PUL ID

PUL0305

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

5371714-5408988

Substrate

homogalacturonan

Loci

BT_4108-BT_4124; (GH105+ CE8+ CE8+ HTCS+ SGBP- SusD-like- SusC-like- PL1- PL1- HP+ HP+ PL1+ HP+ SusC-ilke+ SusD-like+ GH28+ HTCS-)

Species

Bacteroides thetaiotaomicron/818

Degradation or Biosynthesis

degradation

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1200 (+) CAZyme: GH105 Yes
- 1210 - 2178 (+) CAZyme: CE8 Yes
- 2421 - 4031 (+) CAZyme: CE4|CE8|CE12 Yes
- 4097 - 8632 (+) TF: DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0035607 Yes
- 9561 - 11144 (-) other Yes
- 11169 - 13028 (-) other Yes
- 13041 - 16256 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 16476 - 17969 (-) CAZyme: PL1_2|PL1|CE8 Yes
- 17976 - 19547 (-) CAZyme: PL1_2|PL1|CE8 Yes
- 19831 - 20625 (+) TC: gnl|TC-DB|A6ECX8|9.B.116.3.2 Yes
- 20629 - 21441 (+) TF: DBD-Pfam|LytTR Yes
- 21892 - 23571 (+) CAZyme: PL1_2 Yes
- 23601 - 25268 (+) other Yes
- 25295 - 28723 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 28738 - 30813 (+) other Yes
- 31104 - 32690 (+) CAZyme: GH28 Yes
- 32923 - 37275 (-) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607 No

PUL ID

PUL0305

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.