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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0499

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

2482058-2498101

Substrate

capsule polysaccharide

Loci

BF638R_2121-BF638R_2133

Species

Bacteroides fragilis/817

Degradation or Biosynthesis

biosynthesis

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BF638R_RS09990 WP_014298813.1 0 - 1221 (-) NC_016776.1:2482058-2483279 -
- BF638R_RS09995 WP_014298814.1 1217 - 2063 (-) NC_016776.1:2483275-2484121 -
- BF638R_RS10000 WP_014298815.1 2085 - 2997 (-) NC_016776.1:2484143-2485055 -
- BF638R_RS24380 WP_014298816.1 2993 - 4178 (-) NC_016776.1:2485051-2486236 -
- BF638R_RS10010 WP_014298817.1 5257 - 6712 (-) NC_016776.1:2487315-2488770 -
- BF638R_RS10015 WP_014298818.1 6923 - 7874 (-) NC_016776.1:2488981-2489932 -
- BF638R_RS10020 WP_014298819.1 8122 - 8455 (-) NC_016776.1:2490180-2490513 -
- BF638R_RS10025 WP_136199578.1 8514 - 8802 (+) NC_016776.1:2490572-2490860 -
- BF638R_RS24385 WP_133123997.1 8927 - 9119 (+) NC_016776.1:2490985-2491177 -
- BF638R_RS10030 WP_014298821.1 9364 - 10585 (-) NC_016776.1:2491422-2492643 -
- BF638R_RS10035 WP_014298822.1 10799 - 11690 (-) NC_016776.1:2492857-2493748 -
- BF638R_RS10040 WP_014298823.1 11735 - 13073 (-) NC_016776.1:2493793-2495131 -
- BF638R_RS10045 WP_014298824.1 13065 - 15282 (-) NC_016776.1:2495123-2497340 -
- BF638R_RS10050 WP_008659918.1 15294 - 16044 (-) NC_016776.1:2497352-2498102 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1221 (-) CAZyme: GT2_Glyco_tranf_2_3|GT2 Yes
- 1218 - 2063 (-) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 2086 - 2997 (-) CAZyme: GT101|GT0 Yes
- 2994 - 4178 (-) CAZyme: GT4 Yes
- 5258 - 6712 (-) TC: gnl|TC-DB|B0RRI5|2.A.66.2.23 Yes
- 6924 - 7874 (-) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 8123 - 8455 (-) other Yes
- 8515 - 8802 (+) other Yes
- 8928 - 9119 (+) other Yes
- 9365 - 10585 (-) CAZyme: GT2_Glyco_tranf_2_3|GT2 Yes
- 10800 - 11690 (-) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 11736 - 13073 (-) CDS No
- 13066 - 15282 (-) CDS No
- 15295 - 16044 (-) CDS No

PUL ID

PUL0499

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.