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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0340

PubMed

28091525, Sci Rep. 2017 Jan 16;7:40248. doi: 10.1038/srep40248.

Characterization method

fosmid library screen,enzyme activity assay,thin layer chromatography

Genomic accession number

LT674130

Nucelotide position range

36-29087

Substrate

carboxymethylcellulose,xylan,beta-glucan,lichenan

Loci

SIP56454.1-SIP56490.1

Species

uncultured bacterium/77133

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- - SIP56454.1 36 - 309 (+) LT674130.1:72-345 -
- - SIP56455.1 374 - 1535 (-) LT674130.1:410-1571 3.2.1.4
- - SIP56456.1 1556 - 4205 (-) LT674130.1:1592-4241 3.6.3.54
- - SIP56457.1 4260 - 4638 (-) LT674130.1:4296-4674 -
- - SIP56458.1 4662 - 4974 (-) LT674130.1:4698-5010 -
- - SIP56459.1 5701 - 6895 (-) LT674130.1:5737-6931 2.6.1.1
- - SIP56460.1 6981 - 7674 (-) LT674130.1:7017-7710 -
- - SIP56461.1 7848 - 8079 (+) LT674130.1:7884-8115 -
- - SIP56462.1 8160 - 8538 (+) LT674130.1:8196-8574 -
- - SIP56463.1 8537 - 8843 (+) LT674130.1:8573-8879 -
- - SIP56464.1 8818 - 10540 (+) LT674130.1:8854-10576 -
- - SIP56465.1 10478 - 11228 (+) LT674130.1:10514-11264 -
- - SIP56466.1 11358 - 12171 (+) LT674130.1:11394-12207 -
- - SIP56467.1 12171 - 13104 (+) LT674130.1:12207-13140 2.7.13.3
- - SIP56468.1 13458 - 15138 (+) LT674130.1:13494-15174 3.6.4.13
- - SIP56469.1 15178 - 15406 (+) LT674130.1:15214-15442 -
- - SIP56470.1 15527 - 15836 (+) LT674130.1:15563-15872 -
- - SIP56471.1 15789 - 15966 (+) LT674130.1:15825-16002 -
- - SIP56472.1 15955 - 16168 (+) LT674130.1:15991-16204 -
- - SIP56473.1 16222 - 16984 (+) LT674130.1:16258-17020 -
- - SIP56474.1 17064 - 17727 (+) LT674130.1:17100-17763 -
- - SIP56475.1 17727 - 19074 (+) LT674130.1:17763-19110 3.6.4.12
- - SIP56476.1 19063 - 19285 (+) LT674130.1:19099-19321 -
- - SIP56477.1 19357 - 19825 (+) LT674130.1:19393-19861 -
- - SIP56478.1 19824 - 20088 (+) LT674130.1:19860-20124 -
- - SIP56479.1 20107 - 20548 (+) LT674130.1:20143-20584 -
- - SIP56480.1 20593 - 20971 (-) LT674130.1:20629-21007 -
- - SIP56481.1 21230 - 21749 (+) LT674130.1:21266-21785 2.1.1.148
- - SIP56482.1 21808 - 21940 (+) LT674130.1:21844-21976 -
- - SIP56483.1 21939 - 22488 (+) LT674130.1:21975-22524 -
- - SIP56484.1 22480 - 22645 (+) LT674130.1:22516-22681 -
- - SIP56485.1 22638 - 22827 (+) LT674130.1:22674-22863 -
- - SIP56486.1 22877 - 24368 (+) LT674130.1:22913-24404 -
- - SIP56487.1 24427 - 25987 (+) LT674130.1:24463-26023 -
- - SIP56488.1 26021 - 28001 (+) LT674130.1:26057-28037 -
- - SIP56489.1 28000 - 28207 (+) LT674130.1:28036-28243 -
- - SIP56490.1 28418 - 29087 (+) LT674130.1:28454-29123 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 37 - 309 (+) TF: DBD-Pfam|HTH_psq,DBD-SUPERFAMILY|0039384 No
- 375 - 1535 (-) CAZyme: GH5_2|GH5 Yes
- 1557 - 4205 (-) TC: gnl|TC-DB|Q3MNJ6|3.A.3.5.15 Yes
- 4261 - 4638 (-) STP: STP|HMA No
- 4663 - 4974 (-) CDS No
- 5702 - 6895 (-) STP: STP|Aminotran_1_2 No
- 6982 - 7674 (-) TF: DBD-Pfam|HTH_3,DBD-SUPERFAMILY|0043143 No
- 7849 - 8079 (+) CDS No
- 8161 - 8538 (+) CDS No
- 8538 - 8843 (+) CDS No
- 8819 - 10540 (+) CDS No
- 10479 - 11228 (+) CDS No
- 11359 - 12171 (+) TF: DBD-Pfam|Trans_reg_C No
- 12172 - 13104 (+) STP: STP|HisKA,STP|HATPase_c No
- 13459 - 15138 (+) CDS No
- 15179 - 15406 (+) TF: DBD-Pfam|MerR,DBD-SUPERFAMILY|0039468 No
- 15528 - 15836 (+) CDS No
- 15790 - 15966 (+) CDS No
- 15956 - 16168 (+) CDS No
- 16223 - 16984 (+) CDS No
- 17065 - 17727 (+) CDS No
- 17728 - 19074 (+) CDS No
- 19064 - 19285 (+) CDS No
- 19358 - 19825 (+) STP: STP|Sigma70_r4_2 No
- 19825 - 20088 (+) TF: DBD-Pfam|HTH_3,DBD-SUPERFAMILY|0043143 No
- 20108 - 20548 (+) TF: DBD-Pfam|HTH_3,DBD-SUPERFAMILY|0038966 No
- 20594 - 20971 (-) TF: DBD-Pfam|HTH_3,DBD-SUPERFAMILY|0043707 No
- 21231 - 21749 (+) CDS No
- 21809 - 21940 (+) CDS No
- 21940 - 22488 (+) CDS No
- 22481 - 22645 (+) CDS No
- 22639 - 22827 (+) CDS No
- 22878 - 24368 (+) CDS No
- 24428 - 25987 (+) CDS No
- 26022 - 28001 (+) CDS No
- 28001 - 28207 (+) CDS No
- 28419 - 29087 (+) CDS No

