Two Bifunctional β-Xylosidase /α-L-Arabinofuranosidases From GH43 With Different Structures in the xylan Degradation Strain of Paenibacillus Physcomitrellae XB Displayed the Similar xylo-oligosaccharides Degradation Ability

BackgroundThe strain Paenibacillus physcomitrellae XB isolated from moss of Physcomitrella patens was found have the xylan degradation ability, but its degradation characteristics and the related mechanism has not been revealed.ResultsIn this study, Paenibacillus physcomitrellae XB exhibited different xylan degradation ability under the different substrates of corncob xylan (CCX), oat spet xylan (OSX), wheat flour arabinoxylan (AX) and beech wood xylan (BWX). Genomic analysis showed that ~ 38 genes were related to xylan degradation, and quantitative real time RT-PCR showed that two glycoside hydrolase family 43 genes (Pph_0602 and Pph_2344) were up-regulated on 1% CCX and xylose. Substrate-specific experiments with purified proteins Ppxyl43A (Pph_0602) and Ppxyl43B (Pph_2344) revealed that both of them exhibited β-xylosidase activity toward chromogenic substrate p-nitrophenyl–D-xylopyranoside and α-L-arabinofuranosidase activity toward p-nitrophenyl-α-L-arabinofuranoside, indicating at least bifunctionality. Combined their degradation features on the natural substrates of different xylans with the hydrolytic products separated by thin-layer chromatography and high-performance anion exchange chromatography profiles, it was found that both Ppxyl43A and Ppxyl43B were with the similar degradation ability on xylo-oligosaccharides (like CCX, OSX, xylohexaose and xylobiose). Both of them even could hydrolyze xylohexaose and xylobiose completely to xylose, but could not hydrolyze BWX and AX to produce xylooligosaccharides or xylose, suggesting they have no endo-xylanase activity and mainly hydrolyze xylo-oligosaccharides by β-xylosidase activity. Moreover, the kinetic parameters of β-xylosidase and α-L-arabinofuranosidase of both two proteins indicated their affinity with all the detected natural substrate (CCX) and chromogenic substrates were nearly similar. In addition, despite having no signal peptides, both of them might export outside the cell by the nonconventional pathways. However, Ppxy143B exhibited wider temperature and pH ranges, higher pH and thermostability, and was less influenced by metal ions than Ppxyl43A. Given its enzymatic characteristics and predicted structure, it is likely that the C-terminus domain (GH43_C2) of Ppxyl43B enhances the stability of the two enzymes and also restricts the substrates’ or metal ions’ access to the active sites.ConclusionsPpxyl43A and Ppxyl43B were β-xylosidase/α-L-arabinofuranosidase bifunctional enzymes with different structures from Paenibacillus physcomitrellae XB and exhibited similar xylo-oligosaccharides hydrolyse ability, which would be useful in the further lignocellulosic biomass conversion.

Characterization and diversity of the complete set of GH family 3 enzymes from Rhodothermus marinus DSM 4253

The genome of Rhodothermus marinus DSM 4253 encodes six glycoside hydrolases (GH) classified under GH family 3 (GH3): RmBgl3A, RmBgl3B, RmBgl3C, RmXyl3A, RmXyl3B and RmNag3. The biochemical function, modelled 3D-structure, gene cluster and evolutionary relationships of each of these enzymes were studied. The six enzymes were clustered into three major evolutionary lineages of GH3: β-N-acetyl-glucosaminidases, β-1,4-glucosidases/β-xylosidases and macrolide β-glucosidases. The RmNag3 with additional β-lactamase domain clustered with the deepest rooted GH3-lineage of β-N-acetyl-glucosaminidases and was active on acetyl-chitooligosaccharides. RmBgl3B displayed β-1,4-glucosidase activity and was the only representative of the lineage clustered with macrolide β-glucosidases from Actinomycetes. The β-xylosidases, RmXyl3A and RmXyl3B, and the β-glucosidases RmBgl3A and RmBgl3C clustered within the major β-glucosidases/β-xylosidases evolutionary lineage. RmXyl3A and RmXyl3B showed β-xylosidase activity with different specificities for para-nitrophenyl (pNP)-linked substrates and xylooligosaccharides. RmBgl3A displayed β-1,4-glucosidase/β-xylosidase activity while RmBgl3C was active on pNP-β-Glc and β-1,3-1,4-linked glucosyl disaccharides. Putative polysaccharide utilization gene clusters were also investigated for both R. marinus DSM 4253 and DSM 4252T (homolog strain). The analysis showed that in the homolog strain DSM 4252TRmar_1080 (RmXyl3A) and Rmar_1081 (RmXyl3B) are parts of a putative polysaccharide utilization locus (PUL) for xylan utilization.

Experimental Design for Optimization of β-Xylosidase Production by A. fumigatus Isolated from the Atlantic Forest (Brazil)

The production of β-Xylosidase by a new strain of Aspergillus fumigatus (PC-7S-2 M), isolated from the Brazilian Atlantic Forest, was analyzed at 28°C using modified Czapeck media supplemented with different agroindustrial residues at 1% (w/v). Conidia were inoculated for 7 days, and the best activity for β- Xylosidase was obtained in the presence of barley brewing residue after 4 days (15 U mL-1). To optimize the production of β-Xylosidase, this carbon source was used for a central composite rotational design (CCRD) to obtain a significance level of p < 0.10, which predicted an enzyme activity of 245.04 U mL-1. The model validation revealed β-Xylosidase activity was optimized at 229.06 U mL-1. Furthermore, the production of intracellular A. fumigatus β-Xylosidase increased by 1,500% (15 times) over that initially obtained, achieving 93.47% of the predicted model. This finding obtained during two years emphasizes the availability of A. fumigatus β-Xylosidase production with possible applications in biotechnological processes.