β-Xylosidases and α-l-arabinofuranosidases: Accessory enzymes for arabinoxylan degradation

Lagaert, Stijn; Pollet, Annick; Courtin, Christophe M.; Volckaert, Guido

doi:10.1016/j.biotechadv.2013.11.005

Cited by 137 publications

(125 citation statements)

References 190 publications

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“…The overlap of these activities within a subfamily, and in some cases within a single protein, is not altogether unsurprising, as the ␣-L-arabinofuranose and ␤-D-xylose conformations are sterically similar near the glycosidic bond (Fig. 3), and indeed, this cooccurrence has been reported many times previously (24,25).…”

Section: Resultsmentioning

confidence: 67%

Dividing the Large Glycoside Hydrolase Family 43 into Subfamilies: a Motivation for Detailed Enzyme Characterization

Mewis

Lenfant

Lombard

et al. 2016

Appl Environ Microbiol

195

167

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dThe rapid rise in DNA sequencing has led to an expansion in the number of glycoside hydrolase (GH) families. The GH43 family currently contains ␣-L-arabinofuranosidase, ␤-D-xylosidase, ␣-L-arabinanase, and ␤-D-galactosidase enzymes for the debranching and degradation of hemicellulose and pectin polymers. Many studies have revealed finer details about members of GH43 that necessitate the division of GH43 into subfamilies, as was done previously for the GH5 and GH13 families. The work presented here is a robust subfamily classification that assigns over 91% of all complete GH43 domains into 37 subfamilies that correlate with conserved sequence residues and results of biochemical assays and structural studies. Furthermore, cooccurrence analysis of these subfamilies and other functional modules revealed strong associations between some GH43 subfamilies and CBM6 and CBM13 domains. Cooccurrence analysis also revealed the presence of proteins containing up to three GH43 domains and belonging to different subfamilies, suggesting significant functional differences for each subfamily. Overall, the subfamily analysis suggests that the GH43 enzymes probably display a hitherto underestimated variety of subtle specificity features that are not apparent when the enzymes are assayed with simple synthetic substrates, such as pNP-glycosides. Carbohydrates serve a range of functional purposes in biological systems, including energy storage, signal transduction, and intracellular trafficking, among others (1). Importantly, carbohydrates are the main end product of plant primary production, representing a large of majority of carbon fixation by plants (2). As a photosynthetically renewable form of fixed carbon, plant biomass represents a prime target for the replacement of petroleumderived fuels for future sustainability efforts. The enzymatic degradation and modification of carbohydrates have thus been cast to the forefront of biofuel production research (3).As functional efforts to discover plant cell wall polysaccharide (PCWP)-degrading enzymes identify novel activities and mechanisms (4, 5), it is important to derive and maintain a concise classification system for these enzymes. A sequence-based classification of carbohydrate-active enzymes (CAZymes) began in 1991 (6), with the classification of 35 families of glycoside hydrolases (GHs). Today the CAZy database (7) comprises 5 separate enzyme classes, namely, the aforementioned GHs, glycosyltransferases (GTs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), and auxiliary activities (AAs), as well as associated carbohydrate binding modules (CBMs), that together correspond to over 530,000 individual sequences (at the time of submission of this article). The largest of these classes are the glycoside hydrolases, currently represented by over 241,000 sequences classified into 133 families based on amino acid sequence similarity.The rapid advancements in DNA sequencing over the past decade have exponentially increased the number of sequences assigned to each family. Henc...

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Section: Resultsmentioning

confidence: 67%

Dividing the Large Glycoside Hydrolase Family 43 into Subfamilies: a Motivation for Detailed Enzyme Characterization

Mewis

Lenfant

Lombard

et al. 2016

Appl Environ Microbiol

195

167

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“…Interestingly, a GH54 α-L-arabinofuranosidase (ID 4138) was up regulated on wheat bran, but down regulated on duckweed, underlining substrate dependent regulation. A GH54 α-arabinofuranosidases belonging Trichoderma koningii is reported to contain β-D-xylosidase activity [51], while the ones from GH62 are more strictly α-arabinofuranosidases [52]. This indicates that we saw a specialized up and down regulation, where α-arabinofuranosidases with activity towards xylan were up regulated on wheat bran, having a higher xylan content than duckweed.…”

Section: Secretome Comparisonmentioning

confidence: 86%

On-Site Enzyme Production by Trichoderma asperellum for the Degradation of Duckweed

Bech¹,

Herbst²

2015

Fungal Genom Biol

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The on-site production of cell wall degrading enzymes is an important strategy for the development of sustainable bio-refinery processes. This study concerns the optimization of production of plant cell wall-degrading enzymes produced by Trichoderma asperellum. A comparative secretome analysis was performed on T. asperellum growing on PDA agar, wheat bran and duckweed, respectively. T. asperellum proved to be able to produce a wide enzyme profile, including both depolymerization and debranching enzymes, mainly consisting of hemi-cellulases. The secretome analysis showed specific glycoside hydrolase-induction on duckweed compared with growth on wheat bran and PDA, including a GH62 α-L-arabinofuranosidase, a promising candidate enzyme for the degradation of duckweed. The enzyme cocktail from T. asperellum proved capable of degrading pretreated duckweed, obtaining up to 60% of the theoretical glucose yield, making it a potential candidate for on-site enzyme production.

