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PlantCAZyme
Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0560

PubMed

18996345, Cell Host Microbe. 2008 Nov 13;4(5):447-57. doi: 10.1016/j.chom.2008.09.007.
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

AE015928.1

Nucelotide position range

292568-340723

Substrate

arabinogalactan

Loci

BT0262-BT0291

Species

Bacteroides thetaiotaomicron/818

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BT_0262 AAO75369.1 0 - 636 (+) AE015928.1:292568-293204 -
- BT_0263 AAO75370.1 731 - 2144 (+) AE015928.1:293299-294712 -
- BT_0264 AAO75371.1 2269 - 4018 (-) AE015928.1:294837-296586 -
- BT_0265 AAO75372.1 4059 - 5541 (-) AE015928.1:296627-298109 -
- BT_0266 AAO75373.1 5553 - 7014 (-) AE015928.1:298121-299582 -
- BT_0267 AAO75374.1 7296 - 11409 (+) AE015928.1:299864-303977 -
- BT_0268 AAO75375.1 11683 - 14617 (+) AE015928.1:304251-307185 -
- BT_0269 AAO75376.1 14650 - 16189 (+) AE015928.1:307218-308757 -
- BT_0270 AAO75377.1 16202 - 16997 (+) AE015928.1:308770-309565 -
- BT_0271 AAO75378.1 17139 - 18015 (+) AE015928.1:309707-310583 -
- BT_0272 AAO75379.1 18038 - 21209 (+) AE015928.1:310606-313777 -
- BT_0273 AAO75380.1 21233 - 22745 (+) AE015928.1:313801-315313 -
- BT_0274 AAO75381.1 22771 - 23494 (+) AE015928.1:315339-316062 -
- BT_0275 AAO75382.1 23514 - 25200 (+) AE015928.1:316082-317768 -
- BT_0276 AAO75383.1 25240 - 27046 (+) AE015928.1:317808-319614 -
- BT_0277 AAO75384.1 27059 - 29177 (+) AE015928.1:319627-321745 -
- BT_0278 AAO75385.1 29188 - 30961 (+) AE015928.1:321756-323529 -
- BT_0279 AAO75386.1 31107 - 31860 (+) AE015928.1:323675-324428 -
- BT_0280 AAO75387.1 31973 - 33191 (+) AE015928.1:324541-325759 -
- BT_0281 AAO75388.1 33440 - 34082 (-) AE015928.1:326008-326650 -
- BT_0282 AAO75389.1 34383 - 35679 (+) AE015928.1:326951-328247 -
- BT_0283 AAO75390.1 35694 - 35880 (+) AE015928.1:328262-328448 -
- BT_0284 AAO75391.1 35925 - 37377 (+) AE015928.1:328493-329945 -
- BT_0285 AAO75392.1 37606 - 39025 (+) AE015928.1:330174-331593 -
- BT_0286 AAO75393.1 39008 - 39455 (+) AE015928.1:331576-332023 -
- BT_0287 AAO75394.1 39459 - 39885 (+) AE015928.1:332027-332453 -
- BT_0288 AAO75395.1 39859 - 41383 (+) AE015928.1:332427-333951 -
- BT_0289 AAO75396.1 41640 - 44331 (-) AE015928.1:334208-336899 -
- BT_0290 AAO75397.1 44648 - 46988 (+) AE015928.1:337216-339556 -
- BT_0291 AAO75398.1 47190 - 48156 (+) AE015928.1:339758-340724 -

Cluster number

2

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 636 (+) CDS No
- 732 - 2144 (+) CAZyme: PL27 Yes (cluster 1)
- 2270 - 4018 (-) CAZyme: GH43_24 Yes (cluster 1)
- 4060 - 5541 (-) CAZyme: GH43|GH43_24 Yes (cluster 1)
- 5554 - 7014 (-) other Yes (cluster 1)
- 7297 - 11409 (+) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607 Yes (cluster 1)
- 11684 - 14617 (+) other Yes (cluster 1)
- 14651 - 16189 (+) other Yes (cluster 1)
- 16203 - 16997 (+) other Yes (cluster 1)
- 17140 - 18015 (+) other Yes (cluster 1)
- 18039 - 21209 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes (cluster 1)
- 21234 - 22745 (+) CDS No
- 22772 - 23494 (+) CDS No
- 23515 - 25200 (+) CDS No
- 25241 - 27046 (+) CDS No
- 27060 - 29177 (+) CDS No
- 29189 - 30961 (+) CDS No
- 31108 - 31860 (+) CDS No
- 31974 - 33191 (+) CDS No
- 33441 - 34082 (-) CDS No
- 34384 - 35679 (+) CDS No
- 35695 - 35880 (+) CDS No
- 35926 - 37377 (+) CDS No
- 37607 - 39025 (+) TC: gnl|TC-DB|Q8F192|1.A.30.2.9 Yes (cluster 2)
- 39009 - 39455 (+) other Yes (cluster 2)
- 39460 - 39885 (+) other Yes (cluster 2)
- 39860 - 41383 (+) other Yes (cluster 2)
- 41641 - 44331 (-) other Yes (cluster 2)
- 44649 - 46988 (+) CAZyme: GH35|CBM32 Yes (cluster 2)
- 47191 - 48156 (+) CDS No

PUL ID

PUL0560

PubMed

18996345, Cell Host Microbe. 2008 Nov 13;4(5):447-57. doi: 10.1016/j.chom.2008.09.007.

Title

Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont.

Author

Martens EC, Chiang HC, Gordon JI

Abstract

The distal human gut is a microbial bioreactor that digests complex carbohydrates. The strategies evolved by gut microbes to sense and process diverse glycans have important implications for the assembly and operation of this ecosystem. The human gut-derived bacterium Bacteroides thetaiotaomicron forages on both host and dietary glycans. Its ability to target these substrates resides in 88 polysaccharide utilization loci (PULs), encompassing 18% of its genome. Whole genome transcriptional profiling and genetic tests were used to define the mechanisms underlying host glycan foraging in vivo and in vitro. PULs that target all major classes of host glycans were identified. However, mucin O-glycans are the principal host substrate foraged in vivo. Simultaneous deletion of five genes encoding ECF-sigma transcription factors, which activate mucin O-glycan utilization, produces defects in bacterial persistence in the gut and in mother-to-offspring transmission. Thus, PUL-mediated glycan catabolism is an important component in gut colonization and may impact microbiota ecology.

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.