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Glycan complexity dictates microbial resource allocation in the large intestine.

Rogowski A, Briggs JA, Mortimer JC, Tryfona T, Terrapon N, Lowe EC, Baslé A, Morland C, Day AM, Zheng H, Rogers TE, Thompson P, Hawkins AR, Yadav MP, Henrissat B, Martens EC, Dupree P, Gilbert HJ, Bolam DN - Nat Commun (2015)

Bottom Line: We show here, using xylan as a model, that sharing the breakdown products of complex carbohydrates by key members of the microbiota, such as Bacteroides ovatus, is dependent on the complexity of the target glycan.Characterization of the extensive xylan degrading apparatus expressed by B. ovatus reveals that the breakdown of the polysaccharide by the human gut microbiota is significantly more complex than previous models suggested, which were based on the deconstruction of xylans containing limited monosaccharide side chains.Our report presents a highly complex and dynamic xylan degrading apparatus that is fine-tuned to recognize the different forms of the polysaccharide presented to the human gut microbiota.

View Article: PubMed Central - PubMed

Affiliation: Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.

ABSTRACT
The structure of the human gut microbiota is controlled primarily through the degradation of complex dietary carbohydrates, but the extent to which carbohydrate breakdown products are shared between members of the microbiota is unclear. We show here, using xylan as a model, that sharing the breakdown products of complex carbohydrates by key members of the microbiota, such as Bacteroides ovatus, is dependent on the complexity of the target glycan. Characterization of the extensive xylan degrading apparatus expressed by B. ovatus reveals that the breakdown of the polysaccharide by the human gut microbiota is significantly more complex than previous models suggested, which were based on the deconstruction of xylans containing limited monosaccharide side chains. Our report presents a highly complex and dynamic xylan degrading apparatus that is fine-tuned to recognize the different forms of the polysaccharide presented to the human gut microbiota.

No MeSH data available.


Conservation of the B. ovatus ATCC 8483 xylan PULs in other Bacteroides species.CAZymes (green, CBM modules were omitted for clarity), susC-like (yellow), susD-like (orange) and the HTCS sensor-regulator (blue) genes are colour-coded. Genes encoding proteins of unknown function or non-CAZymes (for example, surface glycan binding protein and MFS carbohydrate importer in PUL-XylS) are shown in grey. (a) PUL-XylL. Vertical dotted lines indicate split gene models, while missing gene models are shown in red. Microsyntenic segments are depicted by grey connectors, and include adjacent conserved non-PUL members (shown with dotted lines). Eighteen genes are conserved across all strains, and 17 of these form three highly conserved blocks indicated on top. The major difference between the two groups of the GH98 for GH5_21 swap is indicated. Inset shows a TLC of the activity of the recombinant B. xylanisolvens XBA1 GH5_21 enzyme (BXY_29320; boxed in red) against different xylans (1 μM final enzyme vs 0.5% xylan in 20 mM sodium phosphate buffer, pH 7.0, 16 h at 37 °C). The B. xylanisolvens GH5 enzyme displays endo-xylanase activity against CX, producing a smear of large oligosaccharide products similar to the product profile observed for the B. ovatus GH98 enzyme, BACOVA_03438. The GH5 xylanase also hydrolyses WAX, unlike the GH98 enzyme, but displays no activity against BGX. X1-X5 indicates xylooligosaccharide standards. (b) PUL-XylS. The lower part of the panel shows the strains that contain only the second half of PUL-XylS that encodes the intracellular (periplasmic and cytoplasmic) enzymes only.
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f8: Conservation of the B. ovatus ATCC 8483 xylan PULs in other Bacteroides species.CAZymes (green, CBM modules were omitted for clarity), susC-like (yellow), susD-like (orange) and the HTCS sensor-regulator (blue) genes are colour-coded. Genes encoding proteins of unknown function or non-CAZymes (for example, surface glycan binding protein and MFS carbohydrate importer in PUL-XylS) are shown in grey. (a) PUL-XylL. Vertical dotted lines indicate split gene models, while missing gene models are shown in red. Microsyntenic segments are depicted by grey connectors, and include adjacent conserved non-PUL members (shown with dotted lines). Eighteen genes are conserved across all strains, and 17 of these form three highly conserved blocks indicated on top. The major difference between the two groups of the GH98 for GH5_21 swap is indicated. Inset shows a TLC of the activity of the recombinant B. xylanisolvens XBA1 GH5_21 enzyme (BXY_29320; boxed in red) against different xylans (1 μM final enzyme vs 0.5% xylan in 20 mM sodium phosphate buffer, pH 7.0, 16 h at 37 °C). The B. xylanisolvens GH5 enzyme displays endo-xylanase activity against CX, producing a smear of large oligosaccharide products similar to the product profile observed for the B. ovatus GH98 enzyme, BACOVA_03438. The GH5 xylanase also hydrolyses WAX, unlike the GH98 enzyme, but displays no activity against BGX. X1-X5 indicates xylooligosaccharide standards. (b) PUL-XylS. The lower part of the panel shows the strains that contain only the second half of PUL-XylS that encodes the intracellular (periplasmic and cytoplasmic) enzymes only.