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“…Alternatively, the increase in gene expression that was found could also be the result of a synergistic and, thus, more efficient (A)XOS degradation pattern when both strains are present, as this degradation requires the cooperative action of several carbohydrate-active enzymes encompassing ␣-arabinofuranosidases, ␤-endoxylanases, ␤-xylosidases, and exo-oligoxylanases (57). During cocultivation, the B. longum strain took advantage of the set of (A)XOS-degrading enzymes encoded by the genome of the E. rectale strain (Fig.…”

Section: Discussionmentioning

confidence: 99%

Mutual Cross-Feeding Interactions between Bifidobacterium longum subsp. longum NCC2705 and Eubacterium rectale ATCC 33656 Explain the Bifidogenic and Butyrogenic Effects of Arabinoxylan Oligosaccharides

Rivière

Gagnon

Weckx

et al. 2015

Appl Environ Microbiol

181

140

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Arabinoxylan oligosaccharides (AXOS) are a promising class of prebiotics that have the potential to stimulate the growth of bifidobacteria and the production of butyrate in the human colon, known as the bifidogenic and butyrogenic effects, respectively. Although these dual effects of AXOS are considered beneficial for human health, their underlying mechanisms are still far from being understood. Therefore, this study investigated the metabolic interactions between Bifidobacterium longum subsp. longum NCC2705 (B. longum NCC2705), an acetate producer and arabinose substituent degrader of AXOS, and Eubacterium rectale ATCC 33656, an acetate-converting butyrate producer. Both strains belong to prevalent species of the human colon microbiota. The strains were grown on AXOS during mono-and coculture fermentations, and their growth, AXOS consumption, metabolite production, and expression of key genes were monitored. The results showed that the growth of both strains and gene expression in both strains were affected by cocultivation and that these effects could be linked to changes in carbohydrate consumption and concomitant metabolite production. The consumption of the arabinose substituents of AXOS by B. longum NCC2705 with the concomitant production of acetate allowed E. rectale ATCC 33656 to produce butyrate (by means of a butyryl coenzyme A [CoA]:acetate CoA-transferase), explaining the butyrogenic effect of AXOS. Eubacterium rectale ATCC 33656 released xylose from the AXOS substrate, which favored the B. longum NCC2705 production of acetate, explaining the bifidogenic effect of AXOS. Hence, those interactions represent mutual cross-feeding mechanisms that favor the coexistence of bifidobacterial strains and butyrate producers in the same ecological niche. In conclusion, this study provides new insights into the bifidogenic and butyrogenic effects of AXOS. F ermentation in the human colon is carried out by trillions of bacteria that contribute not only to health and well-being but also to disease (1-4). For instance, a decrease in the relative abundance of bifidobacteria in the human colon has been associated with antibiotic-associated diarrhea, irritable bowel syndrome, inflammatory bowel disease, allergies, and regressive autism (5, 6). Although it is currently not yet clear whether changes in microbial composition are a cause or a consequence of these disorders, there are indications that metabolites, in particular, the short-chain fatty acids (SCFAs), such as acetate, butyrate, and propionate, that are produced during fermentation in the colon play an important role in intestinal homeostasis (3, 7). Among the SCFAs produced in the human colon, butyrate has drawn the most attention, as it is an essential energy source for the colon epithelial cells and has a protective effect against inflammatory bowel disease and colon cancer (3,8,9). Most butyrate producers belong to the Firmicutes phylum and use a butyryl coenzyme A (CoA):acetate CoA-transferase in the final step of butyrate biosynthesis, which involves the n...

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β-Xylosidases and α-l-arabinofuranosidases: Accessory enzymes for arabinoxylan degradation

Cited by 137 publications

References 190 publications

Dividing the Large Glycoside Hydrolase Family 43 into Subfamilies: a Motivation for Detailed Enzyme Characterization

Dividing the Large Glycoside Hydrolase Family 43 into Subfamilies: a Motivation for Detailed Enzyme Characterization

On-Site Enzyme Production by Trichoderma asperellum for the Degradation of Duckweed

Mutual Cross-Feeding Interactions between Bifidobacterium longum subsp. longum NCC2705 and Eubacterium rectale ATCC 33656 Explain the Bifidogenic and Butyrogenic Effects of Arabinoxylan Oligosaccharides

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