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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0491

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_016776.1

Nucelotide position range

1314126-1334368

Substrate

capsule polysaccharide

Loci

BF638R_1076-BF638R_1095

Species

Bacteroides fragilis/817

Degradation or Biosynthesis

biosynthesis

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

rfbA BF638R_RS05055 WP_005795876.1 0 - 885 (+) NC_016776.1:1314126-1315011 2.7.7.24
- BF638R_RS05060 WP_011202254.1 1202 - 2732 (+) NC_016776.1:1315328-1316858 -
- BF638R_RS05065 WP_005795872.1 2728 - 3838 (+) NC_016776.1:1316854-1317964 -
- BF638R_RS05070 WP_005795870.1 3876 - 4824 (+) NC_016776.1:1318002-1318950 -
- BF638R_RS05075 WP_011202256.1 4820 - 6257 (+) NC_016776.1:1318946-1320383 -
wecC BF638R_RS05080 WP_005795861.1 6332 - 7559 (+) NC_016776.1:1320458-1321685 1.1.1.336
wecB BF638R_RS05085 WP_005799504.1 7555 - 8710 (+) NC_016776.1:1321681-1322836 5.1.3.14
- BF638R_RS05090 WP_005795857.1 8706 - 9798 (+) NC_016776.1:1322832-1323924 -
- BF638R_RS05095 WP_005795855.1 9785 - 10217 (+) NC_016776.1:1323911-1324343 -
- BF638R_RS05100 WP_011202258.1 10191 - 10617 (+) NC_016776.1:1324317-1324743 -
- BF638R_RS05105 WP_005795850.1 10613 - 11714 (+) NC_016776.1:1324739-1325840 -
- BF638R_RS05110 WP_011202259.1 11710 - 12706 (+) NC_016776.1:1325836-1326832 -
- BF638R_RS05115 WP_014298345.1 12707 - 13733 (+) NC_016776.1:1326833-1327859 -
- BF638R_RS05120 WP_014298346.1 13777 - 14929 (+) NC_016776.1:1327903-1329055 -
wecB BF638R_RS05125 WP_014298347.1 14936 - 16121 (+) NC_016776.1:1329062-1330247 5.1.3.14
- BF638R_RS05130 WP_014298348.1 16131 - 17340 (+) NC_016776.1:1330257-1331466 -
- BF638R_RS05135 WP_011202264.1 17342 - 17951 (+) NC_016776.1:1331468-1332077 -
- BF638R_RS05140 WP_005795841.1 17963 - 18548 (+) NC_016776.1:1332089-1332674 -
- BF638R_RS05145 WP_005795839.1 18561 - 19692 (+) NC_016776.1:1332687-1333818 -
- BF638R_RS05150 WP_005795836.1 19739 - 20243 (+) NC_016776.1:1333865-1334369 -

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: GT46|GT0 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

PUL0491

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.