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PlantCAZyme
Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0418

PubMed

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

Characterization method

microarray

Genomic accession number

AAXF02000047.1

Nucelotide position range

50166-64939

Substrate

plant polysaccharide

Loci

BACOVA_02051-BACOVA_02059

Species

Bacteroides ovatus/28116

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BACOVA_02051 EDO12162.1 0 - 2871 (+) AAXF02000047.1:50166-53037 -
- BACOVA_02052 EDO12163.1 2886 - 4416 (+) AAXF02000047.1:53052-54582 -
- BACOVA_02053 EDO12164.1 4475 - 6440 (+) AAXF02000047.1:54641-56606 -
- BACOVA_02054 EDO12165.1 6452 - 8060 (+) AAXF02000047.1:56618-58226 -
- BACOVA_02055 EDO12166.1 8066 - 9614 (+) AAXF02000047.1:58232-59780 -
- BACOVA_02056 EDO12167.1 9626 - 11225 (+) AAXF02000047.1:59792-61391 -
- BACOVA_02057 EDO12168.1 11226 - 12747 (+) AAXF02000047.1:61392-62913 -
- BACOVA_02058 EDO12169.1 12816 - 13773 (+) AAXF02000047.1:62982-63939 -
- BACOVA_02059 EDO12170.1 13796 - 14774 (+) AAXF02000047.1:63962-64940 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 2871 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 2887 - 4416 (+) other Yes
- 4476 - 6440 (+) other Yes
- 6453 - 8060 (+) other Yes
- 8067 - 9614 (+) other Yes
- 9627 - 11225 (+) CAZyme: CE1 Yes
- 11227 - 12747 (+) CAZyme: CE1 Yes
- 12817 - 13773 (+) CDS No
- 13797 - 14774 (+) CDS No

PUL ID

PUL0418

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.