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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0118

PubMed

32265336, mBio. 2020 Apr 7;11(2):e00095-20. doi: 10.1128/mBio.00095-20.

Characterization method

qRT-PCR,affinity gel electrophoresis,isothermal titration calorimetry

Genomic accession number

NZ_DS362241.1

Nucelotide position range

149200-163732

Substrate

laminarin,beta-glucan

Loci

BACUNI_RS07655-BACUNI_RS07685

Species

Bacteroides uniformis/820

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

bglX BACUNI_RS07655 WP_005826828.1 0 - 2253 (-) NZ_DS362241.1:149200-151453 3.2.1.21
- BACUNI_RS07660 WP_005826831.1 2255 - 3545 (-) NZ_DS362241.1:151455-152745 -
- BACUNI_RS07665 WP_005826833.1 3633 - 4995 (-) NZ_DS362241.1:152833-154195 -
- BACUNI_RS07670 WP_005826835.1 5133 - 6507 (-) NZ_DS362241.1:154333-155707 -
- BACUNI_RS07675 WP_005826837.1 6538 - 8128 (-) NZ_DS362241.1:155738-157328 -
- BACUNI_RS07680 WP_005826839.1 8146 - 11350 (-) NZ_DS362241.1:157346-160550 -
- BACUNI_RS07685 WP_005826840.1 11641 - 14533 (-) NZ_DS362241.1:160841-163733 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

bglX 1 - 2253 (-) CAZyme: CBM6|GH3 Yes
- 2256 - 3545 (-) CAZyme: GH158 Yes
- 3634 - 4995 (-) CAZyme: GH16 Yes
- 5134 - 6507 (-) other Yes
- 6539 - 8128 (-) other Yes
- 8147 - 11350 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 11642 - 14533 (-) STP: STP|Y_Y_Y,STP|GerE No

PUL ID

PUL0118

PubMed

32265336, mBio. 2020 Apr 7;11(2):e00095-20. doi: 10.1128/mBio.00095-20.

Title

Synergy between Cell Surface Glycosidases and Glycan-Binding Proteins Dictates the Utilization of Specific Beta(1,3)-Glucans by Human Gut Bacteroides.

Author

Dejean G, Tamura K, Cabrera A, Jain N, Pudlo NA, Pereira G, Viborg AH, Van Petegem F, Martens EC, Brumer H

Abstract

The human gut microbiota (HGM) has far-reaching impacts on human health and nutrition, which are fueled primarily by the metabolism of otherwise indigestible complex carbohydrates commonly known as dietary fiber. However, the molecular basis of the ability of individual taxa of the HGM to address specific dietary glycan structures remains largely unclear. In particular, the utilization of beta(1,3)-glucans, which are widespread in the human diet as yeast, seaweed, and plant cell walls, had not previously been resolved. Through a systems-based approach, here we show that the symbiont Bacteroides uniformis deploys a single, exemplar polysaccharide utilization locus (PUL) to access yeast beta(1,3)-glucan, brown seaweed beta(1,3)-glucan (laminarin), and cereal mixed-linkage beta(1,3)/beta(1,4)-glucan. Combined biochemical, enzymatic, and structural analysis of PUL-encoded glycoside hydrolases (GHs) and surface glycan-binding proteins (SGBPs) illuminates a concerted molecular system by which B. uniformis recognizes and saccharifies these distinct beta-glucans. Strikingly, the functional characterization of homologous beta(1,3)-glucan utilization loci (1,3GUL) in other Bacteroides further demonstrated that the ability of individual taxa to utilize beta(1,3)-glucan variants and/or beta(1,3)/beta(1,4)-glucans arises combinatorially from the individual specificities of SGBPs and GHs at the cell surface, which feed corresponding signals to periplasmic hybrid two-component sensors (HTCSs) via TonB-dependent transporters (TBDTs). These data reveal the importance of cooperativity in the adaptive evolution of GH and SGBP cohorts to address individual polysaccharide structures. We anticipate that this fine-grained knowledge of PUL function will inform metabolic network analysis and proactive manipulation of the HGM. Indeed, a survey of 2,441 public human metagenomes revealed the international, yet individual-specific, distribution of each 1,3GUL.IMPORTANCEBacteroidetes are a dominant phylum of the human gut microbiota (HGM) that target otherwise indigestible dietary fiber with an arsenal of polysaccharide utilization loci (PULs), each of which is dedicated to the utilization of a specific complex carbohydrate. Here, we provide novel insight into this paradigm through functional characterization of homologous PULs from three autochthonous Bacteroides species, which target the family of dietary beta(1,3)-glucans. Through detailed biochemical and protein structural analysis, we observed an unexpected diversity in the substrate specificity of PUL glycosidases and glycan-binding proteins with regard to beta(1,3)-glucan linkage and branching patterns. In combination, these individual enzyme and protein specificities support taxon-specific growth on individual beta(1,3)-glucans. This detailed metabolic insight, together with a comprehensive survey of individual 1,3GULs across human populations, further expands the fundamental roadmap of the HGM, with potential application to the future development of microbial intervention therapies.