PUL ID

PUL0517

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

2949015-2969387

Substrate

capsule polysaccharide

Loci

BF2566-BF2583

Species

Bacteroides fragilis/817

Degradation or Biosynthesis

biosynthesis

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BF_RS12180 WP_011202921.1 0 - 954 (-) NC_006347.1:2949015-2949969 -
- BF_RS12185 WP_011202922.1 1071 - 1968 (-) NC_006347.1:2950086-2950983 -
- BF_RS12190 WP_011202923.1 1974 - 3174 (-) NC_006347.1:2950989-2952189 -
- BF_RS12195 WP_011202924.1 3185 - 4043 (-) NC_006347.1:2952200-2953058 -
wecB BF_RS12200 WP_005817161.1 4063 - 5194 (-) NC_006347.1:2953078-2954209 5.1.3.14
- BF_RS12205 WP_011202925.1 5181 - 6204 (-) NC_006347.1:2954196-2955219 -
- BF_RS12210 WP_011202926.1 6173 - 7178 (-) NC_006347.1:2955188-2956193 -
- BF_RS12215 WP_011202927.1 7189 - 8245 (-) NC_006347.1:2956204-2957260 -
- BF_RS12220 WP_011202928.1 8263 - 9079 (-) NC_006347.1:2957278-2958094 -
- BF_RS12225 WP_011202929.1 9044 - 10367 (-) NC_006347.1:2958059-2959382 -
- BF_RS12230 WP_011202930.1 10380 - 11289 (-) NC_006347.1:2959395-2960304 -
- BF_RS12235 WP_011202931.1 11278 - 12415 (-) NC_006347.1:2960293-2961430 -
aepY BF_RS12240 WP_011202932.1 12422 - 13544 (-) NC_006347.1:2961437-2962559 4.1.1.82
aepX BF_RS12245 WP_011202933.1 13551 - 14859 (-) NC_006347.1:2962566-2963874 5.4.2.9
- BF_RS12250 WP_011202934.1 14865 - 15642 (-) NC_006347.1:2963880-2964657 -
- BF_RS12255 WP_011202935.1 15649 - 16921 (-) NC_006347.1:2964664-2965936 -
- BF_RS12260 WP_011202936.1 16924 - 18034 (-) NC_006347.1:2965939-2967049 -
- BF_RS12265 WP_011202937.1 18046 - 19492 (-) NC_006347.1:2967061-2968507 -
rfbA BF_RS12270 WP_011202938.1 19488 - 20373 (-) NC_006347.1:2968503-2969388 2.7.7.24

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 954 (-) CDS No
- 1072 - 1968 (-) CDS No
- 1975 - 3174 (-) CDS No
- 3186 - 4043 (-) CDS No
wecB 4064 - 5194 (-) CDS No
- 5182 - 6204 (-) TC: gnl|TC-DB|Q6MMD5|9.B.18.2.1 Yes
- 6174 - 7178 (-) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 7190 - 8245 (-) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 8264 - 9079 (-) CAZyme: GT11 Yes
- 9045 - 10367 (-) other Yes
- 10381 - 11289 (-) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 11279 - 12415 (-) other Yes
aepY 12423 - 13544 (-) other Yes
aepX 13552 - 14859 (-) other Yes
- 14866 - 15642 (-) other Yes
- 15650 - 16921 (-) other Yes
- 16925 - 18034 (-) other Yes
- 18047 - 19492 (-) TC: gnl|TC-DB|B0RRI5|2.A.66.2.23 Yes
rfbA 19489 - 20373 (-) CDS No

PUL ID

PUL0517

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.