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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0516

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

4458698-4472977

Substrate

capsule polysaccharide

Loci

BF3911-BF3923

Species

Bacteroides fragilis/817

Degradation or Biosynthesis

biosynthesis

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BF_RS18570 WP_011203508.1 0 - 588 (-) NC_006347.1:4458698-4459286 -
- BF_RS18575 WP_011203509.1 619 - 1843 (-) NC_006347.1:4459317-4460541 -
- BF_RS18580 WP_011203510.1 1850 - 2456 (-) NC_006347.1:4460548-4461154 -
- BF_RS18585 WP_011203511.1 2443 - 3658 (-) NC_006347.1:4461141-4462356 -
- BF_RS18590 WP_032588990.1 3664 - 4879 (-) NC_006347.1:4462362-4463577 -
- BF_RS18595 WP_011203513.1 4911 - 5862 (-) NC_006347.1:4463609-4464560 -
- BF_RS18600 WP_011203514.1 5875 - 6940 (-) NC_006347.1:4464573-4465638 -
- BF_RS18605 WP_011203515.1 6863 - 8264 (-) NC_006347.1:4465561-4466962 -
- BF_RS18610 WP_011203516.1 8295 - 9315 (-) NC_006347.1:4466993-4468013 -
- BF_RS18615 WP_011203517.1 9320 - 10634 (-) NC_006347.1:4468018-4469332 -
- BF_RS18620 WP_011203518.1 10648 - 11701 (-) NC_006347.1:4469346-4470399 -
- BF_RS18625 WP_011203519.1 11705 - 12863 (-) NC_006347.1:4470403-4471561 -
- BF_RS18630 WP_011203520.1 12855 - 14280 (-) NC_006347.1:4471553-4472978 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 588 (-) TC: gnl|TC-DB|H8E4X1|9.B.18.1.2 Yes
- 620 - 1843 (-) other Yes
- 1851 - 2456 (-) other Yes
- 2444 - 3658 (-) other Yes
- 3665 - 4879 (-) CAZyme: GT4 Yes
- 4912 - 5862 (-) other Yes
- 5876 - 6940 (-) CAZyme: GT4 Yes
- 6864 - 8264 (-) TC: gnl|TC-DB|F3PUJ6|9.B.67.3.3 Yes
- 8296 - 9315 (-) CAZyme: GT2_Glycos_transf_2|GT2 Yes
- 9321 - 10634 (-) other Yes
- 10649 - 11701 (-) other Yes
- 11706 - 12863 (-) CAZyme: GT4 Yes
- 12856 - 14280 (-) TC: gnl|TC-DB|O32273|2.A.66.2.6 Yes

PUL ID

PUL0516

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.