysis, combined with the whole-genome sequence information, offers a platform for designing advanced T. asperellum ND-1 strains for industrial utilizations, such as bioenergy production.

Glycosyl hydrolases family 5, subfamily 5: Relevance and structural insights for designing improved biomass degrading cocktails

Endoglucanases are carbohydrate-degrading enzymes widely used for bioethanol production as part of the enzymatic cocktail. However, family 5 subfamily 5 (GH5_5) endoglucanases are still poorly explored in depth. The Trichoderma reesei representative is the most studied enzyme, presenting catalytic activity in acidic media and mild temperature conditions. Though biochemically similar, its modular structure and synergy with other components vary greatly compared to other GH5_5 members and there is still a lack of specific studies regarding their interaction with other cellulases and application on novel and better mixtures. In this regard, the threedimensional structure elucidation is a highly valuable tool to both uncover basic catalytic mechanisms and implement engineering techniques, proved by the high success rate GH5_5 endoglucanases show. GH5_5 enzymes must be carefully evaluated to fully uncover their potential in biomass-degrading cocktails: the optimal industrial conditions, synergy with other cellulases, structural studies, and enzyme engineering approaches. We aimed to provide the current understanding of these main topics, collecting all available information about characterized GH5_5 endoglucanases function, structure, and bench experiments, in order to suggest future directions to a better application of these enzymes in the industry.

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.

PTM-ssMP: A Web Server for Predicting Different Types of Post-translational Modification Sites Using Novel Site-specific Modification Profile

Protein post-translational modifications (PTMs) are chemical modifications of a protein after its translation. Owing to its play an important role in deep understanding of various biological processes and the development of effective drugs, PTM site prediction have become a hot topic in bioinformatics. Recently, many online tools are developed to prediction various types of PTM sites, most of which are based on local sequence and some biological information. However, few of existing tools consider the relations between different PTMs for their prediction task. Here, we develop a web server called PTM-ssMP to predict PTM site, which adopts site-specific modification profile (ssMP) to efficiently extract and encode the information of both proximal PTMs and local sequence simultaneously. In PTM-ssMP we provide efficient prediction of multiple types of PTM site including phosphorylation, lysine acetylation, ubiquitination, sumoylation, methylation, O-GalNAc, O-GlcNAc, sulfation and proteolytic cleavage. To assess the performance of PTM-ssMP, a large number of experimentally verified PTM sites are collected from several sources and used to train and test the prediction models. Our results suggest that ssMP consistently contributes to remarkable improvement of prediction performance. In addition, results of independent tests demonstrate that PTM-ssMP compares favorably with other existing tools for different PTM types. PTM-ssMP is implemented as an online web server with user-friendly interface, which is freely available at http://bioinformatics.ustc.edu.cn/PTM-ssMP/index/.

Oxygen Activation by Cu LPMOs in Recalcitrant Carbohydrate Polysaccharide Conversion to Monomer Sugars

Natural carbohydrate polymers such as starch, cellulose, and chitin provide renewable alternatives to fossil fuels as a source for fuels and materials. As such, there is considerable interest in their conversion for industrial purposes, which is evidenced by the established and emerging markets for products derived from these natural polymers. In many cases, this is achieved via industrial processes that use enzymes to break down carbohydrates to monomer sugars. One of the major challenges facing large-scale industrial applications utilizing natural carbohydrate polymers is rooted in the fact that naturally occurring forms of starch, cellulose, and chitin can have tightly packed organizations of polymer chains with low hydration levels, giving rise to crystalline structures that are highly recalcitrant to enzymatic degradation. The topic of this review is oxidative cleavage of carbohydrate polymers by lytic polysaccharide mono-oxygenases (LPMOs). LPMOs are copper-dependent enzymes (EC 1.14.99.53-56) that, with glycoside hydrolases, participate in the degradation of recalcitrant carbohydrate polymers. Their activity and structural underpinnings provide insights into biological mechanisms of polysaccharide degradation.

