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PlantCAZyme
Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0228

PubMed

22686399, Mol Microbiol. 2012 Aug;85(3):478-91. doi: 10.1111/j.1365-2958.2012.08123.x. Epub 2012 Jul 5.
21339299, J Biol Chem. 2011 Apr 29;286(17):15483-95. doi: 10.1074/jbc.M110.215962. Epub 2011 Feb 21.

Characterization method

qRT-PCR,enzyme activity assay,high performance anion exchange chromatography

Genomic accession number

AE015928.1

Nucelotide position range

432012-455321

Substrate

arabinan

Loci

BT_0360-BT_0369

Species

Bacteroides thetaiotaomicron/818

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BT_0360 AAO75467.1 0 - 1926 (-) AE015928.1:432012-433938 -
- BT_0361 AAO75468.1 1960 - 3766 (-) AE015928.1:433972-435778 -
- BT_0362 AAO75469.1 3791 - 6941 (-) AE015928.1:435803-438953 -
- BT_0363 AAO75470.1 6945 - 8721 (-) AE015928.1:438957-440733 -
- BT_0364 AAO75471.1 8733 - 11817 (-) AE015928.1:440745-443829 -
- BT_0365 AAO75472.1 11836 - 14116 (-) AE015928.1:443848-446128 -
- BT_0366 AAO75473.1 14375 - 18638 (-) AE015928.1:446387-450650 -
- BT_0367 AAO75474.1 18793 - 20335 (+) AE015928.1:450805-452347 -
- BT_0368 AAO75475.1 20360 - 22343 (+) AE015928.1:452372-454355 -
- BT_0369 AAO75476.1 22344 - 23310 (+) AE015928.1:454356-455322 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1926 (-) CAZyme: GH43|GH43_4 Yes
- 1961 - 3766 (-) other Yes
- 3792 - 6941 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 6946 - 8721 (-) other Yes
- 8734 - 11817 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 11837 - 14116 (-) other Yes
- 14376 - 18638 (-) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0035607 Yes
- 18794 - 20335 (+) CAZyme: GH43_4 Yes
- 20361 - 22343 (+) CAZyme: GH51 Yes
- 22345 - 23310 (+) CAZyme: GH43_29 Yes

PUL ID

PUL0228

PubMed

22686399, Mol Microbiol. 2012 Aug;85(3):478-91. doi: 10.1111/j.1365-2958.2012.08123.x. Epub 2012 Jul 5.

Title

Prioritization of a plant polysaccharide over a mucus carbohydrate is enforced by a Bacteroides hybrid two-component system.

Author

Lynch JB, Sonnenburg JL

Abstract

Bacteroides is a dominant genus within the intestinal microbiota of healthy humans. Key adaptations of the Bacteroides to the dynamic intestinal ecosystem include a diverse repertoire of genes involved in sensing and processing numerous diet- and host-derived polysaccharides. One such adaptation is the carbohydrate-sensing hybrid two-component system (HTCS) family of signalling sensors, which has been widely expanded within the Bacteroides. Using Bacteroides thetaiotaomicron as a model, we have created a chimeric HTCS consisting of the well-characterized sensing domain of one HTCS, BT1754, and the regulatory domain of another HTCS, BT0366, to explore the regulatory capabilities of these molecules. We found that the BT0366 regulatory region directly binds to and mediates induction of the adjacent polysaccharide utilization locus (PUL) using whole-genome transcriptional profiling after inducing signalling through our chimeric protein. We also found that BT0366 activation simultaneously leads to repression of distal PULs involved in mucus carbohydrate consumption. These results suggest a novel mechanism by which an HTCS enforces a nutrient hierarchy within the Bacteroides via induction and repression of multiple PULs. Thus, hybrid two-component systems provide a mechanism for prioritizing consumption of carbohydrates through simultaneous binding and regulation of multiple polysaccharide utilization loci.

PubMed

21339299, J Biol Chem. 2011 Apr 29;286(17):15483-95. doi: 10.1074/jbc.M110.215962. Epub 2011 Feb 21.

Title

The structure and function of an arabinan-specific alpha-1,2-arabinofuranosidase identified from screening the activities of bacterial GH43 glycoside hydrolases.

Author

Cartmell A, McKee LS, Pena MJ, Larsbrink J, Brumer H, Kaneko S, Ichinose H, Lewis RJ, Vikso-Nielsen A, Gilbert HJ, Marles-Wright J

Abstract

Reflecting the diverse chemistry of plant cell walls, microorganisms that degrade these composite structures synthesize an array of glycoside hydrolases. These enzymes are organized into sequence-, mechanism-, and structure-based families. Genomic data have shown that several organisms that degrade the plant cell wall contain a large number of genes encoding family 43 (GH43) glycoside hydrolases. Here we report the biochemical properties of the GH43 enzymes of a saprophytic soil bacterium, Cellvibrio japonicus, and a human colonic symbiont, Bacteroides thetaiotaomicron. The data show that C. japonicus uses predominantly exo-acting enzymes to degrade arabinan into arabinose, whereas B. thetaiotaomicron deploys a combination of endo- and side chain-cleaving glycoside hydrolases. Both organisms, however, utilize an arabinan-specific alpha-1,2-arabinofuranosidase in the degradative process, an activity that has not previously been reported. The enzyme can cleave alpha-1,2-arabinofuranose decorations in single or double substitutions, the latter being recalcitrant to the action of other arabinofuranosidases. The crystal structure of the C. japonicus arabinan-specific alpha-1,2-arabinofuranosidase, CjAbf43A, displays a five-bladed beta-propeller fold. The specificity of the enzyme for arabinan is conferred by a surface cleft that is complementary to the helical backbone of the polysaccharide. The specificity of CjAbf43A for alpha-1,2-l-arabinofuranose side chains is conferred by a polar residue that orientates the arabinan backbone such that O2 arabinose decorations are directed into the active site pocket. A shelflike structure adjacent to the active site pocket accommodates O3 arabinose side chains, explaining how the enzyme can target O2 linkages that are components of single or double substitutions.