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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0553

PubMed

27142817, BMC Genomics. 2016 May 4;17:326. doi: 10.1186/s12864-016-2680-8.

Characterization method

RT-PCR,qPCR

Genomic accession number

FP929033.1

Nucelotide position range

3588797-3632016

Substrate

xylan

Loci

BXY_29170-BXY_29370

Species

Bacteroides xylanisolvens/371601

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BXY_29170 CBK67940.1 0 - 1605 (+) FP929033.1:3588797-3590402 -
- BXY_29180 CBK67941.1 1701 - 4287 (+) FP929033.1:3590498-3593084 3.2.1.21
- BXY_29190 CBK67942.1 4487 - 4649 (+) FP929033.1:3593284-3593446 -
- BXY_29200 CBK67943.1 4779 - 6447 (+) FP929033.1:3593576-3595244 3.2.1.55
- BXY_29210 CBK67944.1 6472 - 8917 (+) FP929033.1:3595269-3597714 -
- BXY_29220 CBK67945.1 8938 - 10915 (+) FP929033.1:3597735-3599712 -
- BXY_29230 CBK67946.1 10934 - 12266 (+) FP929033.1:3599731-3601063 -
- BXY_29240 CBK67947.1 12554 - 13913 (+) FP929033.1:3601351-3602710 3.2.1.55
- BXY_29250 CBK67948.1 14033 - 17177 (+) FP929033.1:3602830-3605974 -
- BXY_29260 CBK67949.1 17191 - 19093 (+) FP929033.1:3605988-3607890 -
- BXY_29270 CBK67950.1 19124 - 21935 (+) FP929033.1:3607921-3610732 -
- BXY_29280 CBK67951.1 21979 - 23737 (+) FP929033.1:3610776-3612534 -
- BXY_29290 CBK67952.1 23775 - 24849 (+) FP929033.1:3612572-3613646 -
- BXY_29300 CBK67953.1 24879 - 27144 (+) FP929033.1:3613676-3615941 -
- BXY_29310 CBK67954.1 27223 - 27961 (+) FP929033.1:3616020-3616758 -
- BXY_29320 CBK67955.1 28005 - 29964 (+) FP929033.1:3616802-3618761 -
- BXY_29330 CBK67956.1 30088 - 31912 (+) FP929033.1:3618885-3620709 -
- BXY_29340 CBK67957.1 31919 - 33305 (+) FP929033.1:3620716-3622102 -
- BXY_29350 CBK67958.1 33326 - 37346 (-) FP929033.1:3622123-3626143 -
- BXY_29360 CBK67959.1 37504 - 39940 (-) FP929033.1:3626301-3628737 -
- BXY_29370 CBK67960.1 40649 - 43220 (-) FP929033.1:3629446-3632017 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1605 (+) CAZyme: GH43_10|GH43 Yes
- 1702 - 4287 (+) CAZyme: CBM6|GH3 Yes
- 4488 - 4649 (+) other Yes
- 4780 - 6447 (+) CAZyme: GH43|GH43_12 Yes
- 6473 - 8917 (+) CAZyme: GH31 Yes
- 8939 - 10915 (+) CAZyme: GH97 Yes
- 10935 - 12266 (+) CAZyme: CBM66|CBM6|GH43|GH43_29 Yes
- 12555 - 13913 (+) CAZyme: GH43|GH43_12 Yes
- 14034 - 17177 (+) TC: gnl|TC-DB|Q93TH9|1.B.14.6.2 Yes
- 17192 - 19093 (+) other Yes
- 19125 - 21935 (+) other Yes
- 21980 - 23737 (+) other Yes
- 23776 - 24849 (+) other Yes
- 24880 - 27144 (+) CAZyme: CBM4|CBM0|GH10 Yes
- 27224 - 27961 (+) other Yes
- 28006 - 29964 (+) CAZyme: GH5_21 Yes
- 30089 - 31912 (+) CAZyme: CE1|CE6 Yes
- 31920 - 33305 (+) CAZyme: CBM6|GH43_29 Yes
- 33327 - 37346 (-) 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
- 37505 - 39940 (-) CAZyme: GH95 Yes
- 40650 - 43220 (-) CAZyme: GH115 Yes

PUL ID

PUL0553

PubMed

27142817, BMC Genomics. 2016 May 4;17:326. doi: 10.1186/s12864-016-2680-8.

Title

Xylan degradation by the human gut Bacteroides xylanisolvens XB1A(T) involves two distinct gene clusters that are linked at the transcriptional level.

Author

Despres J, Forano E, Lepercq P, Comtet-Marre S, Jubelin G, Chambon C, Yeoman CJ, Berg Miller ME, Fields CJ, Martens E, Terrapon N, Henrissat B, White BA, Mosoni P

Abstract

BACKGROUND: Plant cell wall (PCW) polysaccharides and especially xylans constitute an important part of human diet. Xylans are not degraded by human digestive enzymes in the upper digestive tract and therefore reach the colon where they are subjected to extensive degradation by some members of the symbiotic microbiota. Xylanolytic bacteria are the first degraders of these complex polysaccharides and they release breakdown products that can have beneficial effects on human health. In order to understand better how these bacteria metabolize xylans in the colon, this study was undertaken to investigate xylan breakdown by the prominent human gut symbiont Bacteroides xylanisolvens XB1A(T). RESULTS: Transcriptomic analyses of B. xylanisolvens XB1A(T) grown on insoluble oat-spelt xylan (OSX) at mid- and late-log phases highlighted genes in a polysaccharide utilization locus (PUL), hereafter called PUL 43, and genes in a fragmentary remnant of another PUL, hereafter referred to as rPUL 70, which were highly overexpressed on OSX relative to glucose. Proteomic analyses supported the up-regulation of several genes belonging to PUL 43 and showed the important over-production of a CBM4-containing GH10 endo-xylanase. We also show that PUL 43 is organized in two operons and that the knockout of the PUL 43 sensor/regulator HTCS gene blocked the growth of the mutant on insoluble OSX and soluble wheat arabinoxylan (WAX). The mutation not only repressed gene expression in the PUL 43 operons but also repressed gene expression in rPUL 70. CONCLUSION: This study shows that xylan degradation by B. xylanisolvens XB1A(T) is orchestrated by one PUL and one PUL remnant that are linked at the transcriptional level. Coupled to studies on other xylanolytic Bacteroides species, our data emphasize the importance of one peculiar CBM4-containing GH10 endo-xylanase in xylan breakdown and that this modular enzyme may be used as a functional marker of xylan degradation in the human gut. Our results also suggest that B. xylanisolvens XB1A(T) has specialized in the degradation of xylans of low complexity. This functional feature may provide a niche to all xylanolytic bacteria harboring similar PULs. Further functional and ecological studies on fibrolytic Bacteroides species are needed to better understand their role in dietary fiber degradation and their impact on intestinal health.