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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0101

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_DS990126.1

Nucelotide position range

54056-84377

Substrate

O-glycan,N-glycan

Loci

BACPLE_RS06865-BACPLE_RS06955

Species

Bacteroides plebeius/310297

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BACPLE_RS06865 WP_040312596.1 2 - 3485 (+) NZ_DS990126.1:54058-57541 -
- BACPLE_RS06870 WP_007560193.1 3570 - 4464 (-) NZ_DS990126.1:57626-58520 -
- BACPLE_RS06875 WP_007560197.1 4626 - 6105 (+) NZ_DS990126.1:58682-60161 -
- BACPLE_RS06880 WP_007560199.1 6111 - 7365 (+) NZ_DS990126.1:60167-61421 5.3.1.14
rhaT BACPLE_RS06885 WP_007560200.1 7430 - 8441 (+) NZ_DS990126.1:61486-62497 -
rhaD BACPLE_RS06890 WP_007560202.1 8467 - 9277 (+) NZ_DS990126.1:62523-63333 4.1.2.19
fucO BACPLE_RS06895 WP_040312568.1 9309 - 10464 (+) NZ_DS990126.1:63365-64520 1.1.1.77
- BACPLE_RS06900 WP_040312571.1 10683 - 11589 (-) NZ_DS990126.1:64739-65645 -
rnr BACPLE_RS06905 WP_007560210.1 11878 - 14029 (-) NZ_DS990126.1:65934-68085 -
- BACPLE_RS06910 WP_007560214.1 14177 - 15080 (+) NZ_DS990126.1:68233-69136 -
- BACPLE_RS06915 WP_007560217.1 15084 - 16095 (+) NZ_DS990126.1:69140-70151 -
- BACPLE_RS06920 WP_040312599.1 16091 - 17066 (+) NZ_DS990126.1:70147-71122 -
dusB BACPLE_RS06925 WP_007560221.1 17081 - 18068 (-) NZ_DS990126.1:71137-72124 -
- BACPLE_RS06930 WP_007560223.1 18156 - 19428 (+) NZ_DS990126.1:72212-73484 -
- BACPLE_RS06935 WP_007560225.1 19710 - 21207 (+) NZ_DS990126.1:73766-75263 -
mnmA BACPLE_RS06940 WP_007560227.1 21207 - 22257 (-) NZ_DS990126.1:75263-76313 -
- BACPLE_RS06945 WP_040312574.1 22267 - 25111 (-) NZ_DS990126.1:76323-79167 -
- BACPLE_RS06950 WP_148374610.1 25467 - 27831 (+) NZ_DS990126.1:79523-81887 -
- BACPLE_RS06955 WP_040312576.1 28182 - 30288 (+) NZ_DS990126.1:82238-84344 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 3 - 3485 (+) CAZyme: CBM67|GH78 Yes
- 3571 - 4464 (-) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607 Yes
- 4627 - 6105 (+) other Yes
- 6112 - 7365 (+) other Yes
rhaT 7431 - 8441 (+) TC: gnl|TC-DB|P27125|2.A.7.6.1 Yes
rhaD 8468 - 9277 (+) other Yes
fucO 9310 - 10464 (+) other Yes
- 10684 - 11589 (-) other Yes
rnr 11879 - 14029 (-) other Yes
- 14178 - 15080 (+) TC: gnl|TC-DB|Q8L725|2.A.4.7.2 Yes
- 15085 - 16095 (+) other Yes
- 16092 - 17066 (+) other Yes
dusB 17082 - 18068 (-) other Yes
- 18157 - 19428 (+) other Yes
- 19711 - 21207 (+) other Yes
mnmA 21208 - 22257 (-) other Yes
- 22268 - 25111 (-) CAZyme: GH3 Yes
- 25468 - 27831 (+) CAZyme: GH115 Yes
- 28183 - 30288 (+) CAZyme: GH97 Yes

PUL ID

PUL0101

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.