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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0343

PubMed

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

Characterization method

gene deletion mutant and growth assay,enzyme activity assay,Western Blot,isothermal titration calorimetry

Genomic accession number

LT674132

Nucelotide position range

107-30768

Substrate

carboxymethylcellulose,xylan,beta-glucan,lichenan

Loci

SIP56534.1-SIP56572.1

Species

uncultured bacterium/77133

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- - SIP56534.1 107 - 1037 (+) LT674132.1:214-1144 -
- - SIP56535.1 1095 - 1392 (+) LT674132.1:1202-1499 -
- - SIP56536.1 1535 - 1952 (+) LT674132.1:1642-2059 -
- - SIP56537.1 2059 - 2986 (+) LT674132.1:2166-3093 -
- - SIP56538.1 3071 - 3539 (+) LT674132.1:3178-3646 -
- - SIP56539.1 3571 - 3892 (+) LT674132.1:3678-3999 -
- - SIP56540.1 3891 - 4533 (+) LT674132.1:3998-4640 -
- - SIP56541.1 4525 - 4873 (+) LT674132.1:4632-4980 -
- - SIP56542.1 4878 - 6612 (+) LT674132.1:4985-6719 -
- - SIP56543.1 6615 - 6999 (+) LT674132.1:6722-7106 -
- - SIP56544.1 7371 - 7668 (+) LT674132.1:7478-7775 -
- - SIP56545.1 7850 - 8462 (+) LT674132.1:7957-8569 -
- - SIP56546.1 8458 - 9058 (+) LT674132.1:8565-9165 -
- - SIP56547.1 9148 - 9394 (+) LT674132.1:9255-9501 -
- - SIP56548.1 9684 - 9981 (+) LT674132.1:9791-10088 -
- - SIP56549.1 10052 - 10481 (+) LT674132.1:10159-10588 -
- - SIP56550.1 10480 - 10810 (+) LT674132.1:10587-10917 -
- - SIP56551.1 10827 - 11283 (+) LT674132.1:10934-11390 -
- - SIP56552.1 11285 - 12986 (+) LT674132.1:11392-13093 -
- - SIP56553.1 13002 - 13989 (+) LT674132.1:13109-14096 -
- - SIP56554.1 14129 - 14273 (+) LT674132.1:14236-14380 -
- - SIP56555.1 14269 - 14788 (+) LT674132.1:14376-14895 -
- - SIP56556.1 14790 - 15750 (+) LT674132.1:14897-15857 -
- - SIP56557.1 16693 - 17005 (+) LT674132.1:16800-17112 -
- - SIP56558.1 17029 - 17407 (+) LT674132.1:17136-17514 -
- - SIP56559.1 17462 - 20111 (+) LT674132.1:17569-20218 3.6.3.54
- - SIP56560.1 20132 - 21293 (+) LT674132.1:20239-21400 3.2.1.4
- - SIP56561.1 21358 - 21631 (-) LT674132.1:21465-21738 -
- - SIP56562.1 21835 - 22423 (-) LT674132.1:21942-22530 2.7.4.25
- - SIP56563.1 22702 - 24277 (+) LT674132.1:22809-24384 6.3.5.2
- - SIP56564.1 24544 - 24736 (+) LT674132.1:24651-24843 -
- - SIP56565.1 24746 - 24971 (+) LT674132.1:24853-25078 -
- - SIP56566.1 25120 - 25372 (+) LT674132.1:25227-25479 -
- - SIP56567.1 25748 - 25925 (-) LT674132.1:25855-26032 -
- - SIP56568.1 25982 - 26333 (+) LT674132.1:26089-26440 -
- - SIP56569.1 26432 - 27425 (-) LT674132.1:26539-27532 -
- - SIP56570.1 27784 - 29011 (+) LT674132.1:27891-29118 -
- - SIP56571.1 29026 - 29911 (+) LT674132.1:29133-30018 -
- - SIP56572.1 29934 - 30768 (+) LT674132.1:30041-30875 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 108 - 1037 (+) CDS No
- 1096 - 1392 (+) CDS No
- 1536 - 1952 (+) CDS No
- 2060 - 2986 (+) CDS No
- 3072 - 3539 (+) CDS No
- 3572 - 3892 (+) CDS No
- 3892 - 4533 (+) CDS No
- 4526 - 4873 (+) CDS No
- 4879 - 6612 (+) CDS No
- 6616 - 6999 (+) CDS No
- 7372 - 7668 (+) CDS No
- 7851 - 8462 (+) CDS No
- 8459 - 9058 (+) CDS No
- 9149 - 9394 (+) CDS No
- 9685 - 9981 (+) CDS No
- 10053 - 10481 (+) CDS No
- 10481 - 10810 (+) CDS No
- 10828 - 11283 (+) CDS No
- 11286 - 12986 (+) CDS No
- 13003 - 13989 (+) CDS No
- 14130 - 14273 (+) CDS No
- 14270 - 14788 (+) TC: gnl|TC-DB|Q932J9|3.A.7.17.1 Yes
- 14791 - 15750 (+) other Yes
- 16694 - 17005 (+) other Yes
- 17030 - 17407 (+) STP: STP|HMA Yes
- 17463 - 20111 (+) TC: gnl|TC-DB|Q3MNJ6|3.A.3.5.15 Yes
- 20133 - 21293 (+) CAZyme: GH5|GH5_2 Yes
- 21359 - 21631 (-) TF: DBD-Pfam|HTH_psq,DBD-SUPERFAMILY|0039384 Yes
- 21836 - 22423 (-) TC: gnl|TC-DB|C7N858|2.A.115.2.14 Yes
- 22703 - 24277 (+) other Yes
- 24545 - 24736 (+) STP: STP|TrmB Yes
- 24747 - 24971 (+) other Yes
- 25121 - 25372 (+) other Yes
- 25749 - 25925 (-) other Yes
- 25983 - 26333 (+) TC: gnl|TC-DB|E2YHZ7|3.A.1.135.7 Yes
- 26433 - 27425 (-) TF: DBD-Pfam|LacI,DBD-SUPERFAMILY|0036955 Yes
- 27785 - 29011 (+) STP: STP|SBP_bac_1 Yes
- 29027 - 29911 (+) TC: gnl|TC-DB|Q9WYB4|3.A.1.1.37 Yes
- 29935 - 30768 (+) TC: gnl|TC-DB|Q72H66|3.A.1.1.25 Yes

PUL ID

PUL0343

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.