Mechanism of Cooperative Degradation of Gum Arabic Arabinogalactan Protein by Bifidobacterium longum Surface Enzymes

Sasaki, Yuki; Komeno, Masahiro; Ishiwata, Akihiro; Horigome, Ayako; Odamaki, Toshitaka; Xiao, Jin‐zhong; Tanaka, Katsunori; Ito, Yukishige; Kitahara, Kuninori; Ashida, Hisashi; Fujita, Kiyotaka

doi:10.1128/aem.02187-21

Cited by 10 publications

(9 citation statements)

References 38 publications

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“…These enzymes are required for the degradation of a complex polysaccharide commonly present in plant cell walls, i.e., arabinogalactan, whose degradation has been demonstrated to be strain-dependent within the taxon Bifidobacterium longum subsp. longum ( Fujita et al, 2019 ; Wang and LaPointe, 2020 ; Sasaki et al, 2022 ). Furthermore, PRL2022 was shown to possess various genes involved in the transport/uptake of glycans as well as various glycosyl transferases ( Supplementary Table S6 ).…”

Section: Resultsmentioning

confidence: 99%

Identification of a prototype human gut Bifidobacterium longum subsp. longum strain based on comparative and functional genomic approaches

Alessandri

Fontana²,

Tarracchini³

et al. 2023

Front. Microbiol.

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Bifidobacteria are extensively exploited for the formulation of probiotic food supplements due to their claimed ability to exert health-beneficial effects upon their host. However, most commercialized probiotics are tested and selected for their safety features rather than for their effective abilities to interact with the host and/or other intestinal microbial players. In this study, we applied an ecological and phylogenomic-driven selection to identify novel B. longum subsp. longum strains with a presumed high fitness in the human gut. Such analyses allowed the identification of a prototype microorganism to investigate the genetic traits encompassed by the autochthonous bifidobacterial human gut communities. B. longum subsp. longum PRL2022 was selected due to its close genomic relationship with the calculated model representative of the adult human-gut associated B. longum subsp. longum taxon. The interactomic features of PRL2022 with the human host as well as with key representative intestinal microbial members were assayed using in vitro models, revealing how this bifidobacterial gut strain is able to establish extensive cross-talk with both the host and other microbial residents of the human intestine.

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Section: Resultsmentioning

confidence: 99%

Identification of a prototype human gut Bifidobacterium longum subsp. longum strain based on comparative and functional genomic approaches

Alessandri

Fontana²,

Tarracchini³

et al. 2023

Front. Microbiol.

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“…The increased L-arabinose may selectively enrich resident bacterial strains resulting in the shifts in the abundance of fecal abfA cluster, as they could benefit each other through microbial cross-feeding of L-arabinose released by arabinan degradation. Since these resident bacterial strains commonly harbor an abfA cluster, the abundance change of these key strains typically accompanied with a marked increase in the whole-community-level abfA cluster abundance 51, 52 .…”

Section: Resultsmentioning

confidence: 99%

Identification of a key genetic factor governing arabinan utilization in the gut microbiome suggests a novel therapeutic target for constipation

Zhang

et al. 2022

Preprint

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Probiotics have been widely used to improve impaired gastro-intestinal motility, yet their efficacy varied substantially across strains. Here, by a large-scale genetic screen plus in vivo measurements, we identified a key genetic factor (abfA cluster governing arabinan utilization) in probiotic Bifidobacterium longum harnessing the treatment efficacy against functional constipation (FC). Intriguingly, it also presents in a range of gut resident microbiota and played a protective role against FC. Next, our longitudinal multi-omics study in humans revealed that the exogenous abfA-cluster-carrying B. longum can well establish itself in the gut, and enrich arabinan-utilization residents and beneficial metabolites (e.g., acetate, butyrate, chenodeoxycholic acid and uracil). Finally, transplantation of abfA-cluster-enriched human microbiota to FC-induced germ-free mice recapitulated the marked gut-motility improvement and elevated production of beneficial metabolites. Collectively, our proof-of-concept study actively demonstrated a critical yet underexplored role of microbial abfA cluster in ameliorating FC, establishing generalizable principles for developing functional-genomics-directed probiotic therapies.

