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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0515

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

NC_006347.1

Nucelotide position range

1316575-1336817

Substrate

capsule polysaccharide

Loci

BF1094-BF1113

Species

Bacteroides fragilis/817

Degradation or Biosynthesis

biosynthesis

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

rfbA BF_RS05145 WP_005795876.1 0 - 885 (+) NC_006347.1:1316575-1317460 2.7.7.24
- BF_RS05150 WP_011202254.1 1202 - 2732 (+) NC_006347.1:1317777-1319307 -
- BF_RS05155 WP_011202255.1 2728 - 3838 (+) NC_006347.1:1319303-1320413 -
- BF_RS05160 WP_005795870.1 3876 - 4824 (+) NC_006347.1:1320451-1321399 -
- BF_RS05165 WP_011202256.1 4820 - 6257 (+) NC_006347.1:1321395-1322832 -
wecC BF_RS05170 WP_011202257.1 6332 - 7559 (+) NC_006347.1:1322907-1324134 1.1.1.336
wecB BF_RS05175 WP_005799504.1 7555 - 8710 (+) NC_006347.1:1324130-1325285 5.1.3.14
- BF_RS05180 WP_005795857.1 8706 - 9798 (+) NC_006347.1:1325281-1326373 -
- BF_RS05185 WP_005795855.1 9785 - 10217 (+) NC_006347.1:1326360-1326792 -
- BF_RS05190 WP_011202258.1 10191 - 10617 (+) NC_006347.1:1326766-1327192 -
- BF_RS05195 WP_005795850.1 10613 - 11714 (+) NC_006347.1:1327188-1328289 -
- BF_RS05200 WP_011202259.1 11710 - 12706 (+) NC_006347.1:1328285-1329281 -
- BF_RS05205 WP_011202260.1 12707 - 13733 (+) NC_006347.1:1329282-1330308 -
- BF_RS05210 WP_011202261.1 13777 - 14929 (+) NC_006347.1:1330352-1331504 -
wecB BF_RS05215 WP_011202262.1 14936 - 16121 (+) NC_006347.1:1331511-1332696 5.1.3.14
- BF_RS05220 WP_011202263.1 16131 - 17340 (+) NC_006347.1:1332706-1333915 -
- BF_RS05225 WP_011202264.1 17342 - 17951 (+) NC_006347.1:1333917-1334526 -
- BF_RS05230 WP_005795841.1 17963 - 18548 (+) NC_006347.1:1334538-1335123 -
- BF_RS05235 WP_011202265.1 18561 - 19692 (+) NC_006347.1:1335136-1336267 -
- BF_RS05240 WP_011202266.1 19739 - 20243 (+) NC_006347.1:1336314-1336818 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

rfbA 1 - 885 (+) CDS No
- 1203 - 2732 (+) CDS No
- 2729 - 3838 (+) CDS No
- 3877 - 4824 (+) CDS No
- 4821 - 6257 (+) CDS No
wecC 6333 - 7559 (+) CDS No
wecB 7556 - 8710 (+) CDS No
- 8707 - 9798 (+) CDS No
- 9786 - 10217 (+) CDS No
- 10192 - 10617 (+) CDS No
- 10614 - 11714 (+) CDS No
- 11711 - 12706 (+) CAZyme: GT0|GT46 Yes
- 12708 - 13733 (+) TC: gnl|TC-DB|Q6MMD5|9.B.18.2.1 Yes
- 13778 - 14929 (+) other Yes
wecB 14937 - 16121 (+) other Yes
- 16132 - 17340 (+) other Yes
- 17343 - 17951 (+) TC: gnl|TC-DB|H8E4X1|9.B.18.1.2 Yes
- 17964 - 18548 (+) CDS No
- 18562 - 19692 (+) CDS No
- 19740 - 20243 (+) CDS No

PUL ID

PUL0515

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.