Multiple Transporters and Glycoside Hydrolases Are Involved in Arabinoxylan-Derived Oligosaccharide Utilization in Bifidobacterium pseudocatenulatum

Abstract

Arabinoxylan hydrolysates (AXH) are the hydrolyzed products of the major components of dietary fibers, arabinoxylan. AXH include diverse oligosaccharides varying in xylose polymerization and side residue modifications with arabinose at the O-2 and/or O-3 positions of the xylose unit. Previous studies have reported that AXH exhibit prebiotic properties on gut bifidobacteria; moreover, several adult-associated bifidobacterial species (e.g., Bifidobacterium adolescentis and Bifidobacterium longum ssp. longum) are known to utilize AXH. In this study, we tried to elucidate the molecular mechanisms of AXH utilization by Bifidobacterium pseudocatenulatum, which is a common bifidobacterial species found in adult feces. We performed RNA-seq transcriptomic analysis of B. pseudocatenulatum YIT 4072T, which identified three up-regulated gene clusters during AXH utilization. The gene clusters encoded three sets of ATP-binding cassette (ABC) transporters and five enzymes belonging to the glycoside hydrolase family 43 (GH43). By characterizing the recombinant proteins, we found that three solute-binding proteins of ABC transporters showed either broad or narrow specificity: two arabinofuranosidases hydrolyze either single- or double-decorated arabinoxylooligosaccharides: three xylosidases exhibited functionally identical activity. These data collectively suggest that the transporters and glycoside hydrolases, encoded in the three gene clusters, work together to utilize AXH of different sizes and side residue modifications. Thus, our study sheds light on the overall picture of how these proteins collaborate for utilization of AXH in B. pseudocatenulatum, and may explain the predominance of this symbiont species in the adult human gut. Importance Bifidobacteria commonly reside in the human intestine and possess abundant genes involved in carbohydrate utilization. Arabinoxylan hydrolysates (AXH) are hydrolyzed products of arabinoxylan, one of the most abundant dietary fibers, and they include xylooligosaccharides and those decorated with arabinofuranosyl residues. The molecular mechanism by which B. pseudocatenulatum, a common bifidobacterial species found in adult feces, utilizes structurally and compositionally variable AXH is yet to be extensively investigated. In this study, we identified three gene clusters (encoding five GH43 enzymes and three solute-binding proteins of ABC transporters) that were up-regulated in B. pseudocatenulatum YIT 4072T during AXH utilization. By investigating their substrate specificities, we revealed how these proteins are involved in the uptake and degradation of AXH. These molecular insights may provide a better understanding of how resident bifidobacteria colonize the colon.

Gene–Phenotype Associations Involving Human-Residential Bifidobacteria (HRB) Reveal Significant Species- and Strain-Specificity in Carbohydrate Catabolism

“…Previous studies have identified several GH43 family enzymes in bifidobacteria that degrade xylan-related carbon sources [ 36 ]. In addition, the enzymes belonging to GH8, GH10, and GH120 families may also participate in XOS or xylan degradation [ 37 , 38 ].…”

“…For example, two β-xylosidase, XylB from GH120 family and XylC from GH43 family, with different specificities have been in vitro characterized in B. adolescentis [ 64 ]. Recent study has also characterized three xylosidases from GH43 family in B. pseudocatenulatum and these enzymes exhibit functionally identical activity in XOS degradation [ 36 ]. Moreover, extracellular β-xylanase (GH10) may provide some B. pseudocatenulatum strains stronger long-chain xylan utilization abilities.…”

Exploring the Genomic Diversity and Antimicrobial Susceptibility of Bifidobacterium pseudocatenulatum in a Vietnamese Population

“…In line with this observation, experimental study showed that B . pseudocatenulatum could utilize several components of arabinoxylan hydrolysates (AXH) via the upregulation of three GH43-ABC transporter clusters ( 43 ). This feature likely explains the abundance and persistence of B .…”

Exploring the genomic diversity and antimicrobial susceptibility ofBifidobacterium pseudocatenulatumin the Vietnamese population to aid probiotic design

“…Our results reiterate previous findings on the genomic characterization of the Bifidobacterium genus (6) and Bp in the European population (33), showing that the species harbors an expansive repertoire of enzymes (GH13, GH43) responsible for the assimilation of complex plant-derived carbohydrates, but not host-derived glycan (mucin, HMO). In line with this observation, experimental study showed that Bp could utilize several components of arabinoxylan hydrolysates (AXH), via the upregulation of three GH43 -ABC transporter clusters (34). This feature likely explains the abundance and persistence of Bp through adulthood in the Vietnamese gut microbiota, since the organism may thrive on non-digestible carbohydrates enriched with fruits and vegetables.…”