Characterization of glucose-tolerant β-glucosidases used in biofuel production under the bioinformatics perspective: a systematic review

Abstract

β-glucosidases are enzymes that catalyze the hydrolysis of oligosaccharides and disaccharides, such as cellobiose. These enzymes play a key role in cellulose degrading, such as alleviating product inhibition of cellulases. Consequently, they have been considered essential for the biofuel industry. However, the majority of the characterized β-glucosidases is inhibited by glucose. Hence, glucose-tolerant β-glucosidases have been targeted to improve the production of second-generation biofuels. In this paper, we proceeded a systematic literature review (SLR), collected protein structures and constructed a database of glucose-tolerant β-glucosidases, called betagdb. SLR was performed at PubMed, ScienceDirect and Scopus Library databases and conducted according to PRISMA framework. It was conducted in five steps: i) analysis of duplications, ii) title reading, iii) abstract reading, iv) diagonal reading, and v) full-text reading. The second, third, fourth, and fifth steps were performed independently by two researchers. Besides, we performed bioinformatics analysis on the collected data, such as structural and multiple alignments to detect the most conserved residues in the catalytic pocket, and molecular docking to characterize essential residues for substrate recognizing, glucose tolerance, and the β-glucosidase activity. We selected 27 papers, 23 sequences, and 5 PDB files of glucose-tolerant β-glucosidases. We characterized 11 highly conserved residues: H121, W122, N166, E167, N297, Y299, E355, W402, E409, W410, and F418. The presence of these residues may be essential for β-glucosidases. We also discussed the importance of residues W169, C170, L174, H181, and T226. Furthermore, we proposed that the number of contacts for each residue in the catalytic pocket might be a metric that could be used to suggest mutations. We believe that the herein propositions, together with the sequence and structural data collection, might be helpful for effective engineering of β-glucosidases for biofuel production and may help to shed some light on the degradation of cellulosic biomass.

Proteus: An algorithm for proposing stabilizing mutation pairs based on interactions observed in known protein 3D structures

“…We collected four structures from PDB: (i) Bacillus polymyxa GH1 β-glucosidase (PDB ID: 1BGA): β-glucosidases are vital enzymes in the second-generation biofuel production. They act cleaving cellobiose in two molecules of glucose, which will be used in fermentation for producing bioethanol [3]. The design of thermostable and more efficient β-glucosidases enzymes has excellent value for the industry [4]; (ii) tobacco etch virus protease (PDB ID: 1LVB): proteases (peptidases) hydrolyze the peptide bond producing single amino acids or smaller polypeptides molecules.…”

“…The design of new proteins, known as protein engineering, has many applications for industry. Novel and likely enhanced proteins can benefit the development of new drugs, vaccines, treatment therapies, and improve the enzymes used in digestive processes for new food and biofuel production [1][2][3][4]. Industrial biotechnological applications require enzymes with higher thermal and conformational stability [5].…”

VTR: an algorithm for identifying analogous contacts on protein structures and their complexes

“…Case study 3 -Glucose-tolerant β-glucosidases β-glucosidases (E.C. 3.2.1.21) are enzymes that act in the last step of the saccharification process, cleaving cellobiose into two molecules of glucose 28,29 . Hence, they are considered very important for the second-generation biofuel industrial applications [30][31][32] .…”

“…For GH1 β-glucosidases, a protein class extensively used in industry and with a strong interest in the second-generation bioethanol production 29 , this approach shows itself encouraging. Overall, minimal topological modifications represent a promising strategy for suggesting mutations, especially in the beta-glucosidase loop regions that surround the active site.…”

Highlights of the 2nd Brazilian student council symposium, organized by ISCB Regional Student Group Brazil

“…Finalizing the outstand students oral presentations, Diego Mariano presented a new pontual mutation method of β-glucosidase enzyme, largely applied in biofuel production, based on structural signatures [5]. The methods take into account numerical representations from pairwise residues, and also correlates the euclidean distances of signature variations.…”