PUL ID

PUL0566

PubMed

22205877, PLoS Biol. 2011 Dec;9(12):e1001221. doi: 10.1371/journal.pbio.1001221. Epub 2011 Dec 20.
29255254, Nat Microbiol. 2018 Feb;3(2):210-219. doi: 10.1038/s41564-017-0079-1. Epub 2017 Dec 18.

Characterization method

microarray, qPCR

Genomic accession number

NZ_CP012938.1

Nucelotide position range

6315776-6332245

Substrate

pectin

Loci

Bovatus_04876-Bovatus_04882

Species

Bacteroides ovatus/28116

Degradation or Biosynthesis

degradation

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 2442 (-) CAZyme: GH2 Yes
- 2514 - 3599 (-) CAZyme: GH53 Yes
- 3645 - 5399 (-) other Yes
- 5423 - 7003 (-) TC: gnl|TC-DB|Q8A1G2|8.A.46.1.1 Yes
- 7022 - 9997 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 10221 - 12830 (-) CAZyme: GH147 Yes
- 12946 - 16470 (-) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607,DBD-SUPERFAMILY|0035607 No

PUL ID

PUL0566

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.

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.