Determination of optimal biomass pretreatment strategies for biofuel production: investigation of relationships between surface-exposed polysaccharides and their enzymatic conversion using carbohydrate-binding modules

AbstractExtensive decoration of backbones is a major factor resulting in resistance of enzymatic conversion in hemicellulose and other branched polysaccharides. Employing debranching enzymes is the main strategy to overcome this kind of recalcitrance at present. A carbohydrate-binding module (CBM) is a contiguous amino acid sequence that can promote the binding of enzymes to various carbohydrates, thereby facilitating enzymatic hydrolysis. According to previous studies, CBMs can be classified into four types based on their preference in ligand type, where Type III and IV CBMs prefer to branched polysaccharides than the linear and thus are able to specifically enhance the hydrolysis of substrates containing side chains. With a role in dominating the hydrolysis of branched substrates, Type III and IV CBMs could represent a non-catalytic approach in overcoming side-chain recalcitrance.

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An eco-friendly biomass pretreatment strategy utilizing reusable enzyme mimicking nanoparticles for lignin depolymerization and biofuel production

Green Chemistry ◽

10.1039/d1gc01456k ◽

2021 ◽

Author(s):

Rajiv CHANDRA RAJAK ◽

Pathikrit Saha ◽

Mamata S Singhvi ◽

Darae Kwak ◽

Danil Kim ◽

...

Keyword(s):

Lignocellulosic Biomass ◽

Biofuel Production ◽

Biomass Pretreatment ◽

Enzyme Mimicking ◽

Lignin Depolymerization

Pretreatment of lignocellulosic biomass to specifically depolymerise lignin moieties without loss of carbohydrates as well as to minimize the generation of harmful intermediates during the process is a major challenge...

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Functional diversity of three tandem C-terminal carbohydrate-binding modules of a β-mannanase

Journal of Biological Chemistry ◽

10.1016/j.jbc.2021.100638 ◽

2021 ◽

pp. 100638

Author(s):

Marie Sofie Møller ◽

Souad El Bouaballati ◽

Bernard Henrissat ◽

Birte Svensson

Keyword(s):

Functional Diversity ◽

Carbohydrate Binding ◽

Carbohydrate Binding Modules

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Functionalization of Cellulose-Based Hydrogels with Bi-Functional Fusion Proteins Containing Carbohydrate-Binding Modules

Materials ◽

10.3390/ma14123175 ◽

2021 ◽

Vol 14 (12) ◽

pp. 3175

Author(s):

Mariana Barbosa ◽

Hélvio Simões ◽

Duarte Miguel F. Prazeres

Keyword(s):

Fusion Proteins ◽

Fluorescent Protein ◽

Protein A ◽

Chemical Properties ◽

Main Idea ◽

Bioactive Molecules ◽

Scaffolding Protein ◽

Carbohydrate Binding ◽

Biological Interactions ◽

Carbohydrate Binding Modules

Materials with novel and enhanced functionalities can be obtained by modifying cellulose with a range of biomolecules. This functionalization can deliver tailored cellulose-based materials with enhanced physical and chemical properties and control of biological interactions that match specific applications. One of the foundations for the success of such biomaterials is to efficiently control the capacity to combine relevant biomolecules into cellulose materials in such a way that the desired functionality is attained. In this context, our main goal was to develop bi-functional biomolecular constructs for the precise modification of cellulose hydrogels with bioactive molecules of interest. The main idea was to use biomolecular engineering techniques to generate and purify different recombinant fusions of carbohydrate binding modules (CBMs) with significant biological entities. Specifically, CBM-based fusions were designed to enable the bridging of proteins or oligonucleotides with cellulose hydrogels. The work focused on constructs that combine a family 3 CBM derived from the cellulosomal-scaffolding protein A from Clostridium thermocellum (CBM3) with the following: (i) an N-terminal green fluorescent protein (GFP) domain (GFP-CBM3); (ii) a double Z domain that recognizes IgG antibodies; and (iii) a C-terminal cysteine (CBM3C). The ability of the CBM fusions to bind and/or anchor their counterparts onto the surface of cellulose hydrogels was evaluated with pull-down assays. Capture of GFP-CBM3 by cellulose was first demonstrated qualitatively by fluorescence microscopy. The binding of the fusion proteins, the capture of antibodies (by ZZ-CBM3), and the grafting of an oligonucleotide (to CBM3C) were successfully demonstrated. The bioactive cellulose platform described here enables the precise anchoring of different biomolecules onto cellulose hydrogels and could contribute significatively to the development of advanced medical diagnostic sensors or specialized biomaterials, among others.

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Integrated Counts of Carbohydrate-Active Protein Domains as Metabolic Readouts to Distinguish Probiotic Biology and Human Fecal Metagenomes

Scientific Reports ◽

10.1038/s41598-019-53173-7 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Hong-Hsing Liu ◽

Yu-Chen Lin ◽

Chen-Shuan Chung ◽

Kevin Liu ◽

Ya-Hui Chang ◽

...

Keyword(s):

Markov Models ◽

Protein Domains ◽

Degradation Pathway ◽

The Other ◽

Carbohydrate Binding ◽

Gram Stain ◽

Active Protein ◽

Metabolic Potential ◽

Independent Validation ◽

Carbohydrate Binding Modules

AbstractBowel microbiota is a “metaorgan” of metabolisms on which quantitative readouts must be performed before interventions can be introduced and evaluated. The study of the effects of probiotic Clostridium butyricum MIYAIRI 588 (CBM588) on intestine transplantees indicated an increased percentage of the “other glycan degradation” pathway in 16S-rRNA-inferred metagenomes. To verify the prediction, a scoring system of carbohydrate metabolisms derived from shotgun metagenomes was developed using hidden Markov models. A significant correlation (R = 0.9, p < 0.015) between both modalities was demonstrated. An independent validation revealed a strong complementarity (R = −0.97, p < 0.002) between the scores and the abundance of “glycogen degradation” in bacteria communities. On applying the system to bacteria genomes, CBM588 had only 1 match and ranked higher than the other 8 bacteria evaluated. The gram-stain properties were significantly correlated to the scores (p < 5 × 10−4). The distributions of the scored protein domains indicated that CBM588 had a considerably higher (p < 10−5) proportion of carbohydrate-binding modules than other bacteria, which suggested the superior ability of CBM588 to access carbohydrates as a metabolic driver to the bowel microbiome. These results demonstrated the use of integrated counts of protein domains as a feasible readout for metabolic potential within bacteria genomes and human metagenomes.

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