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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0108

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_NFHS01000001.1

Nucelotide position range

745835-779958

Substrate

O-glycan,N-glycan

Loci

B5G17_RS02980-B5G17_RS03130

Species

Bacteroides uniformis/820

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- B5G17_RS02975 WP_087331937.1 0 - 173 (+) NZ_NFHS01000001.1:745835-746008 -
- B5G17_RS02980 WP_057089731.1 177 - 2442 (+) NZ_NFHS01000001.1:746012-748277 -
- B5G17_RS02985 WP_087331939.1 2688 - 3168 (+) NZ_NFHS01000001.1:748523-749003 -
- B5G17_RS02990 WP_005831704.1 3294 - 3522 (+) NZ_NFHS01000001.1:749129-749357 -
- B5G17_RS02995 WP_087331940.1 3655 - 4108 (+) NZ_NFHS01000001.1:749490-749943 -
- B5G17_RS03000 WP_087331942.1 4169 - 4718 (+) NZ_NFHS01000001.1:750004-750553 -
- B5G17_RS03005 WP_005832639.1 4767 - 5445 (+) NZ_NFHS01000001.1:750602-751280 -
- B5G17_RS03010 WP_005832637.1 5441 - 6731 (+) NZ_NFHS01000001.1:751276-752566 -
- B5G17_RS03015 WP_005831697.1 6823 - 7264 (+) NZ_NFHS01000001.1:752658-753099 -
- B5G17_RS03020 WP_087331944.1 7300 - 7804 (+) NZ_NFHS01000001.1:753135-753639 -
- B5G17_RS03025 WP_087331946.1 7891 - 9103 (-) NZ_NFHS01000001.1:753726-754938 4.3.1.17
- B5G17_RS03030 WP_087331948.1 9159 - 11697 (-) NZ_NFHS01000001.1:754994-757532 -
- B5G17_RS19105 WP_162612921.1 12818 - 12914 (+) NZ_NFHS01000001.1:758653-758749 -
- B5G17_RS03040 WP_087332026.1 13302 - 16026 (+) NZ_NFHS01000001.1:759137-761861 -
- B5G17_RS03045 - 16076 - 16490 (-) NZ_NFHS01000001.1:761911-762325 -
- B5G17_RS03060 WP_087331953.1 16848 - 17139 (+) NZ_NFHS01000001.1:762683-762974 -
- B5G17_RS03065 WP_016272732.1 17530 - 18067 (+) NZ_NFHS01000001.1:763365-763902 -
- B5G17_RS03070 WP_035457791.1 18096 - 19173 (+) NZ_NFHS01000001.1:763931-765008 -
- B5G17_RS03075 WP_087331955.1 19179 - 20235 (-) NZ_NFHS01000001.1:765014-766070 -
- B5G17_RS03085 WP_005832510.1 20423 - 21569 (+) NZ_NFHS01000001.1:766258-767404 -
- B5G17_RS03090 WP_034522675.1 21571 - 22315 (+) NZ_NFHS01000001.1:767406-768150 -
- B5G17_RS03095 WP_008664980.1 22307 - 23264 (+) NZ_NFHS01000001.1:768142-769099 -
- B5G17_RS03105 WP_087331957.1 23926 - 26464 (+) NZ_NFHS01000001.1:769761-772299 -
- B5G17_RS03110 WP_016272717.1 26510 - 29624 (-) NZ_NFHS01000001.1:772345-775459 -
- B5G17_RS03115 WP_005832500.1 29804 - 30509 (-) NZ_NFHS01000001.1:775639-776344 -
- B5G17_RS03120 WP_005831669.1 30690 - 31239 (+) NZ_NFHS01000001.1:776525-777074 -
- B5G17_RS03125 WP_087331959.1 31239 - 32568 (+) NZ_NFHS01000001.1:777074-778403 -
- B5G17_RS03130 WP_087331961.1 32744 - 34124 (+) NZ_NFHS01000001.1:778579-779959 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 173 (+) CDS No
- 178 - 2442 (+) CDS No
- 2689 - 3168 (+) CDS No
- 3295 - 3522 (+) CDS No
- 3656 - 4108 (+) CDS No
- 4170 - 4718 (+) CDS No
- 4768 - 5445 (+) TF: DBD-Pfam|Trans_reg_C No
- 5442 - 6731 (+) STP: STP|HisKA No
- 6824 - 7264 (+) CDS No
- 7301 - 7804 (+) CDS No
- 7892 - 9103 (-) CDS No
- 9160 - 11697 (-) CDS No
- 12819 - 12914 (+) CDS No
- 13303 - 16026 (+) CDS No
- 16849 - 17139 (+) CDS No
- 17531 - 18067 (+) CDS No
- 18097 - 19173 (+) CDS No
- 19180 - 20235 (-) CDS No
- 20424 - 21569 (+) CDS No
- 21572 - 22315 (+) TC: gnl|TC-DB|P42332|3.A.1.131.1 Yes
- 22308 - 23264 (+) other Yes
- 23927 - 26464 (+) CAZyme: GH2 Yes
- 26511 - 29624 (-) TC: gnl|TC-DB|Q93N33|2.A.21.9.2 Yes
- 29805 - 30509 (-) other Yes
- 30691 - 31239 (+) STP: STP|Sigma70_r2,STP|Sigma70_r4_2 Yes
- 31240 - 32568 (+) other Yes
- 32745 - 34124 (+) CAZyme: GH3 Yes

PUL ID

PUL0108

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.