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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0261

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

3580840-3598939

Substrate

capsule polysaccharide

Loci

BT_2862-BT_2878

Species

Bacteroides thetaiotaomicron/818

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BT_2862 AAO77968.1 0 - 2364 (-) AE015928.1:3580840-3583204 -
- BT_2863 AAO77969.1 2398 - 3196 (-) AE015928.1:3583238-3584036 -
- BT_2864 AAO77970.1 3232 - 4384 (-) AE015928.1:3584072-3585224 -
- BT_2865 AAO77971.1 4463 - 5576 (-) AE015928.1:3585303-3586416 -
- BT_2866 AAO77972.1 5572 - 6712 (-) AE015928.1:3586412-3587552 -
- BT_2867 AAO77973.1 6708 - 7953 (-) AE015928.1:3587548-3588793 -
- BT_2868 AAO77974.1 7965 - 8964 (-) AE015928.1:3588805-3589804 -
- BT_2869 AAO77975.1 8960 - 10064 (-) AE015928.1:3589800-3590904 -
- BT_2870 AAO77976.1 10060 - 10927 (-) AE015928.1:3590900-3591767 -
- BT_2871 AAO77977.1 10926 - 11802 (-) AE015928.1:3591766-3592642 -
- BT_2872 AAO77978.1 11794 - 12724 (-) AE015928.1:3592634-3593564 -
- BT_2873 AAO77979.1 12735 - 13665 (-) AE015928.1:3593575-3594505 -
- BT_2874 AAO77980.1 13675 - 14476 (-) AE015928.1:3594515-3595316 -
- BT_2875 AAO77981.1 14475 - 15012 (-) AE015928.1:3595315-3595852 -
- BT_2876 AAO77982.1 15068 - 16052 (-) AE015928.1:3595908-3596892 -
- BT_2877 AAO77983.1 16064 - 16670 (-) AE015928.1:3596904-3597510 -
- BT_2878 AAO77984.1 16666 - 18100 (-) AE015928.1:3597506-3598940 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 2364 (-) TC: gnl|TC-DB|A5FN22|8.A.3.3.4 Yes
- 2399 - 3196 (-) other Yes
- 3233 - 4384 (-) CAZyme: GT4 Yes
- 4464 - 5576 (-) CAZyme: GT0|GT4 Yes
- 5573 - 6712 (-) CAZyme: GT4 Yes
- 6709 - 7953 (-) other Yes
- 7966 - 8964 (-) CAZyme: GT2_Glycos_transf_2|GT2 Yes
- 8961 - 10064 (-) other Yes
- 10061 - 10927 (-) CAZyme: GT14 Yes
- 10927 - 11802 (-) CAZyme: GT14 Yes
- 11795 - 12724 (-) CAZyme: GT32 Yes
- 12736 - 13665 (-) CAZyme: GT8 Yes
- 13676 - 14476 (-) CAZyme: GT2_Glycos_transf_2|GT2 Yes
- 14476 - 15012 (-) other Yes
- 15069 - 16052 (-) CAZyme: GT2_Glycos_transf_2|GT2 Yes
- 16065 - 16670 (-) other Yes
- 16667 - 18100 (-) TC: gnl|TC-DB|B0RRI5|2.A.66.2.23 Yes

PUL ID

PUL0261

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.