Proteomic biomarkers for lung cancer progression

Aim: Lung adenocarcinoma (LUAD) and lung squamous-cell carcinoma (LUSC) are two major subtypes of lung cancer and constitute about 70% of all the lung cancer cases. The patient's lifespan and living quality will be significantly improved if they are diagnosed at an early stage and adequately treated. Methods & results: This study comprehensively screened the proteomic dataset of both LUAD and LUSC, and proposed classification models for the progression stages of LUAD and LUSC with accuracies 86.51 and 89.47%, respectively. Discussion & conclusion: A comparative analysis was also carried out on related transcriptomic datasets, which indicates that the proposed biomarkers provide discerning power for accurate stage prediction, and will be improved when larger-scale proteomic quantitative technologies become available.

Expression and secretion of glycosylated heparin biosynthetic enzymes using Komagataella pastoris

Heparin, an anticoagulant drug, is biosynthesized in selected animal cells. The heparin biosynthetic enzymes mainly consist of sulfotransferases and all are integral transmembrane glycoproteins. These enzymes are generally produced in engineered Escherichia coli as without their transmembrane domains as non-glycosylated fusion proteins. In this study, we used the yeast, Komagataella pastoris, to prepare four sulfotransferases involved in heparin biosynthesis as glycoproteins. While the yields of these yeast-expressed enzymes were considerably lower than E. coli-expressed enzymes, these enzymes were secreted into the fermentation media simplifying their purification and were endotoxin free. The activities of these sulfotransferases, expressed as glycoproteins in yeast, were compared to the bacterially expressed proteins. The yeast-expressed sulfotransferase glycoproteins showed improved kinetic properties than the bacterially expressed proteins.

Extending the linker region increases the activity of the Bacillus subtilis cellulase CelI15

OBJECTIVES

To investigate the effect of the linker region (LR) on the enzymatic activity, stability, and flexibility of Bacillus subtilis cellulase CelI15, six mutants were constructed that contained increasing numbers of the LR.

RESULTS

The CelI15 mutant with three copies of the LR (approx. 57 amino acids) showed the highest activity, which was almost 20 % greater than that of wild type CelI15. The stability of the mutant enzymes increased as the copy number of the LR decreased. However, the substrate affinity of the mutant enzymes increased as the LR copy number increased, and the mutant with four copies of the LR exhibited the highest substrate affinity. Additionally, the flexibility of the CelI15 mutants increased as the LR copy number increased from zero to four copies, although it decreased sharply for the mutant with five copies of the LR.

CONCLUSION

The activity of CelI15 was increased by increasing the LR copy number, which could be a potential way to improve its enzymatic properties.

Analysis of the role of O-glycosylation in GH51 α-L-arabinofuranosidase from Pleurotus ostreatus

In this study, the recombinant α-L-arabinofuranosidase from the fungus Pleurotus ostreatus (rPoAbf) was subjected to site-directed mutagenesis with the aim of elucidating the role of glycosylation on the properties of the enzyme at the level of S160 residue. As a matter of fact, previous mass spectral analyses had led to the localization of a single O-glycosylation at this site. Recombinant expression and characterization of the rPoAbf mutant S160G was therefore performed. It was shown that the catalytic properties are slightly changed by the mutation, with a more evident modification of the Kcat and KM toward the synthetic substrate pN-glucopyranoside. More importantly, the mutation negatively affected the stability of the enzyme at various pHs and temperatures. Circular dichroism (CD) analyses showed a minimum at 210 nm for wild-type (wt) rPoAbf, typical of the beta-sheets structure, whereas this minimum is shifted for rPoAbf S160G, suggesting the presence of an unfolded structure. A similar behavior was revealed when wt rPoAbf was enzymatically deglycosylated. CD structural analyses of both the site-directed mutant and the enzymatically deglycosylated wild-type enzyme indicate a role of the glycosylation at the S160 residue in rPoAbf secondary structure stability.

