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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0105

PubMed

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

Characterization method

fosmid library screen,lectin binding assay

Genomic accession number

LR131284.1

Nucelotide position range

577-44510

Substrate

O-glycan,N-glycan

Loci

VDS02648.1-VDS02683.1

Species

uncultured bacterium/77133

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- - VDS02648.1 577 - 1651 (-) LR131284.1:1154-2228 -
- - VDS02649.1 2095 - 3718 (-) LR131284.1:2672-4295 3.2.1.18
- - VDS02650.1 3733 - 4117 (-) LR131284.1:4310-4694 -
- - VDS02651.1 4199 - 5438 (-) LR131284.1:4776-6015 -
- - VDS02652.1 5476 - 6661 (-) LR131284.1:6053-7238 5.1.3.8
- - VDS02653.1 6671 - 7589 (-) LR131284.1:7248-8166 4.1.3.3
- - VDS02654.1 7680 - 8763 (-) LR131284.1:8257-9340 -
- - VDS02655.1 9062 - 10271 (+) LR131284.1:9639-10848 -
- - VDS02656.1 10333 - 10543 (-) LR131284.1:10910-11120 -
- - VDS02657.1 10549 - 10792 (-) LR131284.1:11126-11369 -
- - VDS02658.1 10806 - 11259 (-) LR131284.1:11383-11836 -
- - VDS02659.1 11270 - 11918 (-) LR131284.1:11847-12495 -
- - VDS02660.1 11934 - 12507 (-) LR131284.1:12511-13084 -
- - VDS02661.1 12535 - 13405 (-) LR131284.1:13112-13982 -
- - VDS02662.1 13430 - 13751 (-) LR131284.1:14007-14328 -
- - VDS02663.1 14285 - 17702 (+) LR131284.1:14862-18279 3.2.1.40
- - VDS02664.1 17782 - 18676 (-) LR131284.1:18359-19253 -
- - VDS02665.1 18650 - 18812 (-) LR131284.1:19227-19389 -
- - VDS02666.1 18838 - 20317 (+) LR131284.1:19415-20894 2.7.1.5
- - VDS02667.1 20323 - 21577 (+) LR131284.1:20900-22154 5.3.1.14
- - VDS02668.1 21642 - 22653 (+) LR131284.1:22219-23230 -
- - VDS02669.1 22679 - 23489 (+) LR131284.1:23256-24066 4.1.2.19
- - VDS02670.1 23521 - 24676 (+) LR131284.1:24098-25253 1.1.1.77
- - VDS02671.1 24896 - 25802 (-) LR131284.1:25473-26379 2.3.1.30
- - VDS02672.1 25890 - 26022 (+) LR131284.1:26467-26599 -
- - VDS02673.1 26101 - 28252 (-) LR131284.1:26678-28829 -
- - VDS02674.1 28400 - 29303 (+) LR131284.1:28977-29880 -
- - VDS02675.1 29307 - 30318 (+) LR131284.1:29884-30895 -
- - VDS02676.1 30308 - 31289 (+) LR131284.1:30885-31866 -
- - VDS02677.1 31303 - 32311 (-) LR131284.1:31880-32888 1.-.-.-
- - VDS02678.1 32351 - 33650 (+) LR131284.1:32928-34227 3.4.-.-
- - VDS02679.1 33932 - 35429 (+) LR131284.1:34509-36006 -
- - VDS02680.1 35429 - 36479 (-) LR131284.1:36006-37056 -
- - VDS02681.1 36489 - 39228 (-) LR131284.1:37066-39805 3.2.1.21
- - VDS02682.1 39749 - 42053 (+) LR131284.1:40326-42630 -
- - VDS02683.1 42404 - 44510 (+) LR131284.1:42981-45087 3.2.1.20

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 578 - 1651 (-) CDS No
- 2096 - 3718 (-) CAZyme: GH33 No
- 3734 - 4117 (-) CDS No
- 4200 - 5438 (-) CDS No
- 5477 - 6661 (-) CDS No
- 6672 - 7589 (-) CDS No
- 7681 - 8763 (-) CDS No
- 9063 - 10271 (+) TF: DBD-Pfam|MarR,DBD-SUPERFAMILY|0043935 No
- 10334 - 10543 (-) TF: DBD-Pfam|HTH_3,DBD-SUPERFAMILY|0043143 No
- 10550 - 10792 (-) CDS No
- 10807 - 11259 (-) CDS No
- 11271 - 11918 (-) CDS No
- 11935 - 12507 (-) CDS No
- 12536 - 13405 (-) CDS No
- 13431 - 13751 (-) CDS No
- 14286 - 17702 (+) CAZyme: CBM67|GH78 Yes
- 17783 - 18676 (-) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607 Yes
- 18651 - 18812 (-) other Yes
- 18839 - 20317 (+) other Yes
- 20324 - 21577 (+) other Yes
- 21643 - 22653 (+) TC: gnl|TC-DB|P27125|2.A.7.6.1 Yes
- 22680 - 23489 (+) other Yes
- 23522 - 24676 (+) other Yes
- 24897 - 25802 (-) other Yes
- 25891 - 26022 (+) other Yes
- 26102 - 28252 (-) other Yes
- 28401 - 29303 (+) TC: gnl|TC-DB|Q8L725|2.A.4.7.2 Yes
- 29308 - 30318 (+) other Yes
- 30309 - 31289 (+) other Yes
- 31304 - 32311 (-) other Yes
- 32352 - 33650 (+) other Yes
- 33933 - 35429 (+) other Yes
- 35430 - 36479 (-) other Yes
- 36490 - 39228 (-) CAZyme: GH3 Yes
- 39750 - 42053 (+) CAZyme: GH115 Yes
- 42405 - 44510 (+) CAZyme: GH97 Yes

PUL ID

PUL0105

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.