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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0493

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

3040104-3055823

Substrate

capsule polysaccharide

Loci

BF638R_2585-BF638R_2598

Species

Bacteroides fragilis/817

Degradation or Biosynthesis

biosynthesis

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BF638R_RS12350 WP_014299007.1 0 - 954 (-) NC_016776.1:3040104-3041058 -
- BF638R_RS12355 WP_014299008.1 1071 - 1968 (-) NC_016776.1:3041175-3042072 -
- BF638R_RS12360 WP_005793465.1 1976 - 2729 (-) NC_016776.1:3042080-3042833 -
- BF638R_RS12365 WP_139104812.1 2725 - 3805 (-) NC_016776.1:3042829-3043909 -
- BF638R_RS12370 WP_144011113.1 3808 - 4939 (-) NC_016776.1:3043912-3045043 -
- BF638R_RS12375 WP_014299011.1 5070 - 6144 (-) NC_016776.1:3045174-3046248 -
- BF638R_RS12380 WP_014299012.1 6152 - 7571 (-) NC_016776.1:3046256-3047675 -
- BF638R_RS12385 WP_014299013.1 7574 - 8576 (-) NC_016776.1:3047678-3048680 -
- BF638R_RS12390 WP_032574388.1 8588 - 9452 (-) NC_016776.1:3048692-3049556 -
- BF638R_RS12395 WP_008657400.1 9837 - 11574 (-) NC_016776.1:3049941-3051678 -
- BF638R_RS12400 WP_005793446.1 11560 - 12481 (-) NC_016776.1:3051664-3052585 -
rfbG BF638R_RS12405 WP_014299015.1 12477 - 13557 (-) NC_016776.1:3052581-3053661 4.2.1.45
rfbF BF638R_RS12410 WP_005781149.1 13562 - 14339 (-) NC_016776.1:3053666-3054443 2.7.7.33
rfbH BF638R_RS12415 WP_005793443.1 14376 - 15720 (-) NC_016776.1:3054480-3055824 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 954 (-) CDS No
- 1072 - 1968 (-) CDS No
- 1977 - 2729 (-) CAZyme: GT2_Glycos_transf_2|GT2 Yes
- 2726 - 3805 (-) CAZyme: GT4 Yes
- 3809 - 4939 (-) other Yes
- 5071 - 6144 (-) CAZyme: GT4 Yes
- 6153 - 7571 (-) TC: gnl|TC-DB|B0RRI5|2.A.66.2.23 Yes
- 7575 - 8576 (-) CAZyme: GT0|GT10 Yes
- 8589 - 9452 (-) CAZyme: GT2_Glycos_transf_2|GT2 Yes
- 9838 - 11574 (-) CDS No
- 11561 - 12481 (-) CDS No
rfbG 12478 - 13557 (-) CDS No
rfbF 13563 - 14339 (-) CDS No
rfbH 14377 - 15720 (-) STP: STP|Aminotran_1_2 No

PUL ID

PUL0493

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.