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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0498

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

3287955-3312742

Substrate

capsule polysaccharide

Loci

BF638R_2800-BF638R_2826

Species

Bacteroides fragilis/817

Degradation or Biosynthesis

biosynthesis

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BF638R_RS13395 WP_014299076.1 0 - 1536 (+) NC_016776.1:3287955-3289491 -
- BF638R_RS13400 WP_011203003.1 1532 - 2288 (+) NC_016776.1:3289487-3290243 -
- BF638R_RS13405 WP_014299077.1 2291 - 3392 (+) NC_016776.1:3290246-3291347 -
- BF638R_RS13410 WP_014299078.1 3403 - 4402 (+) NC_016776.1:3291358-3292357 -
- BF638R_RS24780 WP_162470355.1 4443 - 4875 (+) NC_016776.1:3292398-3292830 -
- BF638R_RS24785 WP_041161390.1 4759 - 5470 (+) NC_016776.1:3292714-3293425 -
- BF638R_RS13420 WP_011203007.1 5466 - 6297 (+) NC_016776.1:3293421-3294252 -
- BF638R_RS13425 WP_014299079.1 6289 - 7252 (+) NC_016776.1:3294244-3295207 -
- BF638R_RS13430 WP_011203009.1 7267 - 8503 (+) NC_016776.1:3295222-3296458 -
- BF638R_RS13435 WP_011203010.1 8508 - 9774 (+) NC_016776.1:3296463-3297729 -
- BF638R_RS13440 WP_011203011.1 9785 - 10346 (+) NC_016776.1:3297740-3298301 -
- BF638R_RS13445 WP_014299081.1 10351 - 11212 (+) NC_016776.1:3298306-3299167 -
- BF638R_RS13450 WP_162470363.1 11430 - 12132 (+) NC_016776.1:3299385-3300087 -
- BF638R_RS13455 WP_011203057.1 12138 - 13257 (+) NC_016776.1:3300093-3301212 -
- BF638R_RS13460 WP_014299083.1 13262 - 14351 (+) NC_016776.1:3301217-3302306 -
- BF638R_RS13465 WP_014299084.1 14364 - 15438 (+) NC_016776.1:3302319-3303393 -
- BF638R_RS13470 WP_005798562.1 15607 - 16327 (+) NC_016776.1:3303562-3304282 -
- BF638R_RS13475 WP_050809234.1 16372 - 17041 (+) NC_016776.1:3304327-3304996 -
- BF638R_RS13480 WP_014299086.1 17046 - 18288 (+) NC_016776.1:3305001-3306243 -
- BF638R_RS13485 WP_005815286.1 18313 - 19600 (+) NC_016776.1:3306268-3307555 -
- BF638R_RS13490 WP_005815284.1 19639 - 20215 (+) NC_016776.1:3307594-3308170 -
gldL BF638R_RS13495 WP_005788660.1 20321 - 20834 (+) NC_016776.1:3308276-3308789 -
- BF638R_RS13500 WP_014299088.1 20845 - 22162 (+) NC_016776.1:3308800-3310117 -
- BF638R_RS13505 WP_014299089.1 22169 - 23267 (+) NC_016776.1:3310124-3311222 -
- BF638R_RS13510 WP_005788667.1 23294 - 23723 (+) NC_016776.1:3311249-3311678 -
- BF638R_RS13515 WP_014299090.1 23738 - 24788 (+) NC_016776.1:3311693-3312743 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1536 (+) CDS No
- 1533 - 2288 (+) CDS No
- 2292 - 3392 (+) CDS No
- 3404 - 4402 (+) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 4444 - 4875 (+) TC: gnl|TC-DB|E8RJP5|9.B.97.1.10 Yes
- 4760 - 5470 (+) other Yes
- 5467 - 6297 (+) other Yes
- 6290 - 7252 (+) other Yes
- 7268 - 8503 (+) other Yes
- 8509 - 9774 (+) CAZyme: GT4 Yes
- 10352 - 11212 (+) other Yes
- 11431 - 12132 (+) CAZyme: GT11 Yes
- 12139 - 13257 (+) CAZyme: GT4 Yes
- 13263 - 14351 (+) CAZyme: GT4 Yes
- 14365 - 15438 (+) CAZyme: GT4 Yes
- 15608 - 16327 (+) CAZyme: GT26 Yes
- 16373 - 17041 (+) other Yes
- 17047 - 18288 (+) other Yes
- 18314 - 19600 (+) other Yes
- 19640 - 20215 (+) other Yes
gldL 20322 - 20834 (+) other Yes
- 20846 - 22162 (+) TC: gnl|TC-DB|Q5EGM3|9.A.25.1.1 Yes
- 22170 - 23267 (+) CDS No
- 23295 - 23723 (+) CDS No
- 23739 - 24788 (+) CDS No

PUL ID

PUL0498

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.