PUL ID

PUL0345

PubMed

27681607, Sci Rep. 2016 Sep 29;6:34360. doi: 10.1038/srep34360.

Characterization method

qRT-PCR, enzyme activity assay

Genomic accession number

ABJL02000008.1

Nucelotide position range

2468545-2529030

Substrate

xylan

Loci

BACINT_04193-BACINT_04223

Species

Bacteroides intestinalis/329854

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BACINT_04193 EDV05050.1 0 - 4095 (-) ABJL02000008.1:2468545-2472640 -
- BACINT_04194 EDV05051.1 4857 - 7998 (+) ABJL02000008.1:2473402-2476543 -
- BACINT_04195 EDV05052.1 8017 - 9757 (+) ABJL02000008.1:2476562-2478302 -
- BACINT_04196 EDV05053.1 9805 - 11173 (+) ABJL02000008.1:2478350-2479718 -
- BACINT_04197 EDV05054.1 11219 - 13568 (+) ABJL02000008.1:2479764-2482113 -
- BACINT_04198 EDV05055.1 13622 - 13745 (-) ABJL02000008.1:2482167-2482290 -
- BACINT_04199 EDV05056.1 13787 - 15536 (+) ABJL02000008.1:2482332-2484081 -
- BACINT_04200 EDV05057.1 15573 - 17244 (+) ABJL02000008.1:2484118-2485789 -
- BACINT_04201 EDV05058.1 17317 - 18814 (+) ABJL02000008.1:2485862-2487359 -
- BACINT_04202 EDV05059.1 18829 - 21562 (+) ABJL02000008.1:2487374-2490107 -
- BACINT_04203 EDV05060.1 21581 - 22559 (+) ABJL02000008.1:2490126-2491104 -
- BACINT_04204 EDV05061.1 22576 - 23557 (+) ABJL02000008.1:2491121-2492102 -
- BACINT_04205 EDV05062.1 23578 - 25609 (+) ABJL02000008.1:2492123-2494154 -
- BACINT_04207 EDV05064.1 25623 - 25851 (-) ABJL02000008.1:2494168-2494396 -
- BACINT_04206 EDV05063.1 25849 - 26908 (+) ABJL02000008.1:2494394-2495453 -
- BACINT_04208 EDV05065.1 27235 - 31231 (+) ABJL02000008.1:2495780-2499776 -
- BACINT_04209 EDV05066.1 31312 - 32974 (-) ABJL02000008.1:2499857-2501519 -
- BACINT_04210 EDV05067.1 33146 - 34403 (-) ABJL02000008.1:2501691-2502948 -
- BACINT_04211 EDV05068.1 34441 - 37627 (-) ABJL02000008.1:2502986-2506172 -
- BACINT_04212 EDV05069.1 37691 - 38576 (-) ABJL02000008.1:2506236-2507121 -
- BACINT_04213 EDV05070.1 38794 - 40777 (-) ABJL02000008.1:2507339-2509322 -
- BACINT_04214 EDV05071.1 41091 - 41832 (-) ABJL02000008.1:2509636-2510377 -
- BACINT_04215 EDV05072.1 41909 - 44150 (-) ABJL02000008.1:2510454-2512695 -
- BACINT_04216 EDV05073.1 44183 - 45218 (-) ABJL02000008.1:2512728-2513763 -
- BACINT_04217 EDV05074.1 45251 - 47057 (-) ABJL02000008.1:2513796-2515602 -
- BACINT_04218 EDV05075.1 47101 - 49930 (-) ABJL02000008.1:2515646-2518475 -
- BACINT_04219 EDV05076.1 49959 - 51822 (-) ABJL02000008.1:2518504-2520367 -
- BACINT_04220 EDV05077.1 51834 - 54978 (-) ABJL02000008.1:2520379-2523523 -
- BACINT_04221 EDV05078.1 55796 - 55955 (+) ABJL02000008.1:2524341-2524500 -
- BACINT_04222 EDV05079.1 55991 - 57917 (-) ABJL02000008.1:2524536-2526462 -
- BACINT_04223 EDV05080.1 57939 - 60486 (-) ABJL02000008.1:2526484-2529031 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 4095 (-) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607 No
- 4858 - 7998 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 8018 - 9757 (+) other Yes
- 9806 - 11173 (+) other Yes
- 11220 - 13568 (+) CAZyme: CBM4|GH10 Yes
- 13623 - 13745 (-) other Yes
- 13788 - 15536 (+) CAZyme: GH35 Yes
- 15574 - 17244 (+) other Yes
- 17318 - 18814 (+) TC: gnl|TC-DB|P31435|2.A.2.3.4 Yes
- 18830 - 21562 (+) CAZyme: GH43_12|GH43|GH10 Yes
- 21582 - 22559 (+) CAZyme: GH43_1|GH43 Yes
- 22577 - 23557 (+) other Yes
- 23579 - 25609 (+) CAZyme: GH67 Yes
- 25624 - 25851 (-) other Yes
- 25850 - 26908 (+) other Yes
- 27236 - 31231 (+) TF: DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607 Yes
- 31313 - 32974 (-) other Yes
- 33147 - 34403 (-) CAZyme: GH8 Yes
- 34442 - 37627 (-) CAZyme: CE6|GH95 Yes
- 37692 - 38576 (-) CAZyme: CE0|CE1 Yes
- 38795 - 40777 (-) CAZyme: GH5|GH5_21 Yes
- 41092 - 41832 (-) other Yes
- 41910 - 44150 (-) CAZyme: GH10|CBM0 Yes
- 44184 - 45218 (-) other Yes
- 45252 - 47057 (-) other Yes
- 47102 - 49930 (-) other Yes
- 49960 - 51822 (-) other Yes
- 51835 - 54978 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 55797 - 55955 (+) other Yes
- 55992 - 57917 (-) other Yes
- 57940 - 60486 (-) CAZyme: GH115 Yes

PUL ID

PUL0345

PubMed

27681607, Sci Rep. 2016 Sep 29;6:34360. doi: 10.1038/srep34360.

Title

Bacteroides intestinalis DSM 17393, a member of the human colonic microbiome, upregulates multiple endoxylanases during growth on xylan.

Author

Wang K, Pereira GV, Cavalcante JJ, Zhang M, Mackie R, Cann I

Abstract

Many human diets contain arabinoxylan, and the ease of genome sequencing coupled with reduced cost have led to unraveling the arsenal of genes utilized by the colonic Bacteroidetes to depolymerize this polysaccharide. The colonic Bacteroidetes with potential to ferment arabinoxylans include Bacteroides intestinalis. In this study, we analyzed the hydrolytic activities of members of a xylan degradation cluster encoded on the genome of Bacteroides intestinalis DSM 17393. Here, it is demonstrated that a cocktail of the xylanolytic enzymes completely hydrolyze arabinoxylans found in human diets. We show that this bacterium and relatives have evolved and secrete a unique bifunctional endoxylanase/arabinofuranosidase in the same polypeptide. The bifunctional enzyme and other secreted enzymes attack the polysaccharides extracellularly to remove the side-chains, exposing the xylan backbone for cleavage to xylo-oligosaccharides and xylose. These end products are transported into the cell where a beta-xylosidase cleaves the oligosaccharides to fermentable sugars. While our experiments focused on B. intestinalis, it is likely that the extracellular enzymes also release nutrients to members of the colonic microbial community that practice cross-feeding. The presence of the genes characterized in this study in other colonic Bacteroidetes suggests a conserved strategy for energy acquisition from arabinoxylan, a component of human diets.