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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0503

PubMed

20829291, Microbiology (Reading). 2010 Nov;156(Pt 11):3255-3269. doi: 10.1099/mic.0.042978-0. Epub 2010 Sep 9.

Characterization method

sequence homology analysis,microscopy

Genomic accession number

CR626927.1

Nucelotide position range

1262011-1277357

Substrate

capsule polysaccharide

Loci

BF1011-BF1026

Species

Bacteroides fragilis/817

Degradation or Biosynthesis

biosynthesis

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

rmlA2 BF9343_0968 CAH06749.1 0 - 888 (+) CR626927.1:1262011-1262899 -
rmlC1 BF9343_0969 CAH06750.1 903 - 1452 (+) CR626927.1:1262914-1263463 -
wcfA BF9343_0970 CAH06751.1 1470 - 1992 (+) CR626927.1:1263481-1264003 -
wzx2 BF9343_0971 CAH06752.1 1984 - 3520 (+) CR626927.1:1263995-1265531 -
wcfB BF9343_0972 CAH06753.1 3523 - 4387 (+) CR626927.1:1265534-1266398 -
wcfC BF9343_0973 CAH06754.1 4362 - 5523 (+) CR626927.1:1266373-1267534 -
wcfD BF9343_0974 CAH06755.1 5540 - 6197 (+) CR626927.1:1267551-1268208 -
wzy2 BF9343_0975 CAH06756.1 6197 - 7304 (+) CR626927.1:1268208-1269315 -
wcfE BF9343_0976 CAH06757.1 7300 - 8176 (+) CR626927.1:1269311-1270187 -
wcfF BF9343_0977 CAH06758.1 8184 - 9462 (+) CR626927.1:1270195-1271473 -
wcfG BF9343_0978 CAH06759.1 9448 - 10582 (+) CR626927.1:1271459-1272593 -
wcfH BF9343_0979 CAH06760.1 10574 - 11354 (+) CR626927.1:1272585-1273365 -
wcfI BF9343_0980 CAH06761.1 11393 - 12632 (+) CR626927.1:1273404-1274643 -
wcfJ BF9343_0981 CAH06762.1 12648 - 13413 (+) CR626927.1:1274659-1275424 -
wcfK BF9343_0982 CAH06763.1 13409 - 14429 (+) CR626927.1:1275420-1276440 -
wcfL BF9343_0983 CAH06764.1 14432 - 15347 (+) CR626927.1:1276443-1277358 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

rmlA2 1 - 888 (+) CDS No
rmlC1 904 - 1452 (+) CDS No
wcfA 1471 - 1992 (+) CDS No
wzx2 1985 - 3520 (+) CDS No
wcfB 3524 - 4387 (+) CAZyme: GT11 Yes
wcfC 4363 - 5523 (+) CAZyme: GT4 Yes
wcfD 5541 - 6197 (+) other Yes
wzy2 6198 - 7304 (+) other Yes
wcfE 7301 - 8176 (+) CAZyme: GT2|GT2_Glycos_transf_2 Yes
wcfF 8185 - 9462 (+) other Yes
wcfG 9449 - 10582 (+) CAZyme: GT4 Yes
wcfH 10575 - 11354 (+) CAZyme: CE4|CE0 Yes
wcfI 11394 - 12632 (+) CAZyme: GT4 Yes
wcfJ 12649 - 13413 (+) CAZyme: GT2|GT2_Glycos_transf_2 Yes
wcfK 13410 - 14429 (+) other Yes
wcfL 14433 - 15347 (+) TC: gnl|TC-DB|P0AC78|9.B.146.1.7 Yes

PUL ID

PUL0503

PubMed

20829291, Microbiology (Reading). 2010 Nov;156(Pt 11):3255-3269. doi: 10.1099/mic.0.042978-0. Epub 2010 Sep 9.

Title

Twenty-eight divergent polysaccharide loci specifying within- and amongst-strain capsule diversity in three strains of Bacteroides fragilis.

Author

Patrick S, Blakely GW, Houston S, Moore J, Abratt VR, Bertalan M, Cerdeno-Tarraga AM, Quail MA, Corton N, Corton C, Bignell A, Barron A, Clark L, Bentley SD, Parkhill J

Abstract

Comparison of the complete genome sequence of Bacteroides fragilis 638R, originally isolated in the USA, was made with two previously sequenced strains isolated in the UK (NCTC 9343) and Japan (YCH46). The presence of 10 loci containing genes associated with polysaccharide (PS) biosynthesis, each including a putative Wzx flippase and Wzy polymerase, was confirmed in all three strains, despite a lack of cross-reactivity between NCTC 9343 and 638R surface PS-specific antibodies by immunolabelling and microscopy. Genomic comparisons revealed an exceptional level of PS biosynthesis locus diversity. Of the 10 divergent PS-associated loci apparent in each strain, none is similar between NCTC 9343 and 638R. YCH46 shares one locus with NCTC 9343, confirmed by mAb labelling, and a second different locus with 638R, making a total of 28 divergent PS biosynthesis loci amongst the three strains. The lack of expression of the phase-variable large capsule (LC) in strain 638R, observed in NCTC 9343, is likely to be due to a point mutation that generates a stop codon within a putative initiating glycosyltransferase, necessary for the expression of the LC in NCTC 9343. Other major sequence differences were observed to arise from different numbers and variety of inserted extra-chromosomal elements, in particular prophages. Extensive horizontal gene transfer has occurred within these strains, despite the presence of a significant number of divergent DNA restriction and modification systems that act to prevent acquisition of foreign DNA. The level of amongst-strain diversity in PS biosynthesis loci is unprecedented.