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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0645

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_JH992941.1

Nucelotide position range

1220565-1238669

Substrate

arabinoxylan

Loci

HMPREF9447_RS12390-HMPREF9447_RS12435

Species

Bacteroides oleiciplenus YIT 12058/626931

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- HMPREF9447_RS12390 WP_009130083.1 0 - 4089 (-) NZ_JH992941.1:1220565-1224654 -
- HMPREF9447_RS12395 WP_009130084.1 4127 - 5459 (-) NZ_JH992941.1:1224692-1226024 -
- HMPREF9447_RS12400 WP_009130085.1 5558 - 8147 (-) NZ_JH992941.1:1226123-1228712 -
- HMPREF9447_RS12405 WP_009130086.1 8198 - 9251 (-) NZ_JH992941.1:1228763-1229816 -
- HMPREF9447_RS12410 WP_009130087.1 9300 - 9609 (-) NZ_JH992941.1:1229865-1230174 -
- HMPREF9447_RS12415 WP_009130088.1 9715 - 11167 (-) NZ_JH992941.1:1230280-1231732 -
- HMPREF9447_RS12420 WP_009130089.1 11169 - 11868 (-) NZ_JH992941.1:1231734-1232433 -
- HMPREF9447_RS12425 WP_009130090.1 11896 - 13054 (-) NZ_JH992941.1:1232461-1233619 -
- HMPREF9447_RS12430 WP_009130091.1 13108 - 14908 (-) NZ_JH992941.1:1233673-1235473 -
- HMPREF9447_RS12435 WP_009130092.1 14928 - 18105 (-) NZ_JH992941.1:1235493-1238670 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 4089 (-) TF: DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0035607 No
- 4128 - 5459 (-) CAZyme: CBM6|CBM6| GH43_2|GH43_2 Yes
- 5559 - 8147 (-) CAZyme: GH3|GH3 Yes
- 8199 - 9251 (-) CAZyme: GH43_17| GH43_17 Yes
- 9301 - 9609 (-) other Yes
- 9716 - 11167 (-) CAZyme: CBM13|GH43_7| GH43_7 Yes
- 11170 - 11868 (-) other Yes
- 11897 - 13054 (-) CAZyme: CBM48|CE0|CE1 Yes
- 13109 - 14908 (-) other Yes
- 14929 - 18105 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes

PUL ID

PUL0645

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.