PUL ID

PUL0192

PubMed

26920945, BMC Genomics. 2016 Feb 27;17:147. doi: 10.1186/s12864-016-2472-1.

Characterization method

RNA-Seq, RT-PCR, qPCR

Genomic accession number

FP929033.1

Nucelotide position range

4024208-4079442

Substrate

pectin

Loci

BXY_32120-BXY_32390

Species

Bacteroides xylanisolvens/371601

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BXY_32120 CBK68219.1 0 - 2766 (-) FP929033.1:4024208-4026974 -
- BXY_32130 CBK68220.1 2765 - 4169 (-) FP929033.1:4026973-4028377 -
- BXY_32140 CBK68221.1 4165 - 4768 (-) FP929033.1:4028373-4028976 -
- BXY_32150 CBK68222.1 4718 - 6254 (-) FP929033.1:4028926-4030462 -
- BXY_32160 CBK68223.1 6309 - 7548 (-) FP929033.1:4030517-4031756 -
- BXY_32170 CBK68224.1 7678 - 10555 (-) FP929033.1:4031886-4034763 -
- BXY_32180 CBK68225.1 10553 - 10682 (+) FP929033.1:4034761-4034890 -
- BXY_32190 CBK68226.1 10843 - 13156 (+) FP929033.1:4035051-4037364 -
- BXY_32200 CBK68227.1 13786 - 15877 (+) FP929033.1:4037994-4040085 3.2.1.23
- BXY_32210 CBK68228.1 15939 - 17322 (+) FP929033.1:4040147-4041530 -
- BXY_32220 CBK68229.1 17410 - 18100 (+) FP929033.1:4041618-4042308 -
- BXY_32230 CBK68230.1 18192 - 20274 (-) FP929033.1:4042400-4044482 -
- BXY_32240 CBK68231.1 20298 - 23430 (-) FP929033.1:4044506-4047638 -
- BXY_32260 CBK68232.1 25046 - 26084 (+) FP929033.1:4049254-4050292 -
- BXY_32270 CBK68233.1 26138 - 27764 (+) FP929033.1:4050346-4051972 -
- BXY_32280 CBK68234.1 27824 - 31004 (+) FP929033.1:4052032-4055212 -
- BXY_32290 CBK68235.1 31025 - 33038 (+) FP929033.1:4055233-4057246 -
- BXY_32300 CBK68236.1 33085 - 36136 (+) FP929033.1:4057293-4060344 -
- BXY_32310 CBK68237.1 36157 - 37879 (+) FP929033.1:4060365-4062087 -
- BXY_32320 CBK68238.1 37956 - 40092 (+) FP929033.1:4062164-4064300 -
- BXY_32330 CBK68239.1 40263 - 43662 (+) FP929033.1:4064471-4067870 -
- BXY_32340 CBK68240.1 43980 - 45615 (-) FP929033.1:4068188-4069823 -
- BXY_32350 CBK68241.1 45744 - 46836 (-) FP929033.1:4069952-4071044 -
- BXY_32360 CBK68242.1 47128 - 48970 (+) FP929033.1:4071336-4073178 -
- BXY_32370 CBK68243.1 48973 - 50383 (+) FP929033.1:4073181-4074591 -
- BXY_32380 CBK68244.1 50402 - 50717 (+) FP929033.1:4074610-4074925 5.1.3.-
- BXY_32390 CBK68245.1 50867 - 55235 (+) FP929033.1:4075075-4079443 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 2766 (-) CAZyme: GH106 Yes
- 2766 - 4169 (-) CAZyme: GH28 Yes
- 4166 - 4768 (-) other Yes
- 4719 - 6254 (-) CAZyme: GH28 Yes
- 6310 - 7548 (-) CAZyme: CE12 Yes
- 7679 - 10555 (-) CAZyme: GH2 Yes
- 10554 - 10682 (+) other Yes
- 10844 - 13156 (+) CAZyme: GH43_18|GH43_34|GH43|CBM32 Yes
- 13787 - 15877 (+) CAZyme: GH42 Yes
- 15940 - 17322 (+) CAZyme: GH28 Yes
- 17411 - 18100 (+) other Yes
- 18193 - 20274 (-) other Yes
- 20299 - 23430 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 25047 - 26084 (+) other Yes
- 26139 - 27764 (+) other Yes
- 27825 - 31004 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 31026 - 33038 (+) other Yes
- 33086 - 36136 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 36158 - 37879 (+) other Yes
- 37957 - 40092 (+) CAZyme: PL11|PL11_1 Yes
- 40264 - 43662 (+) CAZyme: PL26 Yes
- 43981 - 45615 (-) CAZyme: CE12 Yes
- 45745 - 46836 (-) CAZyme: GH105 Yes
- 47129 - 48970 (+) CAZyme: PL11_1 Yes
- 48974 - 50383 (+) CAZyme: GH105 Yes
- 50403 - 50717 (+) CDS No
- 50868 - 55235 (+) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607 No

PUL ID

PUL0192

PubMed

26920945, BMC Genomics. 2016 Feb 27;17:147. doi: 10.1186/s12864-016-2472-1.

Title

Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis.

Author

Despres J, Forano E, Lepercq P, Comtet-Marre S, Jubelin G, Yeoman CJ, Miller ME, Fields CJ, Terrapon N, Le Bourvellec C, Renard CM, Henrissat B, White BA, Mosoni P

Abstract

BACKGROUND: Diet and particularly dietary fibres have an impact on the gut microbiome and play an important role in human health and disease. Pectin is a highly consumed dietary fibre found in fruits and vegetables and is also a widely used additive in the food industry. Yet there is no information on the effect of pectin on the human gut microbiome. Likewise, little is known on gut pectinolytic bacteria and their enzyme systems. This study was undertaken to investigate the mechanisms of pectin degradation by the prominent human gut symbiont Bacteroides xylanisolvens. RESULTS: Transcriptomic analyses of B. xylanisolvens XB1A grown on citrus and apple pectins at mid- and late-log phases highlighted six polysaccharide utilization loci (PUL) that were overexpressed on pectin relative to glucose. The PUL numbers used in this report are those given by Terrapon et al. (Bioinformatics 31(5):647-55, 2015) and found in the PUL database: http://www.cazy.org/PULDB/. Based on their CAZyme composition, we propose that PUL 49 and 50, the most overexpressed PULs on both pectins and at both growth phases, are involved in homogalacturonan (HG) and type I rhamnogalacturonan (RGI) degradation, respectively. PUL 13 and PUL 2 could be involved in the degradation of arabinose-containing side chains and of type II rhamnogalacturonan (RGII), respectively. Considering that HG is the most abundant moiety (>70%) within pectin, the importance of PUL 49 was further investigated by insertion mutagenesis into the susC-like gene. The insertion blocked transcription of the susC-like and the two downstream genes (susD-like/FnIII). The mutant showed strong growth reduction, thus confirming that PUL 49 plays a major role in pectin degradation. CONCLUSION: This study shows the existence of six PULs devoted to pectin degradation by B. xylanisolvens, one of them being particularly important in this function. Hence, this species deploys a very complex enzymatic machinery that probably reflects the structural complexity of pectin. Our findings also highlight the metabolic plasticity of B. xylanisolvens towards dietary fibres that contributes to its competitive fitness within the human gut ecosystem. Wider functional and ecological studies are needed to understand how dietary fibers and especially plant cell wall polysaccharides drive the composition and metabolism of the fibrolytic and non-fibrolytic community within the gut microbial ecosystem.