Characterization of Cryptopygus antarcticus endo-β-1,4-glucanase from Bombyx mori expression systems

Endo-β-1,4-glucanase (CaCel) from Antarctic springtail, Cryptopygus antarcticus, a cellulase with high activity at low temperature, shows potential industrial use. To obtain sufficient active cellulase for characterization, CaCel gene was expressed in Bombyx mori-baculovirus expression systems. Recombinant CaCel (rCaCel) has been expressed in Escherichia coli (Ec-CaCel) at temperatures below 10°C, but the expression yield was low. Here, rCaCel with a silkworm secretion signal (Bm-CaCel) was successfully expressed and secreted into pupal hemolymph and purified to near 90% purity by Ni-affinity chromatography. The yield and specific activity of rCaCel purified from B. mori were estimated at 31 mg/l and 43.2 U/mg, respectively, which is significantly higher than the CaCel yield obtained from E. coli (0.46 mg/l and 35.8 U/mg). The optimal pH and temperature for the rCaCels purified from E. coli and B. mori were 3.5 and 50°C. Both rCaCels were active at a broad range of pH values and temperatures, and retained more than 30% of their maximal activity at 0°C. Oligosaccharide structural analysis revealed that Bm-CaCel contains elaborated N- and O-linked glycans, whereas Ec-CaCel contains putative O-linked glycans. Thermostability of Bm-CaCel from B. mori at 60°C was higher than that from E. coli, probably due to glycosylation.

Predicting protein-protein interactions from primary protein sequences using a novel multi-scale local feature representation scheme and the random forest

The study of protein-protein interactions (PPIs) can be very important for the understanding of biological cellular functions. However, detecting PPIs in the laboratories are both time-consuming and expensive. For this reason, there has been much recent effort to develop techniques for computational prediction of PPIs as this can complement laboratory procedures and provide an inexpensive way of predicting the most likely set of interactions at the entire proteome scale. Although much progress has already been achieved in this direction, the problem is still far from being solved. More effective approaches are still required to overcome the limitations of the current ones. In this study, a novel Multi-scale Local Descriptor (MLD) feature representation scheme is proposed to extract features from a protein sequence. This scheme can capture multi-scale local information by varying the length of protein-sequence segments. Based on the MLD, an ensemble learning method, the Random Forest (RF) method, is used as classifier. The MLD feature representation scheme facilitates the mining of interaction information from multi-scale continuous amino acid segments, making it easier to capture multiple overlapping continuous binding patterns within a protein sequence. When the proposed method is tested with the PPI data of Saccharomyces cerevisiae, it achieves a prediction accuracy of 94.72% with 94.34% sensitivity at the precision of 98.91%. Extensive experiments are performed to compare our method with existing sequence-based method. Experimental results show that the performance of our predictor is better than several other state-of-the-art predictors also with the H. pylori dataset. The reason why such good results are achieved can largely be credited to the learning capabilities of the RF model and the novel MLD feature representation scheme. The experiment results show that the proposed approach can be very promising for predicting PPIs and can be a useful tool for future proteomic studies.

Asn124 of Cel5A from Hypocrea jecorina not only provides the N-glycosylation site but is also essential in maintaining enzymatic activity

To investigate the function of N-glycosylation of Cel5A (endoglucanase II) from Hypocrea jecorina, two N-glycosylation site deletion Cel5A mutants (rN124D and rN124H) were expressed in Saccharomyces cerevisiae. The weights of these recombinant mutants were 54 kDa, which were lower than that of rCel5A. This result was expected to be attributed to deglycosylation. The enzyme activity of rN124H was greatly reduced to 60.6% compared with rCel5A, whereas rN124D showed slightly lower activity (10%) than that of rCel5A. rN124D and rN124H showed different thermal stabilities compared with the glycosylated rCel5A, especially at lower pH value. Thermal stabilities were reduced and improved for rN124D and rN124H, respectively. Circular dichroism spectroscopy showed that the modification of secondary structure by mutation may be the reason for the change in enzymatic activity and thermal stability. [BMB Reports 2014; 47(5): 256-261]

Isolation, identification, and media optimization of high-level cellulase production by Bacillus sp. BCCS A3, in a fermentation system using response surface methodology

