Substrate-Binding Site of Family 11 Xylanase from<i>Bacillus firmus</i>K-1 by Molecular Docking

Jommuengbout, Pattraporn; Pinitglang, Surapong; Kyu, Khin Lay

doi:10.1271/bbb.80731

Cited by 38 publications

(11 citation statements)

References 39 publications

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“…Arabinoxylans are the predominant NSP in wheat and barley ( Izydorczyk and Dexter, 2008 ). Xylanases cleave the internal glycosidic linkages in xylan, producing short-chain xylo-oligosaccharides ( XOS ) ( Jommuengbout et al., 2009 ). These XOS can be utilised more efficiently by gut microbiota, having a direct impact on the overall energy utilisation of cereals.…”

Section: Introductionmentioning

confidence: 99%

Comparing the efficacy of stimbiotic and a combination of xylanase and beta-glucanase, in broilers fed wheat-barley based diets with high or low AME

2021

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A stimbiotic is defined as a product that stimulates a fiber-degrading microbiome to increase fiber fermentability. The aim of this study was to examine if it is more advantageous to feed a stimbiotic (xylanase + xylo-oligosaccharides [ STB ]) or a combination of xylanase and beta-glucanase ( Xyl + BG ) to broilers fed wheat-barley based diets with differing AME levels. Cobb 500 broilers ( n = 480, 80 birds per treatment) were fed 6 dietary treatments in a 2 × 3 factorial arrangement; 2 AME levels, ‘High’ or ‘Low’, which differed by 100 kcal ME/kg, and 3 additive supplementations, with no supplemental additives, STB or Xyl + BG. Diets were fed as 3 phases, starter (d 0–14), grower (d 14–21) and finisher (d 21–35). On bird age d 14, 21 and 35, total pen body weight and feed intake were determined, and feed conversion ratio corrected for mortality ( cFCR ) was calculated. On d 21 and d 35 ileal viscosity and beta-glucan content and caecal SCFA concentration were determined. Additive suplementation had no impact on cFCR in birds fed the low AME diet, but in birds fed the high AME diet the cFCR value was reduced in the presence of the additives ( P = 0.001 and P = 0.015, at d 14–21 and d 21–35, respectively). At d 21, cecal SCFA concentration was consistently higher ( P = 0.015), and ileal beta-glucan level lower ( P = 0.002), in birds fed the diet supplemented with STB compared to those without additives. At d 35, ileal viscosity was lower in birds fed STB compared to those fed the diet without supplementation of additives, irrespective of diet AME level ( P = 0.017). These results suggest that both STB and Xyl + BG ameliorate the antinutritive effects of the non-starch polysaccharides ( NSP ) present in wheat-barley based diets, resulting in improved bird performance. However, supplementation with STB induces a comparatively greater positive effect on NSP hydrolysis and SCFA production.

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Section: Introductionmentioning

confidence: 99%

Comparing the efficacy of stimbiotic and a combination of xylanase and beta-glucanase, in broilers fed wheat-barley based diets with high or low AME

2021

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“…These negative effects can be combatted by supplementing the diet with endo-β1, 4-xylanases, which hydrolyses the xylan backbone. These enzymes cleave the internal β-xylosidic glycosidic linkages uninterrupted by side chains to short-chain xylans or xylo-oligosaccharides ( Jommuengbout et al., 2009 ), resulting in a mixture of low-molecular weight xylans, arabinose-substituted xylo-oligosaccharides (arabinoxylan-oligosaccharides, AXOS) and non-substituted xylo-oligosaccharides (XOS). Partial depolymerisation of AX by enzymes reduces molecular chains containing more than 5,000 sugars to just over 1,000 sugars.…”

Section: Introductionmentioning

confidence: 99%

Effect of arabinoxylo-oligosaccharides and arabinoxylans on net energy and nutrient utilization in broilers

et al. 2019

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Arabinoxylo-oligosaccharides (AXOS) are hydrolytic degradation products of arabinoxylans (AX) that can be fermented by the gut microbiota, thus potentially displaying prebiotic properties. This study examined the effects of AX and AXOS on net energy (NE) and nutrient utilization in broilers. Ross 308 broilers ( n = 90, 30 birds per treatment) were fed wheat-soybean diets supplemented with pure AX, AXOS produced by exposing the AX to xylanase in vitro (AXOS), or AX with xylanase (AX + E) from d 10 to 21. Performance parameters were measured from d 10 to 21. On d 15, 10 birds per treatment were allocated to closed-circuit net energy chambers to assess the impact of AX and AXOS on dietary energy utilization, through assessment of both metabolisable energy (ME) and NE. Ileal and caecal digesta samples were collected on d 21 to determine the effect of AX and AXOS on ileal and total tract dry matter digestibility, ileal digestible energy, digesta pH, short chain fatty acids (SCFA) and microbiota concentration. Feed conversion ratio was numerically the lowest in birds fed the diet supplemented with AXOS, which is 1.26 compared to 1.37 and 1.30 for AX and AX + E, respectively. Ileal dry matter digestibility was higher in birds fed AXOS than those fed AX ( P = 0.047). Ileal digestible energy and total tract dry matter digestibility were higher in birds fed AXOS than those fed AX or AX + E ( P = 0.004 and P = 0.001, respectively). Birds fed AXOS had higher ME intake ( P = 0.049) and nitrogen retention ( P = 0.001) and a strong trend of higher NE ( P = 0.056), NE intake ( P = 0.057) and retained energy ( P = 0.054) compared to those fed AX. Ileal total SCFA, lactic and formic acid concentrations were higher in birds fed AXOS than those fed AX ( P = 0.011, P = 0.012 and P = 0.023, respectively). Birds fed AXOS or AX + E had higher caecal total SCFA, acetic, butyric and isovaleric acid concentrations compared to those fed AX ( P = 0.001, P = 0.004, P = 0.016 and P = 0.008, respectively), and caecal propionic acid concentration was higher in birds fed AX + E than those fed AX ( P = 0.050). Ileal and caecal microbiota concentrations were numerically higher and pH was lower in birds fed AXOS and AX + E than those fed AX. Results from this study indicate that feeding AXOS directly is more efficient than AXOS generation in the gastrointestinal tract, and suggest that AXOS has a potential to be an efficacious prebiotic in broiler diets.

