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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0539

PubMed

23976882, PLoS Biol. 2013;11(8):e1001637. doi: 10.1371/journal.pbio.1001637. Epub 2013 Aug 20.

Characterization method

RNA-Seq

Genomic accession number

CP012801.1

Nucelotide position range

2467595-2494001

Substrate

fucose,galacturonic acid, rhamnose

Loci

BcellWH2_02076-BcellWH2_02091

Species

Bacteroides cellulosilyticus/246787

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BcellWH2_02076 ALJ59319.1 0 - 1377 (-) CP012801.1:2467595-2468972 -
- BcellWH2_02077 ALJ59320.1 1382 - 1523 (+) CP012801.1:2468977-2469118 -
- BcellWH2_02078 ALJ59321.1 1516 - 3514 (-) CP012801.1:2469111-2471109 -
- BcellWH2_02079 ALJ59322.1 3528 - 6735 (-) CP012801.1:2471123-2474330 -
atsA_5 BcellWH2_02080 ALJ59323.1 7067 - 8465 (-) CP012801.1:2474662-2476060 3.1.6.1
pehX_2 BcellWH2_02081 ALJ59324.1 8526 - 9948 (-) CP012801.1:2476121-2477543 3.2.1.82
xylR_2 BcellWH2_02082 ALJ59325.1 10182 - 11103 (-) CP012801.1:2477777-2478698 -
yesR_3 BcellWH2_02083 ALJ59326.1 11236 - 12535 (-) CP012801.1:2478831-2480130 3.2.1.172
rhaD BcellWH2_02084 ALJ59327.1 12559 - 13369 (-) CP012801.1:2480154-2480964 4.1.2.19
rhaT BcellWH2_02085 ALJ59328.1 13470 - 14502 (-) CP012801.1:2481065-2482097 -
rhaA BcellWH2_02086 ALJ59329.1 14601 - 15855 (-) CP012801.1:2482196-2483450 5.3.1.14
rhaB_1 BcellWH2_02087 ALJ59330.1 15921 - 17379 (-) CP012801.1:2483516-2484974 2.7.1.5
pehX_3 BcellWH2_02088 ALJ59331.1 17498 - 19022 (-) CP012801.1:2485093-2486617 3.2.1.82
yesW_1 BcellWH2_02089 ALJ59332.1 19059 - 20889 (-) CP012801.1:2486654-2488484 4.2.2.23
- BcellWH2_02090 ALJ59333.1 21038 - 23867 (-) CP012801.1:2488633-2491462 -
yteR_6 BcellWH2_02091 ALJ59334.1 23875 - 26407 (-) CP012801.1:2491470-2494002 3.2.1.172

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1377 (-) CAZyme: PL1_2|CE8|PL1 Yes
- 1383 - 1523 (+) other Yes
- 1517 - 3514 (-) other Yes
- 3529 - 6735 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
atsA_5 7068 - 8465 (-) other Yes
pehX_2 8527 - 9948 (-) CAZyme: GH28 Yes
xylR_2 10183 - 11103 (-) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607 Yes
yesR_3 11237 - 12535 (-) CAZyme: GH105 Yes
rhaD 12560 - 13369 (-) other Yes
rhaT 13471 - 14502 (-) other Yes
rhaA 14602 - 15855 (-) other Yes
rhaB_1 15922 - 17379 (-) other Yes
pehX_3 17499 - 19022 (-) CAZyme: GH28 Yes
yesW_1 19060 - 20889 (-) CAZyme: PL11 Yes
- 21039 - 23867 (-) CAZyme: GH106 Yes
yteR_6 23876 - 26407 (-) CAZyme: GH105 Yes

PUL ID

PUL0539

PubMed

23976882, PLoS Biol. 2013;11(8):e1001637. doi: 10.1371/journal.pbio.1001637. Epub 2013 Aug 20.

Title

Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome.

Author

McNulty NP, Wu M, Erickson AR, Pan C, Erickson BK, Martens EC, Pudlo NA, Muegge BD, Henrissat B, Hettich RL, Gordon JI

Abstract

The human gut microbiota is an important metabolic organ, yet little is known about how its individual species interact, establish dominant positions, and respond to changes in environmental factors such as diet. In this study, gnotobiotic mice were colonized with an artificial microbiota comprising 12 sequenced human gut bacterial species and fed oscillating diets of disparate composition. Rapid, reproducible, and reversible changes in the structure of this assemblage were observed. Time-series microbial RNA-Seq analyses revealed staggered functional responses to diet shifts throughout the assemblage that were heavily focused on carbohydrate and amino acid metabolism. High-resolution shotgun metaproteomics confirmed many of these responses at a protein level. One member, Bacteroides cellulosilyticus WH2, proved exceptionally fit regardless of diet. Its genome encoded more carbohydrate active enzymes than any previously sequenced member of the Bacteroidetes. Transcriptional profiling indicated that B. cellulosilyticus WH2 is an adaptive forager that tailors its versatile carbohydrate utilization strategy to available dietary polysaccharides, with a strong emphasis on plant-derived xylans abundant in dietary staples like cereal grains. Two highly expressed, diet-specific polysaccharide utilization loci (PULs) in B. cellulosilyticus WH2 were identified, one with characteristics of xylan utilization systems. Introduction of a B. cellulosilyticus WH2 library comprising >90,000 isogenic transposon mutants into gnotobiotic mice, along with the other artificial community members, confirmed that these loci represent critical diet-specific fitness determinants. Carbohydrates that trigger dramatic increases in expression of these two loci and many of the organism's 111 other predicted PULs were identified by RNA-Seq during in vitro growth on 31 distinct carbohydrate substrates, allowing us to better interpret in vivo RNA-Seq and proteomics data. These results offer insight into how gut microbes adapt to dietary perturbations at both a community level and from the perspective of a well-adapted symbiont with exceptional saccharolytic capabilities, and illustrate the value of artificial communities.