Limits...
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.


Related in: MedlinePlus

Schematic of the B. ovatus xylan PULs and differential expression during growth on different xylans.(a,b) schematic of PUL-XylL and PUL-XylS, respectively. Each gene is drawn to scale as a rectangle with its orientation indicated by the arrow head. The numbers below each gene is its locus tag (bacova_XXXXX). Genes encoding known or predicted functionalities are colour-coded and, where appropriate, are also annotated according to their CAZy family number: glycoside hydrolase (GH; green), carbohydrate esterase (CE; purple), carbohydrate-binding module (CBM). Surface located proteins are marked with an asterisk. SGBP=surface glycan binding proteins are coloured orange, or, if also in a CAZy family (BACOVA_03431; inactive GH10), are coloured half orange, half green. UNK=unknown (purple), but distant similarity to CE6 carbohydrate esterases. HTCS=hybrid two component system (light or dark blue). MFS=transporter of the major facilitator superfamily (pink). Grey=unknown function (note, there is a structure of BACOVA_03430, PDB accession code 3N91). SusC-like (yellow) and SusD-like (light tan) proteins are a defining feature of PULs and are responsible for import of complex glycans across the outer membrane18. SusC-like proteins are TonB-dependent transporters, while SusD-like proteins are surface lipoproteins that likely function to deliver the target glycan to their partner SusC. (c) Cells were grown on minimal media with polysaccharide as the sole carbon source, and levels of different susC transcripts (locus tags shown; used as a proxy for expression of the whole PUL) from each PUL were quantified by qRT-PCR. The y-axis shows the Log fold-change relative to a minimal media-glucose reference; x-axis labels indicate the xylans used. WAX= wheat arabinoxylan, CX=corn xylan, BGX=birchwood glucuronoxylan. CX is a highly complex xylan compared to WAX and BGX. All data were analysed by one-way ANOVA followed by Tukey's multiple comparison test (***=P≤0.001).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4491172&req=5

f2: Schematic of the B. ovatus xylan PULs and differential expression during growth on different xylans.(a,b) schematic of PUL-XylL and PUL-XylS, respectively. Each gene is drawn to scale as a rectangle with its orientation indicated by the arrow head. The numbers below each gene is its locus tag (bacova_XXXXX). Genes encoding known or predicted functionalities are colour-coded and, where appropriate, are also annotated according to their CAZy family number: glycoside hydrolase (GH; green), carbohydrate esterase (CE; purple), carbohydrate-binding module (CBM). Surface located proteins are marked with an asterisk. SGBP=surface glycan binding proteins are coloured orange, or, if also in a CAZy family (BACOVA_03431; inactive GH10), are coloured half orange, half green. UNK=unknown (purple), but distant similarity to CE6 carbohydrate esterases. HTCS=hybrid two component system (light or dark blue). MFS=transporter of the major facilitator superfamily (pink). Grey=unknown function (note, there is a structure of BACOVA_03430, PDB accession code 3N91). SusC-like (yellow) and SusD-like (light tan) proteins are a defining feature of PULs and are responsible for import of complex glycans across the outer membrane18. SusC-like proteins are TonB-dependent transporters, while SusD-like proteins are surface lipoproteins that likely function to deliver the target glycan to their partner SusC. (c) Cells were grown on minimal media with polysaccharide as the sole carbon source, and levels of different susC transcripts (locus tags shown; used as a proxy for expression of the whole PUL) from each PUL were quantified by qRT-PCR. The y-axis shows the Log fold-change relative to a minimal media-glucose reference; x-axis labels indicate the xylans used. WAX= wheat arabinoxylan, CX=corn xylan, BGX=birchwood glucuronoxylan. CX is a highly complex xylan compared to WAX and BGX. All data were analysed by one-way ANOVA followed by Tukey's multiple comparison test (***=P≤0.001).

Mentions: The genomes of Bacteroidetes contain numerous polysaccharide utilization loci (PULs) that are optimized to orchestrate the degradation of specific polysaccharides4171819. The glycans targeted by the PULs activate transcription of their cognate loci. Bacteroides ovatus strain ATCC 8483 contains two PULs, spanning locus tags bacova_03417-50 (large xylan PUL or PUL-XylL) and bacova_04385-94 (small xylan PUL or PUL-XylS), that are activated when the organism is grown on wheat arabinoxylan4 (WAX) (Fig. 2a,b). In contrast, linear xylooligosaccharides (preferentially xylotetraose) induce transcription of PUL-XylS alone4. Here we show that growth on CX leads to significant activation of PUL-XylL and only very low activation of PUL-XylS, while glucuronoxylan (from birch; BGX) activates only PUL-XylS (Fig. 2c). These data suggest that the degradative system encoded by PUL-XylS targets simple linear or glucurono-substituted xylans, while the products of PUL-XylL drive the metabolism of more complex decorated forms of the hemicellulose. Bacteroidetes spp. are known to express enzymes capable of breaking down simple forms of xylan2021; however, the mechanisms by which these microorganisms utilize complex cereal GAXs (for example, CX) are not known. Both PULs encode glycanases belonging to GH families16 that are known to contribute to the degradation of simple xylans (GH3, GH10, GH30, GH43, GH67 and GH115)22 (Fig. 2a,b). Significantly, PUL-XylL also directs the synthesis of enzymes belonging to families (GH31, GH95, GH97 and GH98)4 not previously implicated in the deconstruction of the hemicellulose (Fig. 2a).


