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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0644

PubMed

33469030, Nat Commun. 2021 Jan 19;12(1):459. doi: 10.1038/s41467-020-20737-5.

Characterization method

enzyme activity assay,liquid chromatography,high performance anion exchange chromatography,qRT-PCR,crystallization

Genomic accession number

NZ_EQ973490.1

Nucelotide position range

1329075-1352417

Substrate

arabinoxylan

Loci

BACCELL_RS09475-BACCELL_RS09535

Species

Bacteroides cellulosilyticus DSM 14838/246787

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BACCELL_RS09475 WP_149949311.1 0 - 4095 (-) NZ_EQ973490.1:1329075-1333170 -
- BACCELL_RS09480 WP_007211515.1 4114 - 5446 (-) NZ_EQ973490.1:1333189-1334521 -
- BACCELL_RS09485 WP_007211516.1 5622 - 8280 (-) NZ_EQ973490.1:1334697-1337355 -
- BACCELL_RS09490 WP_007211517.1 8328 - 9387 (-) NZ_EQ973490.1:1337403-1338462 -
- BACCELL_RS09495 WP_007211518.1 9433 - 10588 (-) NZ_EQ973490.1:1338508-1339663 -
- BACCELL_RS09500 WP_052309546.1 10595 - 11762 (-) NZ_EQ973490.1:1339670-1340837 -
- BACCELL_RS09510 WP_081450809.1 11998 - 14503 (-) NZ_EQ973490.1:1341073-1343578 -
- BACCELL_RS09515 WP_007211522.1 14831 - 16566 (-) NZ_EQ973490.1:1343906-1345641 -
- BACCELL_RS27335 - 16589 - 17151 (-) NZ_EQ973490.1:1345664-1346226 -
- BACCELL_RS09520 WP_007211524.1 17171 - 19741 (-) NZ_EQ973490.1:1346246-1348816 -
- BACCELL_RS09525 WP_044153754.1 20004 - 21456 (-) NZ_EQ973490.1:1349079-1350531 -
- BACCELL_RS09530 WP_007211527.1 21458 - 22157 (-) NZ_EQ973490.1:1350533-1351232 -
- BACCELL_RS09535 WP_044153756.1 22185 - 23343 (-) NZ_EQ973490.1:1351260-1352418 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 4095 (-) TF: DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0035607 No
- 4115 - 5446 (-) CAZyme: CBM6| GH43_2|GH43_2| CBM6 Yes
- 5623 - 8280 (-) CAZyme: GH3|GH3 Yes
- 8329 - 9387 (-) CAZyme: GH43_17| GH43_17 Yes
- 9434 - 10588 (-) CAZyme: CBM48| CE1|CE1 Yes
- 10596 - 11762 (-) CAZyme: CBM48|CE1 Yes
- 11999 - 14503 (-) CAZyme: GH9 Yes
- 14832 - 16566 (-) other Yes
- 17172 - 19741 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 20005 - 21456 (-) CAZyme: CBM13| GH43_7|GH43_7 Yes
- 21459 - 22157 (-) other Yes
- 22186 - 23343 (-) CAZyme: CE0|CBM48|CE1 Yes

PUL ID

PUL0644

PubMed

33469030, Nat Commun. 2021 Jan 19;12(1):459. doi: 10.1038/s41467-020-20737-5.

Title

Degradation of complex arabinoxylans by human colonic Bacteroidetes.

Author

Pereira GV, Abdel-Hamid AM, Dutta S, D'Alessandro-Gabazza CN, Wefers D, Farris JA, Bajaj S, Wawrzak Z, Atomi H, Mackie RI, Gabazza EC, Shukla D, Koropatkin NM, Cann I

Abstract

Some Bacteroidetes and other human colonic bacteria can degrade arabinoxylans, common polysaccharides found in dietary fiber. Previous work has identified gene clusters (polysaccharide-utilization loci, PULs) for degradation of simple arabinoxylans. However, the degradation of complex arabinoxylans (containing side chains such as ferulic acid, a phenolic compound) is poorly understood. Here, we identify a PUL that encodes multiple esterases for degradation of complex arabinoxylans in Bacteroides species. The PUL is specifically upregulated in the presence of complex arabinoxylans. We characterize some of the esterases biochemically and structurally, and show that they release ferulic acid from complex arabinoxylans. Growth of four different colonic Bacteroidetes members, including Bacteroides intestinalis, on complex arabinoxylans results in accumulation of ferulic acid, a compound known to have antioxidative and immunomodulatory properties.