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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0253

PubMed

23996813, Biotechnol Bioeng. 2014 Jan;111(1):165-73. doi: 10.1002/bit.24994. Epub 2013 Jul 30.

Characterization method

gene chips

Genomic accession number

AE015928.1

Nucelotide position range

34087-66571

Substrate

capsule polysaccharide

Loci

BT_0037-BT_0068

Species

Bacteroides thetaiotaomicron/818

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BT_0037 AAO75144.1 0 - 1056 (+) AE015928.1:34087-35143 -
- BT_0038 AAO75145.1 1179 - 1617 (+) AE015928.1:35266-35704 -
- BT_0039 AAO75146.1 1902 - 2331 (+) AE015928.1:35989-36418 -
- BT_0040 AAO75147.1 2391 - 3933 (+) AE015928.1:36478-38020 -
- BT_0041 AAO75148.1 3929 - 5132 (+) AE015928.1:38016-39219 -
- BT_0042 AAO75149.1 5128 - 6289 (+) AE015928.1:39215-40376 -
- BT_0043 AAO75150.1 6319 - 6496 (+) AE015928.1:40406-40583 -
- BT_0044 AAO75151.1 6506 - 7451 (+) AE015928.1:40593-41538 -
- BT_0045 AAO75152.1 7447 - 8614 (+) AE015928.1:41534-42701 -
- BT_0046 AAO75153.1 8637 - 9570 (+) AE015928.1:42724-43657 -
- BT_0047 AAO75154.1 9584 - 9980 (+) AE015928.1:43671-44067 -
- BT_0048 AAO75155.1 10075 - 10552 (+) AE015928.1:44162-44639 -
- BT_0049 AAO75156.1 10560 - 11496 (+) AE015928.1:44647-45583 -
- BT_0050 AAO75157.1 11507 - 12479 (+) AE015928.1:45594-46566 -
- BT_0051 AAO75158.1 12478 - 13459 (+) AE015928.1:46565-47546 -
- BT_0052 AAO75159.1 13629 - 14748 (+) AE015928.1:47716-48835 -
- BT_0053 AAO75160.1 14747 - 15872 (+) AE015928.1:48834-49959 -
- BT_0054 AAO75161.1 15924 - 17046 (+) AE015928.1:50011-51133 -
- BT_0055 AAO75162.1 17053 - 18169 (+) AE015928.1:51140-52256 -
- BT_0056 AAO75163.1 18189 - 19212 (+) AE015928.1:52276-53299 -
- BT_0057 AAO75164.1 19201 - 19489 (+) AE015928.1:53288-53576 -
- BT_0058 AAO75165.1 19560 - 20691 (+) AE015928.1:53647-54778 -
- BT_0059 AAO75166.1 20687 - 21629 (+) AE015928.1:54774-55716 -
- BT_0060 AAO75167.1 21667 - 22453 (+) AE015928.1:55754-56540 -
- BT_0061 AAO75168.1 22468 - 24808 (+) AE015928.1:56555-58895 -
- BT_0062 AAO75169.1 24804 - 25017 (+) AE015928.1:58891-59104 -
- BT_0063 AAO75170.1 25069 - 25270 (+) AE015928.1:59156-59357 -
- BT_0064 AAO75171.1 25290 - 27465 (+) AE015928.1:59377-61552 -
- BT_0065 AAO75172.1 27534 - 30072 (+) AE015928.1:61621-64159 -
- BT_0066 AAO75173.1 30186 - 31389 (+) AE015928.1:64273-65476 -
- BT_0067 AAO75174.1 31726 - 31978 (+) AE015928.1:65813-66065 -
- BT_0068 AAO75175.1 32005 - 32485 (+) AE015928.1:66092-66572 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1056 (+) CDS No
- 1180 - 1617 (+) CDS No
- 1903 - 2331 (+) CDS No
- 2392 - 3933 (+) CDS No
- 3930 - 5132 (+) STP: STP|Fer4,STP|Fer4 No
- 5129 - 6289 (+) CDS No
- 6320 - 6496 (+) CDS No
- 6507 - 7451 (+) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 7448 - 8614 (+) other Yes
- 8638 - 9570 (+) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 9585 - 9980 (+) other Yes
- 10076 - 10552 (+) other Yes
- 10561 - 11496 (+) CAZyme: GT101|GT0 Yes
- 11508 - 12479 (+) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 12479 - 13459 (+) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 13630 - 14748 (+) other Yes
- 14748 - 15872 (+) CAZyme: GT4 Yes
- 15925 - 17046 (+) other Yes
- 17054 - 18169 (+) CAZyme: GT4 Yes
- 18190 - 19212 (+) other Yes
- 19202 - 19489 (+) other Yes
- 19561 - 20691 (+) other Yes
- 20688 - 21629 (+) other Yes
- 21668 - 22453 (+) other Yes
- 22469 - 24808 (+) TC: gnl|TC-DB|A5FN22|8.A.3.3.4 Yes
- 24805 - 25017 (+) other Yes
- 25070 - 25270 (+) other Yes
- 25291 - 27465 (+) other Yes
- 27535 - 30072 (+) CAZyme: GH27 Yes
- 30187 - 31389 (+) CDS No
- 31727 - 31978 (+) CDS No
- 32006 - 32485 (+) CDS No

PUL ID

PUL0253

PubMed

23996813, Biotechnol Bioeng. 2014 Jan;111(1):165-73. doi: 10.1002/bit.24994. Epub 2013 Jul 30.

Title

Regulated expression of polysaccharide utilization and capsular biosynthesis loci in biofilm and planktonic Bacteroides thetaiotaomicron during growth in chemostats.

Author

TerAvest MA, He Z, Rosenbaum MA, Martens EC, Cotta MA, Gordon JI, Angenent LT

Abstract

Bacteroides thetaiotaomicron is a prominent member of the human distal gut microbiota that specializes in breaking down diet and host-derived polysaccharides. While polysaccharide utilization has been well studied in B. thetaiotaomicron, other aspects of its behavior are less well characterized, including the factors that allow it to maintain itself in the gut. Biofilm formation may be a mechanism for bacterial retention in the gut. Therefore, we used custom GeneChips to compare the transcriptomes of biofilm and planktonic B. thetaiotaomicron during growth in mono-colonized chemostats. We identified 1,154 genes with a fold-change greater than 2, with confidence greater than or equal to 95%. Among the prominent changes observed in biofilm populations were: (i) greater expression of genes in polysaccharide utilization loci that are involved in foraging of O-glycans normally found in the gut mucosa; and (ii) regulated expression of capsular polysaccharide biosynthesis loci. Hierarchical clustering of the data with different datasets, which were obtained during growth under a range of conditions in minimal media and in intestinal tracts of gnotobiotic mice, revealed that within this group of differentially expressed genes, biofilm communities were more similar to the in vivo samples than to planktonic cells and exhibited features of substrate limitation. The current study also validates the use of chemostats as an in vitro "gnotobiotic" model to study gene expression of attached populations of this bacterium. This is important to gut microbiota research, because bacterial attachment and the consequences of disruptions in attachment are difficult to study in vivo.