Cellulases are important glycosyl hydrolase enzymes, which break down cellulose to β-glucose. They have been used widely in biotechnological processing such as bioethanol production. In this work we studied maximizing cellulase production by Bacillus sp. BCCS A3 using response surface methodology (RSM). A good result was attained with these conditions (% w/v): tryptone 0.1, Na₂PO₄ 0.25, (NH₄)₂SO₄ 0.2, MgSO₄ · 7H₂O 0.005, CaCl₂ 0.005, KH₂PO₄ 0.1, NaCl 0.1, sodium carboxymethylcellulose (CMC) 0.75, and pH 9. The cellulase activity in optimized medium was 49.80 U/ml. Moreover, high level of enzyme production was obtained by using fermentor system (50.30 U/ml). Thus, according to the obtained results, this statistical method provided quick identification and integration of key medium details for Bacillus sp. BCCS A3, leading to more cellulase production.

Deciphering the effect of the different N-glycosylation sites on the secretion, activity, and stability of cellobiohydrolase I from Trichoderma reesei

N-linked glycosylation modulates and diversifies the structures and functions of the eukaryotic proteome through both intrinsic and extrinsic effects on proteins. We investigated the significance of the three N-linked glycans on the catalytic domain of cellobiohydrolase I (CBH1) from the filamentous fungus Trichoderma reesei in its secretion and activity. While the removal of one or two N-glycosylation sites hardly affected the extracellular secretion of CBH1, eliminating all of the glycosylation sites did induce expression of the unfolded protein response (UPR) target genes, and secretion of this CBH1 variant was severely compromised in a calnexin gene deletion strain. Further characterization of the purified CBH1 variants showed that, compared to Asn270, the thermal reactivity of CBH1 was significantly decreased by removal of either Asn45 or Asn384 glycosylation site during the catalyzed hydrolysis of soluble substrate. Combinatorial loss of these two N-linked glycans further exacerbated the temperature-dependent inactivation. In contrast, this thermal labile property was less severe when hydrolyzing insoluble cellulose. Analysis of the structural integrity of CBH1 variants revealed that removal of N-glycosylation at Asn384 had a more pronounced effect on the integrity of regular secondary structure compared to the loss of Asn45 or Asn270. These data implicate differential roles of N-glycosylation modifications in contributing to the stability of specific functional regions of CBH1 and highlight the potential of improving the thermostability of CBH1 by tuning proper interactions between glycans and functional residues.

GH11 xylanases: Structure/function/properties relationships and applications

For technical, environmental and economical reasons, industrial demands for process-fitted enzymes have evolved drastically in the last decade. Therefore, continuous efforts are made in order to get insights into enzyme structure/function relationships to create improved biocatalysts. Xylanases are hemicellulolytic enzymes, which are responsible for the degradation of the heteroxylans constituting the lignocellulosic plant cell wall. Due to their variety, xylanases have been classified in glycoside hydrolase families GH5, GH8, GH10, GH11, GH30 and GH43 in the CAZy database. In this review, we focus on GH11 family, which is one of the best characterized GH families with bacterial and fungal members considered as true xylanases compared to the other families because of their high substrate specificity. Based on an exhaustive analysis of the sequences and 3D structures available so far, in relation with biochemical properties, we assess biochemical aspects of GH11 xylanases: structure, catalytic machinery, focus on their "thumb" loop of major importance in catalytic efficiency and substrate selectivity, inhibition, stability to pH and temperature. GH11 xylanases have for a long time been used as biotechnological tools in various industrial applications and represent in addition promising candidates for future other uses.

Cellulases: ambiguous nonhomologous enzymes in a genomic perspective

The key material for bioethanol production is cellulose, which is one of the main components of the plant cell wall. Enzymatic depolymerization of cellulose is an essential step in bioethanol production, and can be accomplished by fungal and bacterial cellulases. Most of the biochemically characterized bacterial cellulases come from only a few cellulose-degrading bacteria, thus limiting our knowledge of a range of cellulolytic activities that exist in nature. The recent explosion of genomic data offers a unique opportunity to search for novel cellulolytic activities; however, the absence of clear understanding of structural and functional features that are important for reliable computational identification of cellulases precludes their exploration in the genomic datasets. Here, we explore the diversity of cellulases and propose a genomic approach to overcome this bottleneck.