Home Repository Download Help About Statistics Taxonomy Blastx
Links
PULDB
CAZy
dbCAN2
dbCAN-seq
run_dbcan
CAZypedia
PlantCAZyme
Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0562

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

4749697-4765579

Substrate

host glycan,rhamnogalacturonan

Loci

BT3662-BT3672

Species

Bacteroides thetaiotaomicron/818

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BT_3662 AAO78767.1 0 - 1386 (+) AE015928.1:4749697-4751083 -
- BT_3663 AAO78768.1 1640 - 3002 (+) AE015928.1:4751337-4752699 -
- BT_3664 AAO78769.1 3013 - 4930 (+) AE015928.1:4752710-4754627 -
- BT_3665 AAO78770.1 5048 - 6692 (+) AE015928.1:4754745-4756389 -
- BT_3666 AAO78771.1 6703 - 7093 (+) AE015928.1:4756400-4756790 -
- BT_3667 AAO78772.1 7169 - 8030 (-) AE015928.1:4756866-4757727 -
- BT_3668 AAO78773.1 8246 - 8981 (+) AE015928.1:4757943-4758678 -
- BT_3669 AAO78774.1 9061 - 9652 (+) AE015928.1:4758758-4759349 -
- BT_3670 AAO78775.1 9651 - 12792 (+) AE015928.1:4759348-4762489 -
- BT_3671 AAO78776.1 12816 - 14892 (+) AE015928.1:4762513-4764589 -
- BT_3672 AAO78777.1 14923 - 15883 (+) AE015928.1:4764620-4765580 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1386 (+) CAZyme: CBM32|GH43_34 Yes
- 1641 - 3002 (+) CAZyme: GH43_10 Yes
- 3014 - 4930 (+) CAZyme: GH97 Yes
- 5049 - 6692 (+) CAZyme: GH29 Yes
- 6704 - 7093 (+) other Yes
- 7170 - 8030 (-) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607 Yes
- 8247 - 8981 (+) other Yes
- 9062 - 9652 (+) other Yes
- 9652 - 12792 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 12817 - 14892 (+) CDS No
- 14924 - 15883 (+) CDS No

PUL ID

PUL0562

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.