PUL ID

PUL0489

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

1698150-1720386

Substrate

capsule polysaccharide

Loci

BF638R_1435-BF638R_1460

Species

Bacteroides fragilis/817

Degradation or Biosynthesis

biosynthesis

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BF638R_RS06690 WP_014298514.1 0 - 879 (+) NC_016776.1:1698150-1699029 -
- BF638R_RS06695 WP_008768177.1 907 - 1369 (+) NC_016776.1:1699057-1699519 -
- BF638R_RS06700 WP_014298515.1 1394 - 2522 (+) NC_016776.1:1699544-1700672 -
- BF638R_RS06705 WP_014298516.1 2549 - 4085 (+) NC_016776.1:1700699-1702235 -
- BF638R_RS06710 WP_014298517.1 4188 - 5604 (+) NC_016776.1:1702338-1703754 -
- BF638R_RS06715 WP_014298518.1 5734 - 6802 (+) NC_016776.1:1703884-1704952 -
- BF638R_RS06720 WP_008768182.1 6814 - 7831 (+) NC_016776.1:1704964-1705981 -
- BF638R_RS06725 WP_014298519.1 7835 - 8792 (+) NC_016776.1:1705985-1706942 -
- BF638R_RS06730 WP_014298520.1 9322 - 9862 (+) NC_016776.1:1707472-1708012 -
- BF638R_RS06735 WP_014298521.1 9866 - 10511 (+) NC_016776.1:1708016-1708661 -
- BF638R_RS06740 WP_014298522.1 10512 - 11226 (+) NC_016776.1:1708662-1709376 -
- BF638R_RS06745 WP_014298523.1 11268 - 12396 (+) NC_016776.1:1709418-1710546 -
- BF638R_RS06750 WP_014298524.1 12406 - 13198 (+) NC_016776.1:1710556-1711348 -
- BF638R_RS06755 - 13208 - 14533 (+) NC_016776.1:1711358-1712683 -
- BF638R_RS06770 WP_022348520.1 14987 - 16253 (+) NC_016776.1:1713137-1714403 -
rfbA BF638R_RS06775 WP_014298528.1 16680 - 17562 (+) NC_016776.1:1714830-1715712 2.7.7.24
- BF638R_RS06780 WP_014298529.1 17561 - 18188 (+) NC_016776.1:1715711-1716338 -
- BF638R_RS06785 WP_014298530.1 18195 - 18429 (+) NC_016776.1:1716345-1716579 -
- BF638R_RS06790 WP_008768195.1 18428 - 19187 (+) NC_016776.1:1716578-1717337 -
- BF638R_RS06795 WP_014298531.1 19350 - 20352 (+) NC_016776.1:1717500-1718502 -
- BF638R_RS06800 WP_041161352.1 20394 - 21618 (+) NC_016776.1:1718544-1719768 -
- BF638R_RS06805 WP_005795339.1 21649 - 22237 (+) NC_016776.1:1719799-1720387 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 879 (+) CDS No
- 908 - 1369 (+) CDS No
- 1395 - 2522 (+) CDS No
- 2550 - 4085 (+) CDS No
- 4189 - 5604 (+) CDS No
- 5735 - 6802 (+) CDS No
- 6815 - 7831 (+) CDS No
- 7836 - 8792 (+) CDS No
- 9323 - 9862 (+) CDS No
- 9867 - 10511 (+) STP: STP|SIS No
- 10513 - 11226 (+) CDS No
- 11269 - 12396 (+) CAZyme: GT4 Yes
- 12407 - 13198 (+) other Yes
- 14988 - 16253 (+) other Yes
rfbA 16681 - 17562 (+) other Yes
- 17562 - 18188 (+) other Yes
- 18196 - 18429 (+) other Yes
- 18429 - 19187 (+) other Yes
- 19351 - 20352 (+) other Yes
- 20395 - 21618 (+) other Yes
- 21650 - 22237 (+) TC: gnl|TC-DB|H8E4X1|9.B.18.1.2 Yes

PUL ID

PUL0489

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.