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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0668

PubMed

34420703, Carbohydr Polym. 2021 Nov 15;272:118534. doi: 10.1016/j.carbpol.2021.118534. Epub 2021 Aug 6.

Characterization method

UHPLC-MS,RNA-seq,RT-qPCR

Genomic accession number

NC_004663.1

Nucelotide position range

5446660-5500444

Substrate

pectin

Loci

BT_4149-BT_4177

Species

Bacteroides thetaiotaomicron VPI-5482/818

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BT_RS20935 - 0 - 1059 (-) NC_004663.1:5446660-5447719 -
- BT_RS20940 WP_011109136.1 1083 - 2322 (-) NC_004663.1:5447743-5448982 -
- BT_RS20945 WP_011109137.1 2339 - 5216 (-) NC_004663.1:5448999-5451876 -
- BT_RS20950 WP_225011864.1 5458 - 8440 (+) NC_004663.1:5452118-5455100 3.2.1.23
- BT_RS20955 WP_011109139.1 8483 - 9782 (+) NC_004663.1:5455143-5456442 -
- BT_RS20960 WP_011109140.1 9794 - 10763 (+) NC_004663.1:5456454-5457423 3.-.-.-
- BT_RS20965 WP_162303131.1 10796 - 12176 (+) NC_004663.1:5457456-5458836 -
- BT_RS20970 WP_011109142.1 12300 - 15186 (-) NC_004663.1:5458960-5461846 -
- BT_RS20975 WP_055229316.1 15210 - 16794 (-) NC_004663.1:5461870-5463454 3.2.1.22
- BT_RS20980 WP_008764375.1 17037 - 17730 (+) NC_004663.1:5463697-5464390 -
- BT_RS20985 WP_008764376.1 17970 - 19632 (+) NC_004663.1:5464630-5466292 -
- BT_RS20990 WP_011109145.1 19660 - 21757 (+) NC_004663.1:5466320-5468417 3.2.1.23
- BT_RS20995 WP_011109146.1 21895 - 22498 (-) NC_004663.1:5468555-5469158 -
- BT_RS21000 WP_011109147.1 22910 - 24989 (+) NC_004663.1:5469570-5471649 -
- BT_RS21005 WP_008764380.1 25547 - 27881 (+) NC_004663.1:5472207-5474541 -
- BT_RS21010 WP_008764381.1 27899 - 31166 (+) NC_004663.1:5474559-5477826 -
- BT_RS21015 WP_032840505.1 31178 - 32765 (+) NC_004663.1:5477838-5479425 -
- BT_RS21020 WP_011109149.1 32773 - 34519 (+) NC_004663.1:5479433-5481179 -
- BT_RS21025 WP_008764384.1 34524 - 36267 (+) NC_004663.1:5481184-5482927 -
- BT_RS21030 WP_008764385.1 36283 - 39436 (+) NC_004663.1:5482943-5486096 -
- BT_RS21035 WP_008764386.1 39441 - 41193 (+) NC_004663.1:5486101-5487853 -
- BT_RS21040 WP_008764387.1 41225 - 42833 (+) NC_004663.1:5487885-5489493 -
- BT_RS21045 WP_008764388.1 42854 - 43508 (+) NC_004663.1:5489514-5490168 -
- BT_RS21050 WP_008764390.1 43760 - 47057 (+) NC_004663.1:5490420-5493717 -
- BT_RS21055 WP_032840507.1 47135 - 48770 (-) NC_004663.1:5493795-5495430 -
- BT_RS21060 - 48790 - 49931 (-) NC_004663.1:5495450-5496591 -
- BT_RS21065 WP_008764392.1 50197 - 52039 (+) NC_004663.1:5496857-5498699 -
- BT_RS21070 WP_011109152.1 52042 - 53440 (+) NC_004663.1:5498702-5500100 -
rhaM BT_RS21075 WP_008759851.1 53470 - 53785 (+) NC_004663.1:5500130-5500445 5.1.3.32

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1084 - 2322 (-) CAZyme: CE12|CE12 Yes
- 2340 - 5216 (-) CAZyme: GH2|3.2.1.23| GH2 Yes
- 5459 - 8440 (+) CAZyme: GH42|GH42| GH43_18|GH43_18 Yes
- 8484 - 9782 (+) CAZyme: GH28| GH28 Yes
- 9795 - 10763 (+) CAZyme: CE4|CE12 Yes
- 10797 - 12176 (+) CAZyme: GH28| GH28 Yes
- 12301 - 15186 (-) CAZyme: GH2|3.2.1.23| GH2 Yes
- 15211 - 16794 (-) CAZyme: GH27|CBM35|GH27 Yes
- 17038 - 17730 (+) other Yes
- 17971 - 19632 (+) other Yes
- 19661 - 21757 (+) CAZyme: GH35| GH35|3.2.1.23 Yes
- 21896 - 22498 (-) other Yes
- 22911 - 24989 (+) other Yes
- 25548 - 27881 (+) other Yes
- 27900 - 31166 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 31179 - 32765 (+) TC: gnl|TC-DB|Q5LEN2|8.A.46.1.4 Yes
- 32774 - 34519 (+) other Yes
- 34525 - 36267 (+) other Yes
- 36284 - 39436 (+) TC: gnl|TC-DB|Q93TH9|1.B.14.6.2 Yes
- 39442 - 41193 (+) other Yes
- 41226 - 42833 (+) CAZyme: PL9_1|PL9 Yes
- 42855 - 43508 (+) other Yes
- 43761 - 47057 (+) CAZyme: PL26|PL26 Yes
- 47136 - 48770 (-) CAZyme: CE12|CE12 Yes
- 50198 - 52039 (+) CAZyme: PL11_1|PL11_1 Yes
- 52043 - 53440 (+) CAZyme: GH105| GH105 Yes
rhaM 53471 - 53785 (+) CDS No

PUL ID

PUL0668

PubMed

34420703, Carbohydr Polym. 2021 Nov 15;272:118534. doi: 10.1016/j.carbpol.2021.118534. Epub 2021 Aug 6.

Title

Discrete genetic loci in human gut Bacteroides thetaiotaomicron confer pectin metabolism.

Author

Li M, Li S, Guo X, Guo C, Wang Y, Du Z, Zhang Z, Xie C, Ding K

Abstract

Although the polysaccharide utilization loci (PULs) activated by pectin have been defined, due to the complex of side-chain structure, the degradative mechanisms still remain vague. Thus, we hypothesize that there may have other specific PULs to target pectin. Here, we characterize loci-encoded proteins expressed by Bacteroides thetaiotaomicron (BT) that are involved in the pectin capturing, importation, de-branching and degradation into monosaccharides. Totally, four PULs contain ten enzymes and four glycan binding proteins which including a novel surface enzyme and a surface glycan binding protein are identified. Notably, PUL2 and PUL3 have not been reported so far. Further, we show that the degradation products support the growth of other Bacteroides spp. and probiotics. In addition, genes involved in this process are conservative in other Bacteroides spp. Our results further highlight the contribution of Bacteroides spp. to metabolism the pectic network.