Mentions: To identify PULs similar to PUL-XylL and -XylS in other genomes, we examined not only the gene family composition but also gene synteny in 260 Bacteroidetes species (Supplementary Table 8). Comparative genomics revealed a high degree of conservation of PUL-XylL in B. ovatus and B. xylanisolvens strains. Indeed, PULs with a high level of synteny with PUL-XylL was observed in 22 of the 23 strains examined. In these PULs, 17 genes show strict conservation with those present in PUL-XylL, which are arranged into three syntenic blocks (Fig. 8a). These 22 PUL-XylL homologues can be subdivided into two groups that differ by the presence of a tandem array of three genes. The three genes in group one PUL-XylLs, which encode GH30_8 (subfamily 8)45, GH98 and GH115 enzymes (including B. ovatus ATCC 8483), are replaced in group two PUL-XylLs by a single gene encoding a GH5 subfamily 21 (GH5_21)46 glycanase (Fig. 8a). Significantly, the GH5_21 enzyme from B. xylanisolvens XBA1 displays activity on CX (Fig. 8a inset), similar to the B. ovatus GH98 enzyme BACOVA_03433. This suggests that both forms of PUL-XylL retain the capacity to hydrolyse the backbone of complex GAXs without the need for extensive debranching. The high synteny described above for PUL-XylL in the B. ovatus and B. xylanisolvens strains was not found in any of the other 260 Bacteroidetes genomes analysed. In particular, the distribution of the GH98-encoding gene is extremely narrow, being present in only five of the 260 genomes analysed.


Glycan complexity dictates microbial resource allocation in the large intestine.

Rogowski A, Briggs JA, Mortimer JC, Tryfona T, Terrapon N, Lowe EC, Baslé A, Morland C, Day AM, Zheng H, Rogers TE, Thompson P, Hawkins AR, Yadav MP, Henrissat B, Martens EC, Dupree P, Gilbert HJ, Bolam DN - Nat Commun (2015)

