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PlantCAZyme
Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0528

PubMed

22205877, PLoS Biol. 2011 Dec;9(12):e1001221. doi: 10.1371/journal.pbio.1001221. Epub 2011 Dec 20.

Characterization method

microarray,qPCR

Genomic accession number

NZ_CP012938.1

Nucelotide position range

3918991-3935883

Substrate

beta-glucan

Loci

Bovatus_03146-Bovatus_03153

Species

Bacteroides ovatus/28116

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- Bovatus_RS15280 WP_004298554.1 0 - 2403 (+) NZ_CP012938.1:3918991-3921394 -
- Bovatus_RS15285 WP_004298556.1 2900 - 6872 (+) NZ_CP012938.1:3921891-3925863 -
- Bovatus_RS15290 WP_004298557.1 7490 - 8306 (+) NZ_CP012938.1:3926481-3927297 -
- Bovatus_RS15295 WP_004298558.1 8326 - 11515 (+) NZ_CP012938.1:3927317-3930506 -
- Bovatus_RS15300 WP_004298559.1 11526 - 13203 (+) NZ_CP012938.1:3930517-3932194 -
- Bovatus_RS15305 WP_004298560.1 13223 - 14486 (+) NZ_CP012938.1:3932214-3933477 -
- Bovatus_RS15310 WP_004298561.1 14598 - 16893 (+) NZ_CP012938.1:3933589-3935884 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 2403 (+) CAZyme: GH3 Yes
- 2901 - 6872 (+) TF: DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0035607 Yes
- 7491 - 8306 (+) CAZyme: GH16 Yes
- 8327 - 11515 (+) TC: gnl|TC-DB|Q93TH9|1.B.14.6.2 Yes
- 11527 - 13203 (+) TC: gnl|TC-DB|Q8A8X0|8.A.46.2.1 Yes
- 13224 - 14486 (+) other Yes
- 14599 - 16893 (+) CAZyme: GH3 Yes

PUL ID

PUL0528

PubMed

22205877, PLoS Biol. 2011 Dec;9(12):e1001221. doi: 10.1371/journal.pbio.1001221. Epub 2011 Dec 20.

Title

Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts.

Author

Martens EC, Lowe EC, Chiang H, Pudlo NA, Wu M, McNulty NP, Abbott DW, Henrissat B, Gilbert HJ, Bolam DN, Gordon JI

Abstract

Symbiotic bacteria inhabiting the human gut have evolved under intense pressure to utilize complex carbohydrates, primarily plant cell wall glycans in our diets. These polysaccharides are not digested by human enzymes, but are processed to absorbable short chain fatty acids by gut bacteria. The Bacteroidetes, one of two dominant bacterial phyla in the adult gut, possess broad glycan-degrading abilities. These species use a series of membrane protein complexes, termed Sus-like systems, for catabolism of many complex carbohydrates. However, the role of these systems in degrading the chemically diverse repertoire of plant cell wall glycans remains unknown. Here we show that two closely related human gut Bacteroides, B. thetaiotaomicron and B. ovatus, are capable of utilizing nearly all of the major plant and host glycans, including rhamnogalacturonan II, a highly complex polymer thought to be recalcitrant to microbial degradation. Transcriptional profiling and gene inactivation experiments revealed the identity and specificity of the polysaccharide utilization loci (PULs) that encode individual Sus-like systems that target various plant polysaccharides. Comparative genomic analysis indicated that B. ovatus possesses several unique PULs that enable degradation of hemicellulosic polysaccharides, a phenotype absent from B. thetaiotaomicron. In contrast, the B. thetaiotaomicron genome has been shaped by increased numbers of PULs involved in metabolism of host mucin O-glycans, a phenotype that is undetectable in B. ovatus. Binding studies of the purified sensor domains of PUL-associated hybrid two-component systems in conjunction with transcriptional analyses demonstrate that complex oligosaccharides provide the regulatory cues that induce PUL activation and that each PUL is highly specific for a defined cell wall polymer. These results provide a view of how these species have diverged into different carbohydrate niches by evolving genes that target unique suites of available polysaccharides, a theme that likely applies to disparate bacteria from the gut and other habitats.