Home Repository Download Help About Statistics Taxonomy Blastx
Links
PULDB
CAZy
dbCAN2
dbCAN-seq
run_dbcan
CAZypedia
PlantCAZyme
Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0254

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

462368-490843

Substrate

capsule polysaccharide

Loci

BT_0375-BT_0402

Species

Bacteroides thetaiotaomicron/818

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BT_0375 AAO75482.1 0 - 690 (+) AE015928.1:462368-463058 -
- BT_0376 AAO75483.1 1041 - 1620 (+) AE015928.1:463409-463988 -
- BT_0377 AAO75484.1 1626 - 1986 (+) AE015928.1:463994-464354 -
- BT_0378 AAO75485.1 2039 - 3965 (+) AE015928.1:464407-466333 -
- BT_0379 AAO75486.1 3999 - 5316 (+) AE015928.1:466367-467684 -
- BT_0380 AAO75487.1 5320 - 6394 (+) AE015928.1:467688-468762 -
- BT_0381 AAO75488.1 6428 - 7478 (+) AE015928.1:468796-469846 -
- BT_0382 AAO75489.1 7485 - 8691 (+) AE015928.1:469853-471059 -
- BT_0383 AAO75490.1 8693 - 9887 (+) AE015928.1:471061-472255 -
- BT_0384 AAO75491.1 10608 - 11742 (+) AE015928.1:472976-474110 -
- BT_0385 AAO75492.1 11744 - 12905 (+) AE015928.1:474112-475273 -
- BT_0386 AAO75493.1 12901 - 14095 (+) AE015928.1:475269-476463 -
- BT_0387 AAO75494.1 14094 - 15411 (+) AE015928.1:476462-477779 -
- BT_0388 AAO75495.1 15435 - 16059 (+) AE015928.1:477803-478427 -
- BT_0389 AAO75496.1 16063 - 16609 (+) AE015928.1:478431-478977 -
- BT_0390 AAO75497.1 16613 - 17978 (+) AE015928.1:478981-480346 -
- BT_0391 AAO75498.1 18186 - 19338 (+) AE015928.1:480554-481706 -
- BT_0392 AAO75499.1 19354 - 20461 (+) AE015928.1:481722-482829 -
- BT_0393 AAO75500.1 20462 - 21068 (+) AE015928.1:482830-483436 -
- BT_0394 AAO75501.1 21085 - 22180 (+) AE015928.1:483453-484548 -
- BT_0395 AAO75502.1 22350 - 22578 (+) AE015928.1:484718-484946 -
- BT_0396 AAO75503.1 22760 - 23750 (+) AE015928.1:485128-486118 -
- BT_0397 AAO75504.1 23755 - 24202 (+) AE015928.1:486123-486570 -
- BT_0398 AAO75505.1 24243 - 25038 (+) AE015928.1:486611-487406 -
- BT_0399 AAO75506.1 25050 - 26196 (+) AE015928.1:487418-488564 -
- BT_0400 AAO75507.1 26210 - 27500 (+) AE015928.1:488578-489868 -
- BT_0401 AAO75508.1 27496 - 27715 (-) AE015928.1:489864-490083 -
- BT_0402 AAO75509.1 27966 - 28476 (+) AE015928.1:490334-490844 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 690 (+) CDS No
- 1042 - 1620 (+) CDS No
- 1627 - 1986 (+) CDS No
- 2040 - 3965 (+) TC: gnl|TC-DB|Q6MMD5|9.B.18.2.1 Yes
- 4000 - 5316 (+) other Yes
- 5321 - 6394 (+) other Yes
- 6429 - 7478 (+) TC: gnl|TC-DB|Q6MMD5|9.B.18.2.1 Yes
- 7486 - 8691 (+) other Yes
- 8694 - 9887 (+) other Yes
- 10609 - 11742 (+) other Yes
- 11745 - 12905 (+) other Yes
- 12902 - 14095 (+) STP: STP|Fer4 Yes
- 14095 - 15411 (+) other Yes
- 15436 - 16059 (+) other Yes
- 16064 - 16609 (+) other Yes
- 16614 - 17978 (+) other Yes
- 18187 - 19338 (+) CAZyme: GT4 Yes
- 19355 - 20461 (+) other Yes
- 20463 - 21068 (+) other Yes
- 21086 - 22180 (+) CAZyme: GT4 Yes
- 22351 - 22578 (+) other Yes
- 22761 - 23750 (+) other Yes
- 23756 - 24202 (+) other Yes
- 24244 - 25038 (+) TC: gnl|TC-DB|A5FN23|1.B.18.3.3 Yes
- 25051 - 26196 (+) other Yes
- 26211 - 27500 (+) TC: gnl|TC-DB|A5FN22|8.A.3.3.4 Yes
- 27497 - 27715 (-) CDS No
- 27967 - 28476 (+) CDS No

PUL ID

PUL0254

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.