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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0097

PubMed

31275257, Front Microbiol. 2019 Jun 7;10:1286. doi: 10.3389/fmicb.2019.01286. eCollection 2019.

Characterization method

sequence homology analysis

Genomic accession number

NZ_KB905472.1

Nucelotide position range

535723-561211

Substrate

O-glycan,N-glycan

Loci

None

Species

Bacteroides massiliensis/204516

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- HMPREF1534_RS16690 WP_005936482.1 0 - 1853 (+) NZ_KB905472.1:535723-537576 -
nanU HMPREF1534_RS16685 WP_005936484.1 1883 - 3398 (+) NZ_KB905472.1:537606-539121 -
- HMPREF1534_RS16680 WP_005936486.1 3525 - 5166 (+) NZ_KB905472.1:539248-540889 -
- HMPREF1534_RS16675 WP_025066736.1 5166 - 7176 (+) NZ_KB905472.1:540889-542899 -
- HMPREF1534_RS16670 WP_005936493.1 7177 - 7843 (+) NZ_KB905472.1:542900-543566 -
- HMPREF1534_RS16665 WP_005936496.1 7839 - 9909 (+) NZ_KB905472.1:543562-545632 -
- HMPREF1534_RS16660 WP_005936499.1 9961 - 12562 (+) NZ_KB905472.1:545684-548285 -
- HMPREF1534_RS16655 WP_005936501.1 12577 - 14902 (+) NZ_KB905472.1:548300-550625 -
- HMPREF1534_RS16650 WP_005936504.1 14918 - 16058 (+) NZ_KB905472.1:550641-551781 -
- HMPREF1534_RS16645 WP_005936507.1 16054 - 18115 (+) NZ_KB905472.1:551777-553838 -
- HMPREF1534_RS16640 WP_005936510.1 18121 - 20374 (+) NZ_KB905472.1:553844-556097 -
- HMPREF1534_RS16635 WP_005936513.1 20382 - 22887 (+) NZ_KB905472.1:556105-558610 -
nagA HMPREF1534_RS16630 WP_005936515.1 23065 - 24229 (+) NZ_KB905472.1:558788-559952 3.5.1.25
- HMPREF1534_RS16625 WP_005936518.1 24452 - 25106 (-) NZ_KB905472.1:560175-560829 -
- HMPREF1534_RS16620 WP_005936521.1 25102 - 25489 (-) NZ_KB905472.1:560825-561212 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1853 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
nanU 1884 - 3398 (+) TC: gnl|TC-DB|Q5LEN2|8.A.46.1.4 Yes
- 3526 - 5166 (+) CAZyme: GH33 Yes
- 5167 - 7176 (+) CAZyme: GH20 Yes
- 7178 - 7843 (+) other Yes
- 7840 - 9909 (+) other Yes
- 9962 - 12562 (+) CAZyme: GH2 Yes
- 12578 - 14902 (+) CAZyme: GH20 Yes
- 14919 - 16058 (+) other Yes
- 16055 - 18115 (+) CAZyme: GH20 Yes
- 18122 - 20374 (+) CAZyme: GH92 Yes
- 20383 - 22887 (+) CAZyme: GH2 Yes
nagA 23066 - 24229 (+) CAZyme: CE9 Yes
- 24453 - 25106 (-) TC: gnl|TC-DB|Q18BL2|3.A.1.124.6 Yes
- 25103 - 25489 (-) CDS No

PUL ID

PUL0097

PubMed

31275257, Front Microbiol. 2019 Jun 7;10:1286. doi: 10.3389/fmicb.2019.01286. eCollection 2019.

Title

Investigating Host Microbiota Relationships Through Functional Metagenomics.

Author

Laville E, Perrier J, Bejar N, Maresca M, Esque J, Tauzin AS, Bouhajja E, Leclerc M, Drula E, Henrissat B, Berdah S, Di Pasquale E, Robe P, Potocki-Veronese G

Abstract

The human Intestinal mucus is formed by glycoproteins, the O- and N-linked glycans which constitute a crucial source of carbon for commensal gut bacteria, especially when deprived of dietary glycans of plant origin. In recent years, a dozen carbohydrate-active enzymes from cultivated mucin degraders have been characterized. But yet, considering the fact that uncultured species predominate in the human gut microbiota, these biochemical data are far from exhaustive. In this study, we used functional metagenomics to identify new metabolic pathways in uncultured bacteria involved in harvesting mucin glycans. First, we performed a high-throughput screening of a fosmid metagenomic library constructed from the ileum mucosa microbiota using chromogenic substrates. The screening resulted in the isolation of 124 clones producing activities crucial in the degradation of human O- and N-glycans, namely sialidases, beta-D-N-acetyl-glucosaminidase, beta-D-N-acetyl-galactosaminidase, and/or beta-D-mannosidase. Thirteen of these clones were selected based on their diversified functional profiles and were further analyzed on a secondary screening. This step consisted of lectin binding assays to demonstrate the ability of the clones to degrade human intestinal mucus. In total, the structural modification of several mucin motifs, sialylated mucin ones in particular, was evidenced for nine clones. Sequencing their metagenomic loci highlighted complex catabolic pathways involving the complementary functions of glycan sensing, transport, hydrolysis, deacetylation, and deamination, which were sometimes associated with amino acid metabolism machinery. These loci are assigned to several Bacteroides and Feacalibacterium species highly prevalent and abundant in the gut microbiome and explain the metabolic flexibility of gut bacteria feeding both on dietary and human glycans.