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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

PUL0257

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

1665404-1680617

Substrate

capsule polysaccharide

Loci

BT_1340-BT_1354

Species

Bacteroides thetaiotaomicron/818

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BT_1340 AAO76447.1 0 - 813 (-) AE015928.1:1665404-1666217 -
- BT_1341 AAO76448.1 838 - 2152 (-) AE015928.1:1666242-1667556 -
- BT_1342 AAO76449.1 2159 - 3221 (-) AE015928.1:1667563-1668625 -
- BT_1343 AAO76450.1 3249 - 4317 (-) AE015928.1:1668653-1669721 -
- BT_1344 AAO76451.1 4313 - 5417 (-) AE015928.1:1669717-1670821 -
- BT_1345 AAO76452.1 5416 - 6310 (-) AE015928.1:1670820-1671714 -
- BT_1346 AAO76453.1 6327 - 7353 (-) AE015928.1:1671731-1672757 -
- BT_1347 AAO76454.1 7361 - 8219 (-) AE015928.1:1672765-1673623 -
- BT_1348 AAO76455.1 8244 - 9135 (-) AE015928.1:1673648-1674539 -
- BT_1349 AAO76456.1 9131 - 9578 (-) AE015928.1:1674535-1674982 -
- BT_1350 AAO76457.1 9565 - 10666 (-) AE015928.1:1674969-1676070 -
- BT_1351 AAO76458.1 10677 - 11451 (-) AE015928.1:1676081-1676855 -
- BT_1352 AAO76459.1 11452 - 12622 (-) AE015928.1:1676856-1678026 -
- BT_1353 AAO76460.1 12635 - 13673 (-) AE015928.1:1678039-1679077 -
- BT_1354 AAO76461.1 13672 - 15214 (-) AE015928.1:1679076-1680618 -

Cluster number

0

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 813 (-) CDS No
- 839 - 2152 (-) STP: STP|Pyr_redox No
- 2160 - 3221 (-) CDS No
- 3250 - 4317 (-) CDS No
- 4314 - 5417 (-) CAZyme: GT4 No
- 5417 - 6310 (-) CDS No
- 6328 - 7353 (-) CDS No
- 7362 - 8219 (-) CAZyme: GT2|GT2_Glycos_transf_2 No
- 8245 - 9135 (-) CDS No
- 9132 - 9578 (-) CDS No
- 9566 - 10666 (-) CDS No
- 10678 - 11451 (-) CDS No
- 11453 - 12622 (-) CAZyme: GT4 No
- 12636 - 13673 (-) CAZyme: GT2|GT2_Glycos_transf_2 No
- 13673 - 15214 (-) CDS No

PUL ID

PUL0257

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.