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“…The precipitate was collected via glass fiber filtration, washed several times, and resolved in water. The oligosaccharides (S3-GA, S3-AA, and S5-GA) were obtained from the supernatant following the ethanol precipitation of gum arabic reagent [8] , based on the method described by Tischer et al [15] β-L-Arap-(1→3)-α-L-Araf-OMe and α-D-Galp-(1→3)-α-L-Araf-OMe were prepared via the transglycosylation of GAfase with gum arabic and larch AGP, respectively [8] . pET23d_GAfase plasmid and recombinant GAfase were prepared as described previously [8] .…”

Section: Methodsmentioning

confidence: 99%

“…However, several Bifidobacterium species, particularly the adult type (Bifidobacterium longum subsp. longum, B. adolescentis, B. pseudocatenulatum, and B. catenulatum), possess extracellular carbohydrate-hydrolyzing enzymes that can access polysaccharides and glycoproteins directly, thereby enabling the production of transportable small saccharides from those such as resistant starch [2] , arabinan [3] , mannan [4] , extensin [5,6] , arabinogalactan protein (AGP) [7][8][9] , and arabinoxylan [10] .…”

Section: Introductionmentioning

confidence: 99%

“…In particular, the structures of type II arabinogalactan (AG) moieties from gum arabic and larch wood have been well studied and comprise a β-1,3-galactan backbone and β-1,6-galactan side chains with several modifications of other sugars [11][12][13] . Recently, we elucidated the molecular basis of assimilating gum arabic AGP in B. longum JCM7052 [8,9] . The extracellular glycoside hydrolase (GH) family 39 enzyme "3-O-α-D-galactosyl-α-L-arabinofuranosidase (GAfase)" can act on gum arabic AGP and facilitate the action of other enzymes for degrading the AGP backbone and modified sugar.…”

Section: Introductionmentioning

confidence: 99%

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Assimilation of arabinogalactan side chains with novel 3-O-β-L-arabinopyranosyl-α-L-arabinofuranosidase in bifidobacterium pseudocatenulatum

Sasaki¹,

Yanagita²,

Hashiguchi³

et al. 2023

Microbiome Res Rep

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Aim: Dietary plant fibers affect gut microbiota composition; however, the underlying microbial degradation pathways are not fully understood. We previously discovered 3-O-α-D-galactosyl-α-L-arabinofuranosidase (GAfase), a glycoside hydrolase family 39 enzyme involved in the assimilation of side chains of arabinogalactan protein (AGP), from Bifidobacterium longum subsp. longum JCM7052. Although GAfase homologs are not highly prevalent in the Bifidobacterium genus, several Bifidobacterium strains possess the homologs. To explore the differences in substrate specificity among the homologs, a homolog of B. longum GAfase in Bifidobacterium pseudocatenulatum MCC10289 (MCC10289_0425) was characterized. Methods: Gum arabic, larch, wheat AGP, and sugar beet arabinan were used to determine the substrate specificity of the MCC10289_0425 protein. An amino acid replacement was introduced into GAfase to identify a critical residue that governs the differentiation of substrate specificity. The growth of several Bifidobacterium strains on β-L-arabinopyranosyl disaccharide and larch AGP was examined. Results: MCC10289_0425 was identified to be an unprecedented 3-O-β-L-arabinopyranosyl-α-L-arabinofuranosidase (AAfase) with low GAfase activity. A single amino acid replacement (Asn119 to Tyr) at the catalytic site converted GAfase into AAfase. AAfase releases sugar source from AGP, thereby allowing B. pseudocatenulatum growth. Conclusion: Bifidobacteria have evolved several homologous enzymes with overlapping but distinct substrate specificities depending on the species. They have acquired different fitness abilities to respond to diverse plant polysaccharide structures.

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Mechanism of Cooperative Degradation of Gum Arabic Arabinogalactan Protein by Bifidobacterium longum Surface Enzymes

Cited by 10 publications

References 38 publications

Identification of a prototype human gut Bifidobacterium longum subsp. longum strain based on comparative and functional genomic approaches

Identification of a prototype human gut Bifidobacterium longum subsp. longum strain based on comparative and functional genomic approaches

Identification of a key genetic factor governing arabinan utilization in the gut microbiome suggests a novel therapeutic target for constipation

Assimilation of arabinogalactan side chains with novel 3-O-β-L-arabinopyranosyl-α-L-arabinofuranosidase in bifidobacterium pseudocatenulatum

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