PUL ID

PUL0510

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

3250670-3278126

Substrate

capsule polysaccharide

Loci

BF2791-BF2817

Species

Bacteroides fragilis/817

Degradation or Biosynthesis

biosynthesis

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BF9343_2704 CAH08485.1 0 - 147 (+) CR626927.1:3250670-3250817 -
- BF9343_2705 CAH08486.1 148 - 1186 (+) CR626927.1:3250818-3251856 -
- BF9343_2706 CAH08487.1 1352 - 2351 (+) CR626927.1:3252022-3253021 -
- BF9343_2707 CAH08488.1 2347 - 3442 (+) CR626927.1:3253017-3254112 -
- BF9343_2708 CAH08489.1 3475 - 4558 (+) CR626927.1:3254145-3255228 -
- BF9343_2709 CAH08490.1 4563 - 5553 (+) CR626927.1:3255233-3256223 -
- BF9343_2710 CAH08491.1 5562 - 6552 (+) CR626927.1:3256232-3257222 -
- BF9343_2711 CAH08492.1 6565 - 7117 (+) CR626927.1:3257235-3257787 -
- BF9343_2712 CAH08493.1 7113 - 8160 (+) CR626927.1:3257783-3258830 -
- BF9343_2713 CAH08494.1 8159 - 9326 (+) CR626927.1:3258829-3259996 -
- BF9343_2714 CAH08495.1 9367 - 10396 (+) CR626927.1:3260037-3261066 -
- BF9343_2715 CAH08496.1 10400 - 11423 (+) CR626927.1:3261070-3262093 -
- BF9343_2716 CAH08497.1 11435 - 11999 (+) CR626927.1:3262105-3262669 -
- BF9343_2717 CAH08498.1 12013 - 13045 (+) CR626927.1:3262683-3263715 -
- BF9343_2718 CAH08499.1 13019 - 14294 (+) CR626927.1:3263689-3264964 -
- BF9343_2719 CAH08500.1 14324 - 15488 (+) CR626927.1:3264994-3266158 -
- BF9343_2720 CAH08501.1 15481 - 16702 (+) CR626927.1:3266151-3267372 -
- BF9343_2721 CAH08502.1 16879 - 17599 (+) CR626927.1:3267549-3268269 -
- BF9343_2722 CAH08503.1 17608 - 18313 (+) CR626927.1:3268278-3268983 -
- BF9343_2723 CAH08504.1 18318 - 19560 (+) CR626927.1:3268988-3270230 -
- BF9343_2724 CAH08505.1 19570 - 20872 (+) CR626927.1:3270240-3271542 -
- BF9343_2725 CAH08506.1 20911 - 21487 (+) CR626927.1:3271581-3272157 -
- BF9343_2726 CAH08507.1 21592 - 22105 (+) CR626927.1:3272262-3272775 -
- BF9343_2727 CAH08508.1 22116 - 23433 (+) CR626927.1:3272786-3274103 -
- BF9343_2728 CAH08509.1 23440 - 24538 (+) CR626927.1:3274110-3275208 -
- BF9343_2729 CAH08510.1 24565 - 24994 (+) CR626927.1:3275235-3275664 -
- BF9343_2730 CAH08511.1 25009 - 26059 (+) CR626927.1:3275679-3276729 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 147 (+) CDS No
- 149 - 1186 (+) CDS No
- 1353 - 2351 (+) CDS No
- 2348 - 3442 (+) CDS No
- 3476 - 4558 (+) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 4564 - 5553 (+) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 5563 - 6552 (+) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 6566 - 7117 (+) other Yes
- 7114 - 8160 (+) other Yes
- 8160 - 9326 (+) other Yes
- 9368 - 10396 (+) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 10401 - 11423 (+) other Yes
- 11436 - 11999 (+) other Yes
- 12014 - 13045 (+) CAZyme: GT4 Yes
- 13020 - 14294 (+) STP: STP|Fer4,STP|Fer4 Yes
- 14325 - 15488 (+) other Yes
- 15482 - 16702 (+) CAZyme: GT4 Yes
- 16880 - 17599 (+) CAZyme: GT26 Yes
- 17609 - 18313 (+) other Yes
- 18319 - 19560 (+) other Yes
- 19571 - 20872 (+) other Yes
- 20912 - 21487 (+) other Yes
- 21593 - 22105 (+) other Yes
- 22117 - 23433 (+) TC: gnl|TC-DB|Q5EGM3|9.A.25.1.1 Yes
- 23441 - 24538 (+) CDS No
- 24566 - 24994 (+) CDS No
- 25010 - 26059 (+) CDS No

PUL ID

PUL0510

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.