<i>Bacteroides thetaiotaomicron</i> VPI‐5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions

Kim, Young Min; Yamamoto, Eiji; Kang, Min Sun; Nakai, Hiroyuki; Saburi, Wataru; Okuyama, Masayuki; Mori, Haruhide; Funane, Kazumi; Momma, Mitsuru; Fujimoto, Zui; Kobayashi, Mikihiko; Kim, Doman; Kimura, Atsuo

doi:10.1111/j.1742-4658.2012.08698.x

Cited by 20 publications

(8 citation statements)

References 25 publications

(50 reference statements)

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“…Of particular interest is a PUL encoding proteins with GH97, CBM20, and CBM69 domains, all of which have documented activity on starch (47, 48). While the only outer-membrane localized hydrolase in this PUL is a GH66, and members of this family have characterized activity on the alpha-1,6 linkages between glucose monomers in dextran (49), it is plausible that this PUL can be repurposed and confers some ability to grow on starch.…”

Section: Discussionmentioning

confidence: 99%

Muribaculaceae genomes assembled from metagenomes suggest genetic drivers of differential response to acarbose treatment in mice

Smith¹,

Miller

Schmidt

2020

Preprint

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AbstractThe drug acarbose (ACA) is used to treat diabetes, and by inhibiting alpha-amylase in the small intestine increases the amount of starch entering the lower digestive tract. This results in changes to the composition of the microbiota and its fermentation products. Acarbose also increases longevity in mice, an effect that could be related to increased production of the short-chain fatty acids propionate and butyrate. In experiments replicated across three study sites, two distantly related species in the bacterial family Muribaculaceae were dramatically more abundant in ACA treated mice, distinguishing these responders from other members of the family. Members of the Muribaculaceae likely produce propionate and are abundant and diverse in the guts of mice, although few isolates are available. We reconstructed genomes from metagenomes (MAGs) for eight populations of Muribaculaceae to examine what distinguishes species that respond positively to acarbose. We found two closely related MAGs (B1-A and B1-B) from one responsive species that both contain a polysaccharide utilization locus with a predicted extracellular alpha-amylase. These also shared a periplasmic neopullulanase with another, distantly related MAG (B2) representative of the only other responsive species. This gene differentiated these three MAGs from MAGs representative of non-responding species. Differential gene content in B1-A and B1-B may be associated with the inconsistent response of this species to acarbose across study sites. This work demonstrates the utility of culture-free genomics for inferring the ecological roles of gut bacteria including their response to pharmaceutical perturbations.ImportanceThe drug acarbose is used to treat diabetes by preventing the breakdown of starch in the small intestine, resulting in dramatic changes in the abundance of some members of the gut microbiome and its fermentation products. In mice, several of the bacteria that respond most positively are classified in the family Muribaculaceae, members of which produce propionate as a primary fermentation product. Propionate has been associated with gut health and increased longevity in mice. We found that genomes of the most responsive Muribaculaceae showed signs of specialization for starch fermentation, presumably providing them a competitive advantage in the large intestine of animals consuming acarbose. Comparisons among genomes support existing models for the ecological niches occupied by members of this family. In addition, genes encoding one type of enzyme known to participate in starch breakdown were found in all three genomes from responding species, but none of the others.

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Section: Discussionmentioning

confidence: 99%

Muribaculaceae genomes assembled from metagenomes suggest genetic drivers of differential response to acarbose treatment in mice

Smith¹,

Miller

Schmidt

2020

Preprint

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“…In addition, there are couple of reports about cloning and expression of the dextranase from Bacteroides spp., such as B. thetaiotaomicron 489 and B. thetaiotaomicron VPI‐5482. 31,32 Dextranase from B. thetaiotaomicron VPI‐5482 showed endo‐dextranase activity to synthesize isomaltooligosaccharides (DP>4) as well as cyclic form of oligomers . Dextran‐oligosaccharides could be produced by acid treatment of dextran .…”

Section: Discussionmentioning

confidence: 99%

Isolation of dextran‐hydrolyzing intestinal bacteria and characterization of their dextranolytic activities

et al. 2015

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The aim of this study was to isolate dextran-hydrolyzing bacteria from the human intestines and to identify their dextranolytic enzymes. For this, dextranase-producing microorganisms were screened from fecal samples by using blue dextran-containing media. Colonies producing a decolorized zone were isolated and they were grouped using RAPD-PCR. 16S rRNA gene sequencing analysis revealed the isolates were Bacteroides (B.) thetaiotaomicron, B. ovatus, B. vulgatus, B. dorei, B. xylanisolvens, B. uniformis, and Veillonella (V.) rogosae. Thin layer chromatography analysis showed that the dextranases exhibit mainly endo-type activity and produce various oligosaccharides including isomaltose and isomaltotriose. Zymogram analysis demonstrated that enzymes localized mainly in the cell membrane fraction and the molecular weight was 50-70 kDa. When cultured in a dextran-containing medium, all strains isolated in this study produced short-chain fatty acids, with butyric acid as the major compound. This is the first study to report that human intestinal B. xylanisolvens, B. dorei, and V. rogosae metabolize dextran utilizing dextranolytic enzymes.

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“…Recently, both Bacteroides thetaiotaomicron dextranase lacking this inserted domain and Paenibacillus sp. endo-dextranases containing the CBM35 domain have been reported to show CI producing activity, although the activity of these two enzymes is reduced when compared with the activity of BcCITase (48,49). Furthermore, deletion mutants, in which BcCBM35-1 is removed from BcCITase, still retain approximately one-twentieth of the CI producing activity of the wildtype enzyme (21).…”

Section: Discussionmentioning

confidence: 99%

Structural Elucidation of the Cyclization Mechanism of α-1,6-Glucan by Bacillus circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase

Suzuki

Fujimoto

Kim

et al. 2014

Journal of Biological Chemistry

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Background: Cycloisomaltooligosaccharide glucanotransferase catalyzes an intramolecular transglucosylation reaction and produces cycloisomaltooligosaccharides from dextran. Results: The crystal structure of Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase was determined. Conclusion:The enzyme structures complexed with isomaltooligosaccharides and cycloisomaltooctaose revealed the molecular mechanism of action. Significance: CBM35 functions in the product size determination and substrate recruitment.

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Bacteroides thetaiotaomicron VPI‐5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions

Cited by 20 publications

References 25 publications

Muribaculaceae genomes assembled from metagenomes suggest genetic drivers of differential response to acarbose treatment in mice

Muribaculaceae genomes assembled from metagenomes suggest genetic drivers of differential response to acarbose treatment in mice

Isolation of dextran‐hydrolyzing intestinal bacteria and characterization of their dextranolytic activities

Structural Elucidation of the Cyclization Mechanism of α-1,6-Glucan by Bacillus circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase

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