PUL ID

PUL0193

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

4080557-4141706

Substrate

pectin

Loci

BXY_32430-BXY_32730

Species

Bacteroides xylanisolvens/371601

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BXY_32430 CBK68249.1 0 - 2964 (-) FP929033.1:4080557-4083521 3.2.1.23
- BXY_32440 CBK68250.1 2978 - 4844 (-) FP929033.1:4083535-4085401 -
- BXY_32450 CBK68251.1 5100 - 6564 (+) FP929033.1:4085657-4087121 -
- BXY_32460 CBK68252.1 6632 - 9803 (-) FP929033.1:4087189-4090360 -
- BXY_32470 CBK68253.1 9768 - 10278 (-) FP929033.1:4090325-4090835 -
- BXY_32480 CBK68254.1 10317 - 11394 (-) FP929033.1:4090874-4091951 -
- BXY_32490 CBK68255.1 12057 - 12837 (-) FP929033.1:4092614-4093394 -
- BXY_32500 CBK68256.1 12961 - 17320 (-) FP929033.1:4093518-4097877 -
- BXY_32510 CBK68257.1 17682 - 20763 (+) FP929033.1:4098239-4101320 -
- BXY_32520 CBK68258.1 20813 - 22394 (+) FP929033.1:4101370-4102951 -
- BXY_32530 CBK68259.1 22432 - 25675 (+) FP929033.1:4102989-4106232 -
- BXY_32540 CBK68260.1 25717 - 26710 (+) FP929033.1:4106274-4107267 -
- BXY_32550 CBK68261.1 26731 - 28321 (+) FP929033.1:4107288-4108878 -
- BXY_32560 CBK68262.1 28417 - 30241 (-) FP929033.1:4108974-4110798 -
- BXY_32570 CBK68263.1 30648 - 31026 (+) FP929033.1:4111205-4111583 -
- BXY_32580 CBK68264.1 31304 - 32615 (+) FP929033.1:4111861-4113172 -
- BXY_32590 CBK68265.1 32917 - 35347 (+) FP929033.1:4113474-4115904 -
- BXY_32600 CBK68266.1 35416 - 36529 (+) FP929033.1:4115973-4117086 -
- BXY_32620 CBK68267.1 37733 - 38396 (+) FP929033.1:4118290-4118953 -
- BXY_32630 CBK68268.1 38573 - 40757 (+) FP929033.1:4119130-4121314 -
- BXY_32640 CBK68269.1 40777 - 44029 (+) FP929033.1:4121334-4124586 -
- BXY_32650 CBK68270.1 44087 - 45581 (+) FP929033.1:4124644-4126138 -
- BXY_32660 CBK68271.1 45598 - 47305 (+) FP929033.1:4126155-4127862 -
- BXY_32670 CBK68272.1 47308 - 48979 (+) FP929033.1:4127865-4129536 -
- BXY_32680 CBK68273.1 49000 - 52144 (+) FP929033.1:4129557-4132701 -
- BXY_32690 CBK68274.1 52143 - 53826 (+) FP929033.1:4132700-4134383 -
- BXY_32700 CBK68275.1 53947 - 56059 (+) FP929033.1:4134504-4136616 -
- BXY_32710 CBK68276.1 56075 - 59339 (+) FP929033.1:4136632-4139896 -
- BXY_32720 CBK68277.1 59404 - 60784 (+) FP929033.1:4139961-4141341 -
- BXY_32730 CBK68278.1 60814 - 61150 (+) FP929033.1:4141371-4141707 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 2964 (-) CAZyme: GH2 Yes
- 2979 - 4844 (-) CAZyme: PL11_1|PL11 Yes
- 5101 - 6564 (+) CAZyme: GH28 Yes
- 6633 - 9803 (-) other Yes
- 9769 - 10278 (-) other Yes
- 10318 - 11394 (-) CAZyme: GH117 Yes
- 12058 - 12837 (-) other Yes
- 12962 - 17320 (-) TF: DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0035607 Yes
- 17683 - 20763 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 20814 - 22394 (+) TC: gnl|TC-DB|C6Y217|8.A.46.1.3 Yes
- 22433 - 25675 (+) other Yes
- 25718 - 26710 (+) other Yes
- 26732 - 28321 (+) other Yes
- 28418 - 30241 (-) CAZyme: PL11_1|PL11 Yes
- 30649 - 31026 (+) other Yes
- 31305 - 32615 (+) CAZyme: GH28 Yes
- 32918 - 35347 (+) CAZyme: GH105 Yes
- 35417 - 36529 (+) other Yes
- 37734 - 38396 (+) other Yes
- 38574 - 40757 (+) other Yes
- 40778 - 44029 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 44088 - 45581 (+) other Yes
- 45599 - 47305 (+) other Yes
- 47309 - 48979 (+) other Yes
- 49001 - 52144 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 52144 - 53826 (+) other Yes
- 53948 - 56059 (+) other Yes
- 56076 - 59339 (+) other Yes
- 59405 - 60784 (+) CAZyme: GH28 Yes
- 60815 - 61150 (+) CDS No

PUL ID

PUL0193

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.