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)

Schematic of the B. ovatus xylan PULs and differential expression during growth on different xylans.(a,b) schematic of PUL-XylL and PUL-XylS, respectively. Each gene is drawn to scale as a rectangle with its orientation indicated by the arrow head. The numbers below each gene is its locus tag (bacova_XXXXX). Genes encoding known or predicted functionalities are colour-coded and, where appropriate, are also annotated according to their CAZy family number: glycoside hydrolase (GH; green), carbohydrate esterase (CE; purple), carbohydrate-binding module (CBM). Surface located proteins are marked with an asterisk. SGBP=surface glycan binding proteins are coloured orange, or, if also in a CAZy family (BACOVA_03431; inactive GH10), are coloured half orange, half green. UNK=unknown (purple), but distant similarity to CE6 carbohydrate esterases. HTCS=hybrid two component system (light or dark blue). MFS=transporter of the major facilitator superfamily (pink). Grey=unknown function (note, there is a structure of BACOVA_03430, PDB accession code 3N91). SusC-like (yellow) and SusD-like (light tan) proteins are a defining feature of PULs and are responsible for import of complex glycans across the outer membrane18. SusC-like proteins are TonB-dependent transporters, while SusD-like proteins are surface lipoproteins that likely function to deliver the target glycan to their partner SusC. (c) Cells were grown on minimal media with polysaccharide as the sole carbon source, and levels of different susC transcripts (locus tags shown; used as a proxy for expression of the whole PUL) from each PUL were quantified by qRT-PCR. The y-axis shows the Log fold-change relative to a minimal media-glucose reference; x-axis labels indicate the xylans used. WAX= wheat arabinoxylan, CX=corn xylan, BGX=birchwood glucuronoxylan. CX is a highly complex xylan compared to WAX and BGX. All data were analysed by one-way ANOVA followed by Tukey's multiple comparison test (***=P≤0.001).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4491172&req=5

f2: Schematic of the B. ovatus xylan PULs and differential expression during growth on different xylans.(a,b) schematic of PUL-XylL and PUL-XylS, respectively. Each gene is drawn to scale as a rectangle with its orientation indicated by the arrow head. The numbers below each gene is its locus tag (bacova_XXXXX). Genes encoding known or predicted functionalities are colour-coded and, where appropriate, are also annotated according to their CAZy family number: glycoside hydrolase (GH; green), carbohydrate esterase (CE; purple), carbohydrate-binding module (CBM). Surface located proteins are marked with an asterisk. SGBP=surface glycan binding proteins are coloured orange, or, if also in a CAZy family (BACOVA_03431; inactive GH10), are coloured half orange, half green. UNK=unknown (purple), but distant similarity to CE6 carbohydrate esterases. HTCS=hybrid two component system (light or dark blue). MFS=transporter of the major facilitator superfamily (pink). Grey=unknown function (note, there is a structure of BACOVA_03430, PDB accession code 3N91). SusC-like (yellow) and SusD-like (light tan) proteins are a defining feature of PULs and are responsible for import of complex glycans across the outer membrane18. SusC-like proteins are TonB-dependent transporters, while SusD-like proteins are surface lipoproteins that likely function to deliver the target glycan to their partner SusC. (c) Cells were grown on minimal media with polysaccharide as the sole carbon source, and levels of different susC transcripts (locus tags shown; used as a proxy for expression of the whole PUL) from each PUL were quantified by qRT-PCR. The y-axis shows the Log fold-change relative to a minimal media-glucose reference; x-axis labels indicate the xylans used. WAX= wheat arabinoxylan, CX=corn xylan, BGX=birchwood glucuronoxylan. CX is a highly complex xylan compared to WAX and BGX. All data were analysed by one-way ANOVA followed by Tukey's multiple comparison test (***=P≤0.001).
Mentions: The genomes of Bacteroidetes contain numerous polysaccharide utilization loci (PULs) that are optimized to orchestrate the degradation of specific polysaccharides4171819. The glycans targeted by the PULs activate transcription of their cognate loci. Bacteroides ovatus strain ATCC 8483 contains two PULs, spanning locus tags bacova_03417-50 (large xylan PUL or PUL-XylL) and bacova_04385-94 (small xylan PUL or PUL-XylS), that are activated when the organism is grown on wheat arabinoxylan4 (WAX) (Fig. 2a,b). In contrast, linear xylooligosaccharides (preferentially xylotetraose) induce transcription of PUL-XylS alone4. Here we show that growth on CX leads to significant activation of PUL-XylL and only very low activation of PUL-XylS, while glucuronoxylan (from birch; BGX) activates only PUL-XylS (Fig. 2c). These data suggest that the degradative system encoded by PUL-XylS targets simple linear or glucurono-substituted xylans, while the products of PUL-XylL drive the metabolism of more complex decorated forms of the hemicellulose. Bacteroidetes spp. are known to express enzymes capable of breaking down simple forms of xylan2021; however, the mechanisms by which these microorganisms utilize complex cereal GAXs (for example, CX) are not known. Both PULs encode glycanases belonging to GH families16 that are known to contribute to the degradation of simple xylans (GH3, GH10, GH30, GH43, GH67 and GH115)22 (Fig. 2a,b). Significantly, PUL-XylL also directs the synthesis of enzymes belonging to families (GH31, GH95, GH97 and GH98)4 not previously implicated in the deconstruction of the hemicellulose (Fig. 2a).

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.


Related in: MedlinePlus