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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0145

PubMed

30262663, J Biol Chem. 2018 Nov 16;293(46):17906-17916. doi: 10.1074/jbc.RA118.004510. Epub 2018 Sep 27.

Characterization method

enzyme activity assay

Genomic accession number

AE015928.1

Nucelotide position range

4269304-4322090

Substrate

glycosaminoglycan,chondroitin sulfate

Loci

BT_3324-BT_3350

Species

Bacteroides thetaiotaomicron/818

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BT_3324 AAO78430.1 0 - 3045 (+) AE015928.1:4269304-4272349 -
- BT_3325 AAO78431.1 3839 - 5069 (-) AE015928.1:4273143-4274373 -
- BT_3326 AAO78432.1 5155 - 6100 (-) AE015928.1:4274459-4275404 -
- BT_3327 AAO78433.1 6127 - 7585 (-) AE015928.1:4275431-4276889 -
- BT_3328 AAO78434.1 7765 - 10372 (-) AE015928.1:4277069-4279676 -
- BT_3329 AAO78435.1 10385 - 12323 (-) AE015928.1:4279689-4281627 -
- BT_3330 AAO78436.1 12361 - 13405 (-) AE015928.1:4281665-4282709 -
- BT_3331 AAO78437.1 13438 - 15157 (-) AE015928.1:4282742-4284461 -
- BT_3332 AAO78438.1 15197 - 18359 (-) AE015928.1:4284501-4287663 -
- BT_3333 AAO78439.1 18518 - 20054 (-) AE015928.1:4287822-4289358 -
- BT_3334 AAO78440.1 20353 - 24418 (-) AE015928.1:4289657-4293722 -
- BT_3335 AAO78441.1 24529 - 25171 (+) AE015928.1:4293833-4294475 -
- BT_3336 AAO78442.1 25231 - 26002 (-) AE015928.1:4294535-4295306 -
- BT_3337 AAO78443.1 26020 - 27406 (-) AE015928.1:4295324-4296710 -
- BT_3338 AAO78444.1 27417 - 30633 (-) AE015928.1:4296721-4299937 -
- BT_3339 AAO78445.1 30649 - 31825 (-) AE015928.1:4299953-4301129 -
- BT_3340 AAO78446.1 32004 - 35115 (-) AE015928.1:4301308-4304419 -
- BT_3341 AAO78447.1 35265 - 37194 (+) AE015928.1:4304569-4306498 -
- BT_3342 AAO78448.1 37234 - 38014 (+) AE015928.1:4306538-4307318 -
- BT_3343 AAO78449.1 38019 - 38424 (-) AE015928.1:4307323-4307728 -
- BT_3344 AAO78450.1 38729 - 39740 (-) AE015928.1:4308033-4309044 -
- BT_3345 AAO78451.1 39768 - 41808 (-) AE015928.1:4309072-4311112 -
- BT_3346 AAO78452.1 41830 - 44914 (-) AE015928.1:4311134-4314218 -
- BT_3347 AAO78453.1 44937 - 46347 (-) AE015928.1:4314241-4315651 -
- BT_3348 AAO78454.1 46951 - 48154 (+) AE015928.1:4316255-4317458 -
- BT_3349 AAO78455.1 48260 - 49787 (+) AE015928.1:4317564-4319091 -
- BT_3350 AAO78456.1 49925 - 52787 (+) AE015928.1:4319229-4322091 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 3045 (+) CAZyme: PL8|PL8_2 Yes
- 3840 - 5069 (-) other Yes
- 5156 - 6100 (-) other Yes
- 6128 - 7585 (-) other Yes
- 7766 - 10372 (-) CAZyme: PL29 Yes
- 10386 - 12323 (-) other Yes
- 12362 - 13405 (-) other Yes
- 13439 - 15157 (-) TC: gnl|TC-DB|C6Y217|8.A.46.1.3 Yes
- 15198 - 18359 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 18519 - 20054 (-) other Yes
- 20354 - 24418 (-) STP: STP|Reg_prop,STP|Reg_prop,STP|Reg_prop,STP|Y_Y_Y,STP|HisKA,STP|HATPase_c,STP|Response_reg,STP|HTH_18 Yes
- 24530 - 25171 (+) other Yes
- 25232 - 26002 (-) other Yes
- 26021 - 27406 (-) TC: gnl|TC-DB|Q8ZRH0|2.A.6.2.25 Yes
- 27418 - 30633 (-) TC: gnl|TC-DB|Q8RTE4|2.A.6.2.22 Yes
- 30650 - 31825 (-) TC: gnl|TC-DB|P52477|2.A.6.2.6 Yes
- 32005 - 35115 (-) CAZyme: GH2 Yes
- 35266 - 37194 (+) other Yes
- 37235 - 38014 (+) other Yes
- 38020 - 38424 (-) other Yes
- 38730 - 39740 (-) other Yes
- 39769 - 41808 (-) other Yes
- 41831 - 44914 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 44938 - 46347 (-) other Yes
- 46952 - 48154 (+) CAZyme: GH88 Yes
- 48261 - 49787 (+) other Yes
- 49926 - 52787 (+) CAZyme: PL8_2 Yes

PUL ID

PUL0145

PubMed

30262663, J Biol Chem. 2018 Nov 16;293(46):17906-17916. doi: 10.1074/jbc.RA118.004510. Epub 2018 Sep 27.

Title

The human gut microbe Bacteroides thetaiotaomicron encodes the founding member of a novel glycosaminoglycan-degrading polysaccharide lyase family PL29.

Author

Ndeh D, Munoz Munoz J, Cartmell A, Bulmer D, Wills C, Henrissat B, Gray J

Abstract

Glycosaminoglycans (GAGs) and GAG-degrading enzymes have wide-ranging applications in the medical and biotechnological industries. The former are also an important nutrient source for select species of the human gut microbiota (HGM), a key player in host-microbial interactions. How GAGs are metabolized by the HGM is therefore of interest and has been extensively investigated in the model human gut microbe Bacteroides thetaiotaomicron. The presence of as-yet uncharacterized GAG-inducible genes in its genome and of related species, however, is testament to our incomplete understanding of this process. Nevertheless, it presents a potential opportunity for the discovery of additional GAG-degrading enzymes. Here, we investigated a gene of unknown function (BT_3328) from the chondroitin sulfate (CS) utilization locus of B. thetaiotaomicron NMR and UV spectroscopic assays revealed that it encodes a novel polysaccharide lyase (PL), hereafter referred to as BtCDH, reflecting its source (B. thetaiotaomicron (Bt)) and its ability to degrade the GAGs CS, dermatan sulfate (DS), and hyaluronic acid (HA). When incubated with HA, BtCDH generated a series of unsaturated HA sugars, including Delta(4,5)UA-GlcNAc, Delta(4,5)UA-GlcNAc-GlcA-GlcNac, Delta(4,5)UA-[GlcNAc-GlcA](2)-GlcNac, and Delta(4,5)UA-[GlcNAc-GlcA](3)-GlcNac, as end products and hence was classed as endo-acting. A combination of genetic and biochemical assays revealed that BtCDH localizes to the cell surface of B. thetaiotaomicron where it enables extracellular GAG degradation. BtCDH homologs were also detected in several other HGM species, and we therefore propose that it represents the founding member of a new polysaccharide lyase family (PL29). The current discovery also contributes new insights into CS metabolism by the HGM.