PUL ID

PUL0521

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

957305-978417

Substrate

capsule polysaccharide

Loci

BF0805-BF0827

Species

Bacteroides fragilis/817

Degradation or Biosynthesis

biosynthesis

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

rfbA BF_RS03800 WP_011202141.1 0 - 888 (+) NC_006347.1:957305-958193 2.7.7.24
rfbC BF_RS03805 WP_011202142.1 890 - 1460 (+) NC_006347.1:958195-958765 5.1.3.13
rfbB BF_RS03810 WP_011202143.1 1461 - 2532 (+) NC_006347.1:958766-959837 4.2.1.46
- BF_RS03815 WP_011202144.1 2539 - 3988 (+) NC_006347.1:959844-961293 -
- BF_RS03820 WP_011202145.1 3994 - 5377 (+) NC_006347.1:961299-962682 -
- BF_RS03825 WP_011202146.1 5381 - 6362 (+) NC_006347.1:962686-963667 -
- BF_RS03830 WP_011202147.1 6348 - 7431 (+) NC_006347.1:963653-964736 -
- BF_RS03835 WP_032591456.1 7456 - 8599 (+) NC_006347.1:964761-965904 -
- BF_RS03840 WP_162484906.1 8632 - 9475 (+) NC_006347.1:965937-966780 -
- BF_RS03845 WP_011202150.1 9476 - 10493 (+) NC_006347.1:966781-967798 -
- BF_RS03850 WP_011202151.1 10496 - 11594 (+) NC_006347.1:967801-968899 -
- BF_RS03855 WP_011202152.1 11597 - 12719 (+) NC_006347.1:968902-970024 -
- BF_RS03860 WP_011202153.1 12708 - 13317 (+) NC_006347.1:970013-970622 -
- BF_RS03865 WP_005775527.1 13320 - 13962 (+) NC_006347.1:970625-971267 -
- BF_RS03870 WP_005775528.1 13974 - 14205 (+) NC_006347.1:971279-971510 -
- BF_RS03875 WP_011202154.1 14204 - 15260 (+) NC_006347.1:971509-972565 -
- BF_RS03880 WP_005801362.1 15265 - 16018 (+) NC_006347.1:972570-973323 -
- BF_RS03885 WP_005775532.1 16021 - 17071 (+) NC_006347.1:973326-974376 -
- BF_RS03890 WP_005775533.1 17074 - 17476 (+) NC_006347.1:974379-974781 -
- BF_RS03895 WP_011202156.1 17486 - 19076 (+) NC_006347.1:974791-976381 -
- BF_RS03900 WP_005796132.1 19077 - 19293 (+) NC_006347.1:976382-976598 -
- BF_RS03905 WP_005801359.1 19293 - 19893 (+) NC_006347.1:976598-977198 -
- BF_RS03910 WP_011202157.1 19979 - 21113 (+) NC_006347.1:977284-978418 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

rfbA 1 - 888 (+) CDS No
rfbC 891 - 1460 (+) CDS No
rfbB 1462 - 2532 (+) CDS No
- 2540 - 3988 (+) TC: gnl|TC-DB|O32273|2.A.66.2.6 Yes
- 3995 - 5377 (+) other Yes
- 5382 - 6362 (+) other Yes
- 6349 - 7431 (+) STP: STP|Aminotran_1_2 Yes
- 7457 - 8599 (+) other Yes
- 8633 - 9475 (+) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 9477 - 10493 (+) CAZyme: GT4 Yes
- 10497 - 11594 (+) other Yes
- 11598 - 12719 (+) other Yes
- 12709 - 13317 (+) TC: gnl|TC-DB|H8E4X1|9.B.18.1.2 Yes
- 13321 - 13962 (+) CDS No
- 13975 - 14205 (+) CDS No
- 14205 - 15260 (+) CDS No
- 15266 - 16018 (+) CDS No
- 16022 - 17071 (+) CDS No
- 17075 - 17476 (+) CDS No
- 17487 - 19076 (+) CDS No
- 19078 - 19293 (+) CDS No
- 19294 - 19893 (+) CDS No
- 19980 - 21113 (+) CDS No

PUL ID

PUL0521

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.