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PlantCAZyme
Cite: NAR/gkaa742 2020

Because CGCFinder predicted no CGC for this PUL, the gene cluster depicted below contains dbCAN2 and CGC signature predictions for all genes in the PUL, instead of a predicted CGC.


PUL General Information

Literature Information

PUL ID

PUL0260

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

2108693-2124231

Substrate

capsule polysaccharide

Loci

BT_1712-BT_1725

Species

Bacteroides thetaiotaomicron/818

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BT_1712 AAO76819.1 0 - 1179 (-) AE015928.1:2108693-2109872 -
- BT_1713 AAO76820.1 1191 - 1686 (-) AE015928.1:2109884-2110379 -
- BT_1714 AAO76821.1 1778 - 2819 (-) AE015928.1:2110471-2111512 -
- BT_1715 AAO76822.1 2818 - 3568 (-) AE015928.1:2111511-2112261 -
- BT_1716 AAO76823.1 3576 - 4836 (-) AE015928.1:2112269-2113529 -
- BT_1717 AAO76824.1 4789 - 6274 (-) AE015928.1:2113482-2114967 -
- BT_1718 AAO76825.1 6616 - 7738 (-) AE015928.1:2115309-2116431 -
- BT_1719 AAO76826.1 7747 - 8872 (-) AE015928.1:2116440-2117565 -
- BT_1720 AAO76827.1 8888 - 10190 (-) AE015928.1:2117581-2118883 -
- BT_1721 AAO76828.1 10210 - 10930 (-) AE015928.1:2118903-2119623 -
- BT_1722 AAO76829.1 10993 - 12142 (-) AE015928.1:2119686-2120835 -
- BT_1723 AAO76830.1 12152 - 14522 (-) AE015928.1:2120845-2123215 -
- BT_1724 AAO76831.1 14581 - 14950 (-) AE015928.1:2123274-2123643 -
- BT_1725 AAO76832.1 14960 - 15539 (-) AE015928.1:2123653-2124232 -

Cluster number

0

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1179 (-) CAZyme: GT4 No
- 1192 - 1686 (-) CDS No
- 1779 - 2819 (-) CDS No
- 2819 - 3568 (-) CDS No
- 3577 - 4836 (-) CDS No
- 4790 - 6274 (-) CDS No
- 6617 - 7738 (-) CDS No
- 7748 - 8872 (-) CDS No
- 8889 - 10190 (-) CDS No
- 10211 - 10930 (-) CDS No
- 10994 - 12142 (-) CDS No
- 12153 - 14522 (-) CDS No
- 14582 - 14950 (-) CDS No
- 14961 - 15539 (-) CDS No

PUL ID

PUL0260

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.