PUL ID

PUL0529

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

5623780-5679732

Substrate

homogalacturonan

Loci

Bovatus_04357-Bovatus_04384

Species

Bacteroides ovatus/28116

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- Bovatus_RS21315 WP_004320969.1 0 - 1200 (+) NZ_CP012938.1:5623780-5624980 -
- Bovatus_RS21320 WP_004301505.1 1209 - 2181 (+) NZ_CP012938.1:5624989-5625961 -
- Bovatus_RS21325 WP_004301507.1 2540 - 4289 (+) NZ_CP012938.1:5626320-5628069 -
- Bovatus_RS21330 WP_004301508.1 4454 - 8990 (+) NZ_CP012938.1:5628234-5632770 -
- Bovatus_RS21335 WP_004301509.1 9134 - 10631 (-) NZ_CP012938.1:5632914-5634411 -
- Bovatus_RS21340 WP_004301510.1 10666 - 12328 (-) NZ_CP012938.1:5634446-5636108 -
- Bovatus_RS21345 WP_004301511.1 12359 - 13943 (-) NZ_CP012938.1:5636139-5637723 -
- Bovatus_RS21350 WP_004301512.1 14036 - 15665 (-) NZ_CP012938.1:5637816-5639445 -
- Bovatus_RS21355 WP_004301513.1 15749 - 17669 (-) NZ_CP012938.1:5639529-5641449 -
- Bovatus_RS21360 WP_004301514.1 17684 - 19592 (-) NZ_CP012938.1:5641464-5643372 -
- Bovatus_RS21365 WP_004301515.1 19617 - 22875 (-) NZ_CP012938.1:5643397-5646655 -
- Bovatus_RS21370 WP_004301517.1 23221 - 24016 (+) NZ_CP012938.1:5647001-5647796 -
- Bovatus_RS21375 WP_004301518.1 24019 - 24838 (+) NZ_CP012938.1:5647799-5648618 -
- Bovatus_RS21380 WP_004320967.1 24956 - 26486 (+) NZ_CP012938.1:5648736-5650266 -
- Bovatus_RS21385 WP_004320966.1 26881 - 27766 (+) NZ_CP012938.1:5650661-5651546 -
- Bovatus_RS21390 WP_004301523.1 27778 - 29584 (+) NZ_CP012938.1:5651558-5653364 -
- Bovatus_RS21395 WP_004301524.1 29618 - 32006 (+) NZ_CP012938.1:5653398-5655786 -
- Bovatus_RS21400 WP_004320965.1 32050 - 35263 (+) NZ_CP012938.1:5655830-5659043 -
- Bovatus_RS21405 WP_004301526.1 35288 - 37190 (+) NZ_CP012938.1:5659068-5660970 -
- Bovatus_RS21410 WP_004301527.1 37210 - 38863 (+) NZ_CP012938.1:5660990-5662643 -
- Bovatus_RS21415 WP_004320964.1 38918 - 40775 (+) NZ_CP012938.1:5662698-5664555 -
- Bovatus_RS21420 WP_004301529.1 40816 - 43228 (+) NZ_CP012938.1:5664596-5667008 -
- Bovatus_RS21425 WP_004320963.1 43253 - 44828 (+) NZ_CP012938.1:5667033-5668608 -
- Bovatus_RS21430 WP_004301531.1 45551 - 48143 (-) NZ_CP012938.1:5669331-5671923 -
- Bovatus_RS21435 WP_004320962.1 48481 - 50488 (+) NZ_CP012938.1:5672261-5674268 -
- Bovatus_RS21440 WP_004301534.1 50711 - 51479 (+) NZ_CP012938.1:5674491-5675259 -
- Bovatus_RS21445 WP_004301535.1 51612 - 55953 (-) NZ_CP012938.1:5675392-5679733 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1200 (+) CAZyme: GH105 Yes
- 1210 - 2181 (+) CAZyme: CE8 Yes
- 2541 - 4289 (+) CAZyme: CE12|CE4|CE8 Yes
- 4455 - 8990 (+) TF: DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0035607 Yes
- 9135 - 10631 (-) CAZyme: PL1|CE8|PL1_2 Yes
- 10667 - 12328 (-) CAZyme: PL1|PL1_2 Yes
- 12360 - 13943 (-) CAZyme: PL1|PL1_2 Yes
- 14037 - 15665 (-) CAZyme: CE8 Yes
- 15750 - 17669 (-) other Yes
- 17685 - 19592 (-) other Yes
- 19618 - 22875 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 23222 - 24016 (+) TC: gnl|TC-DB|A6ECX8|9.B.116.3.2 Yes
- 24020 - 24838 (+) TF: DBD-Pfam|LytTR Yes
- 24957 - 26486 (+) CAZyme: PL1|PL1_2 Yes
- 26882 - 27766 (+) other Yes
- 27779 - 29584 (+) other Yes
- 29619 - 32006 (+) CAZyme: PL1|CE8|PL1_2 Yes
- 32051 - 35263 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 35289 - 37190 (+) TC: gnl|TC-DB|C6Y217|8.A.46.1.3 Yes
- 37211 - 38863 (+) other Yes
- 38919 - 40775 (+) other Yes
- 40817 - 43228 (+) CAZyme: CE8 Yes
- 43254 - 44828 (+) CAZyme: GH28 Yes
- 45552 - 48143 (-) CAZyme: GH3 Yes
- 48482 - 50488 (+) CAZyme: GH43_10|CBM6 Yes
- 50712 - 51479 (+) CDS No
- 51613 - 55953 (-) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607 No

PUL ID

PUL0529

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.