PUL ID

PUL0340

PubMed

28091525, Sci Rep. 2017 Jan 16;7:40248. doi: 10.1038/srep40248.

Title

A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic.

Author

Patrascu O, Beguet-Crespel F, Marinelli L, Le Chatelier E, Abraham AL, Leclerc M, Klopp C, Terrapon N, Henrissat B, Blottiere HM, Dore J, Bera-Maillet C

Abstract

The digestion of dietary fibers is a major function of the human intestinal microbiota. So far this function has been attributed to the microorganisms inhabiting the colon, and many studies have focused on this distal part of the gastrointestinal tract using easily accessible fecal material. However, microbial fermentations, supported by the presence of short-chain fatty acids, are suspected to occur in the upper small intestine, particularly in the ileum. Using a fosmid library from the human ileal mucosa, we screened 20,000 clones for their activities against carboxymethylcellulose and xylans chosen as models of the major plant cell wall (PCW) polysaccharides from dietary fibres. Eleven positive clones revealed a broad range of CAZyme encoding genes from Bacteroides and Clostridiales species, as well as Polysaccharide Utilization Loci (PULs). The functional glycoside hydrolase genes were identified, and oligosaccharide break-down products examined from different polysaccharides including mixed-linkage beta-glucans. CAZymes and PULs were also examined for their prevalence in human gut microbiome. Several clusters of genes of low prevalence in fecal microbiome suggested they belong to unidentified strains rather specifically established upstream the colon, in the ileum. Thus, the ileal mucosa-associated microbiota encompasses the enzymatic potential for PCW polysaccharide degradation in the small intestine.