Conservation of the B. ovatus ATCC 8483 xylan PULs in other Bacteroides species.CAZymes (green, CBM modules were omitted for clarity), susC-like (yellow), susD-like (orange) and the HTCS sensor-regulator (blue) genes are colour-coded. Genes encoding proteins of unknown function or non-CAZymes (for example, surface glycan binding protein and MFS carbohydrate importer in PUL-XylS) are shown in grey. (a) PUL-XylL. Vertical dotted lines indicate split gene models, while missing gene models are shown in red. Microsyntenic segments are depicted by grey connectors, and include adjacent conserved non-PUL members (shown with dotted lines). Eighteen genes are conserved across all strains, and 17 of these form three highly conserved blocks indicated on top. The major difference between the two groups of the GH98 for GH5_21 swap is indicated. Inset shows a TLC of the activity of the recombinant B. xylanisolvens XBA1 GH5_21 enzyme (BXY_29320; boxed in red) against different xylans (1 μM final enzyme vs 0.5% xylan in 20 mM sodium phosphate buffer, pH 7.0, 16 h at 37 °C). The B. xylanisolvens GH5 enzyme displays endo-xylanase activity against CX, producing a smear of large oligosaccharide products similar to the product profile observed for the B. ovatus GH98 enzyme, BACOVA_03438. The GH5 xylanase also hydrolyses WAX, unlike the GH98 enzyme, but displays no activity against BGX. X1-X5 indicates xylooligosaccharide standards. (b) PUL-XylS. The lower part of the panel shows the strains that contain only the second half of PUL-XylS that encodes the intracellular (periplasmic and cytoplasmic) enzymes only.
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f8: Conservation of the B. ovatus ATCC 8483 xylan PULs in other Bacteroides species.CAZymes (green, CBM modules were omitted for clarity), susC-like (yellow), susD-like (orange) and the HTCS sensor-regulator (blue) genes are colour-coded. Genes encoding proteins of unknown function or non-CAZymes (for example, surface glycan binding protein and MFS carbohydrate importer in PUL-XylS) are shown in grey. (a) PUL-XylL. Vertical dotted lines indicate split gene models, while missing gene models are shown in red. Microsyntenic segments are depicted by grey connectors, and include adjacent conserved non-PUL members (shown with dotted lines). Eighteen genes are conserved across all strains, and 17 of these form three highly conserved blocks indicated on top. The major difference between the two groups of the GH98 for GH5_21 swap is indicated. Inset shows a TLC of the activity of the recombinant B. xylanisolvens XBA1 GH5_21 enzyme (BXY_29320; boxed in red) against different xylans (1 μM final enzyme vs 0.5% xylan in 20 mM sodium phosphate buffer, pH 7.0, 16 h at 37 °C). The B. xylanisolvens GH5 enzyme displays endo-xylanase activity against CX, producing a smear of large oligosaccharide products similar to the product profile observed for the B. ovatus GH98 enzyme, BACOVA_03438. The GH5 xylanase also hydrolyses WAX, unlike the GH98 enzyme, but displays no activity against BGX. X1-X5 indicates xylooligosaccharide standards. (b) PUL-XylS. The lower part of the panel shows the strains that contain only the second half of PUL-XylS that encodes the intracellular (periplasmic and cytoplasmic) enzymes only.
Mentions: To identify PULs similar to PUL-XylL and -XylS in other genomes, we examined not only the gene family composition but also gene synteny in 260 Bacteroidetes species (Supplementary Table 8). Comparative genomics revealed a high degree of conservation of PUL-XylL in B. ovatus and B. xylanisolvens strains. Indeed, PULs with a high level of synteny with PUL-XylL was observed in 22 of the 23 strains examined. In these PULs, 17 genes show strict conservation with those present in PUL-XylL, which are arranged into three syntenic blocks (Fig. 8a). These 22 PUL-XylL homologues can be subdivided into two groups that differ by the presence of a tandem array of three genes. The three genes in group one PUL-XylLs, which encode GH30_8 (subfamily 8)45, GH98 and GH115 enzymes (including B. ovatus ATCC 8483), are replaced in group two PUL-XylLs by a single gene encoding a GH5 subfamily 21 (GH5_21)46 glycanase (Fig. 8a). Significantly, the GH5_21 enzyme from B. xylanisolvens XBA1 displays activity on CX (Fig. 8a inset), similar to the B. ovatus GH98 enzyme BACOVA_03433. This suggests that both forms of PUL-XylL retain the capacity to hydrolyse the backbone of complex GAXs without the need for extensive debranching. The high synteny described above for PUL-XylL in the B. ovatus and B. xylanisolvens strains was not found in any of the other 260 Bacteroidetes genomes analysed. In particular, the distribution of the GH98-encoding gene is extremely narrow, being present in only five of the 260 genomes analysed.

Bottom Line: We show here, using xylan as a model, that sharing the breakdown products of complex carbohydrates by key members of the microbiota, such as Bacteroides ovatus, is dependent on the complexity of the target glycan.Characterization of the extensive xylan degrading apparatus expressed by B. ovatus reveals that the breakdown of the polysaccharide by the human gut microbiota is significantly more complex than previous models suggested, which were based on the deconstruction of xylans containing limited monosaccharide side chains.Our report presents a highly complex and dynamic xylan degrading apparatus that is fine-tuned to recognize the different forms of the polysaccharide presented to the human gut microbiota.

View Article: PubMed Central - PubMed

Affiliation: Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.

ABSTRACT
The structure of the human gut microbiota is controlled primarily through the degradation of complex dietary carbohydrates, but the extent to which carbohydrate breakdown products are shared between members of the microbiota is unclear. We show here, using xylan as a model, that sharing the breakdown products of complex carbohydrates by key members of the microbiota, such as Bacteroides ovatus, is dependent on the complexity of the target glycan. Characterization of the extensive xylan degrading apparatus expressed by B. ovatus reveals that the breakdown of the polysaccharide by the human gut microbiota is significantly more complex than previous models suggested, which were based on the deconstruction of xylans containing limited monosaccharide side chains. Our report presents a highly complex and dynamic xylan degrading apparatus that is fine-tuned to recognize the different forms of the polysaccharide presented to the human gut microbiota.

No MeSH data available.