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“…However, endo-1,4β-xylanases (gene loci; CT4_03195 and CT4_04894), the main enzymes to attack the xylan backbone of strain CT4 T could not find the CBM. To explain how those xylanases were able to degrade xylan in cassava pulp, the enzymes might have other substrate-binding regions which are located at a certain distance from the active site and are called secondary xylan-binding sites (SXS), which function similarly to the CBM (Jommuengbout et al, 2009). Based on the amino acid sequence alignment of endo-1,4-β-xylanase (CT4_04894) with an endo-1,4-β-xylanase in the glycoside hydrolase family 10 (Xyn10) from Penicillium simplicissimum, which is capable of binding to insoluble xylan via the SXS, it was found that the residues E60, N61, K64, H97, W101, N142, E143, Y187, Q218, H220, E250, W283 and W291 of an endo-1,4-β-xylanase from strain CT4 T (CT4_04894) were conserved with the SXS of Xyn10 from P. simplicissimum (Schmidt, Gübitz & Kratky, 1999).…”

Section: Discussionmentioning

confidence: 99%

Clostridium manihotivorumsp. nov., a novel mesophilic anaerobic bacterium that produces cassava pulp-degrading enzymes

Cheawchanlertfa

Sutheeworapong

Jenjaroenpun

et al. 2020

PeerJ

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Background Cassava pulp is a promising starch-based biomasses, which consists of residual starch granules entrapped in plant cell wall containing non-starch polysaccharides, cellulose and hemicellulose. Strain CT4T, a novel mesophilic anaerobic bacterium isolated from soil collected from a cassava pulp landfill, has a strong ability to degrade polysaccharides in cassava pulp. This study explored a rarely described species within the genus Clostridium that possessed a group of cassava pulp-degrading enzymes. Methods A novel mesophilic anaerobic bacterium, the strain CT4T, was identified based on phylogenetic, genomic, phenotypic and chemotaxonomic analysis. The complete genome of the strain CT4T was obtained following whole-genome sequencing, assembly and annotation using both Illumina and Oxford Nanopore Technology (ONT) platforms. Results Analysis based on the 16S rRNA gene sequence indicated that strain CT4T is a species of genus Clostridium. Analysis of the whole-genome average amino acid identity (AAI) of strain CT4T and the other 665 closely related species of the genus Clostridium revealed a separated strain CT4T from the others. The results revealed that the genome consisted of a 6.3 Mb circular chromosome with 5,664 protein-coding sequences. Genome analysis result of strain CT4T revealed that it contained a set of genes encoding amylolytic-, hemicellulolytic-, cellulolytic- and pectinolytic enzymes. A comparative genomic analysis of strain CT4T with closely related species with available genomic information, C. amylolyticum SW408T, showed that strain CT4T contained more genes encoding cassava pulp-degrading enzymes, which comprised a complex mixture of amylolytic-, hemicellulolytic-, cellulolytic- and pectinolytic enzymes. This work presents the potential for saccharification of strain CT4T in the utilization of cassava pulp. Based on phylogenetic, genomic, phenotypic and chemotaxonomic data, we propose a novel species for which the name Clostridium manihotivorum sp. nov. is suggested, with the type strain CT4T (= TBRC 11758T = NBRC 114534T).

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Substrate-Binding Site of Family 11 Xylanase fromBacillus firmusK-1 by Molecular Docking

Cited by 38 publications

References 39 publications

Comparing the efficacy of stimbiotic and a combination of xylanase and beta-glucanase, in broilers fed wheat-barley based diets with high or low AME

Comparing the efficacy of stimbiotic and a combination of xylanase and beta-glucanase, in broilers fed wheat-barley based diets with high or low AME

Effect of arabinoxylo-oligosaccharides and arabinoxylans on net energy and nutrient utilization in broilers

Clostridium manihotivorumsp. nov., a novel mesophilic anaerobic bacterium that produces cassava pulp-degrading enzymes

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