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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0302

PubMed

29255254, Nat Microbiol. 2018 Feb;3(2):210-219. doi: 10.1038/s41564-017-0079-1. Epub 2017 Dec 18.

Characterization method

RT-qPCR,isothermal titration calorimetry,enzyme activity assay,gene deletion mutant and growth assay

Genomic accession number

AE015928.1

Nucelotide position range

417722-455321

Substrate

arabinan

Loci

BT_0348-BT_0369

Species

Bacteroides thetaiotaomicron/818

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BT_0348 AAO75455.1 0 - 1545 (-) AE015928.1:417722-419267 -
- BT_0349 AAO75456.1 1614 - 4023 (-) AE015928.1:419336-421745 -
- BT_0350 AAO75457.1 4127 - 5723 (-) AE015928.1:421849-423445 -
- BT_0351 AAO75458.1 5912 - 7442 (-) AE015928.1:423634-425164 -
- BT_0352 AAO75459.1 7522 - 7885 (-) AE015928.1:425244-425607 -
- BT_0353 AAO75460.1 7921 - 8605 (-) AE015928.1:425643-426327 -
- BT_0354 AAO75461.1 8610 - 9288 (-) AE015928.1:426332-427010 -
- BT_0355 AAO75462.1 9309 - 11004 (-) AE015928.1:427031-428726 -
- BT_0356 AAO75463.1 11029 - 12169 (-) AE015928.1:428751-429891 -
- BT_0357 AAO75464.1 12504 - 12753 (+) AE015928.1:430226-430475 -
- BT_0358 AAO75465.1 12773 - 13667 (-) AE015928.1:430495-431389 -
- BT_0359 AAO75466.1 13699 - 14047 (-) AE015928.1:431421-431769 -
- BT_0360 AAO75467.1 14290 - 16216 (-) AE015928.1:432012-433938 -
- BT_0361 AAO75468.1 16250 - 18056 (-) AE015928.1:433972-435778 -
- BT_0362 AAO75469.1 18081 - 21231 (-) AE015928.1:435803-438953 -
- BT_0363 AAO75470.1 21235 - 23011 (-) AE015928.1:438957-440733 -
- BT_0364 AAO75471.1 23023 - 26107 (-) AE015928.1:440745-443829 -
- BT_0365 AAO75472.1 26126 - 28406 (-) AE015928.1:443848-446128 -
- BT_0366 AAO75473.1 28665 - 32928 (-) AE015928.1:446387-450650 -
- BT_0367 AAO75474.1 33083 - 34625 (+) AE015928.1:450805-452347 -
- BT_0368 AAO75475.1 34650 - 36633 (+) AE015928.1:452372-454355 -
- BT_0369 AAO75476.1 36634 - 37600 (+) AE015928.1:454356-455322 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1545 (-) CAZyme: GH51 Yes
- 1615 - 4023 (-) CAZyme: GH146 Yes
- 4128 - 5723 (-) other Yes
- 5913 - 7442 (-) other Yes
- 7523 - 7885 (-) other Yes
- 7922 - 8605 (-) other Yes
- 8611 - 9288 (-) STP: STP|NUDIX Yes
- 9310 - 11004 (-) TC: gnl|TC-DB|Q8AAV7|2.A.21.3.19 Yes
- 11030 - 12169 (-) other Yes
- 12505 - 12753 (+) other Yes
- 12774 - 13667 (-) other Yes
- 13700 - 14047 (-) other Yes
- 14291 - 16216 (-) CAZyme: GH43_4|GH43 Yes
- 16251 - 18056 (-) other Yes
- 18082 - 21231 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 21236 - 23011 (-) other Yes
- 23024 - 26107 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 26127 - 28406 (-) other Yes
- 28666 - 32928 (-) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0035607 Yes
- 33084 - 34625 (+) CAZyme: GH43_4 Yes
- 34651 - 36633 (+) CAZyme: GH51 Yes
- 36635 - 37600 (+) CAZyme: GH43_29 Yes

PUL ID

PUL0302

PubMed

29255254, Nat Microbiol. 2018 Feb;3(2):210-219. doi: 10.1038/s41564-017-0079-1. Epub 2017 Dec 18.

Title

Dietary pectic glycans are degraded by coordinated enzyme pathways in human colonic Bacteroides.

Author

Luis AS, Briggs J, Zhang X, Farnell B, Ndeh D, Labourel A, Basle A, Cartmell A, Terrapon N, Stott K, Lowe EC, McLean R, Shearer K, Schuckel J, Venditto I, Ralet MC, Henrissat B, Martens EC, Mosimann SC, Abbott DW, Gilbert HJ

Abstract

The major nutrients available to human colonic Bacteroides species are glycans, exemplified by pectins, a network of covalently linked plant cell wall polysaccharides containing galacturonic acid (GalA). Metabolism of complex carbohydrates by the Bacteroides genus is orchestrated by polysaccharide utilization loci (PULs). In Bacteroides thetaiotaomicron, a human colonic bacterium, the PULs activated by different pectin domains have been identified; however, the mechanism by which these loci contribute to the degradation of these GalA-containing polysaccharides is poorly understood. Here we show that each PUL orchestrates the metabolism of specific pectin molecules, recruiting enzymes from two previously unknown glycoside hydrolase families. The apparatus that depolymerizes the backbone of rhamnogalacturonan-I is particularly complex. This system contains several glycoside hydrolases that trim the remnants of other pectin domains attached to rhamnogalacturonan-I, and nine enzymes that contribute to the degradation of the backbone that makes up a rhamnose-GalA repeating unit. The catalytic properties of the pectin-degrading enzymes are optimized to protect the glycan cues that activate the specific PULs ensuring a continuous supply of inducing molecules throughout growth. The contribution of Bacteroides spp. to metabolism of the pectic network is illustrated by cross-feeding between organisms.