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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0518

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

1777755-1802668

Substrate

capsule polysaccharide

Loci

BF1530-BF1551

Species

Bacteroides fragilis/817

Degradation or Biosynthesis

biosynthesis

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BF_RS07190 WP_011202462.1 0 - 1824 (+) NC_006347.1:1777755-1779579 -
- BF_RS07195 WP_009291950.1 1829 - 3557 (+) NC_006347.1:1779584-1781312 -
- BF_RS07200 WP_009291951.1 3576 - 3819 (+) NC_006347.1:1781331-1781574 -
- BF_RS07205 WP_050443750.1 3864 - 5352 (+) NC_006347.1:1781619-1783107 -
rfbF BF_RS07210 WP_005816687.1 5386 - 6199 (+) NC_006347.1:1783141-1783954 2.7.7.33
- BF_RS07215 WP_005816689.1 6137 - 6593 (+) NC_006347.1:1783892-1784348 -
rfbG BF_RS07220 WP_011202465.1 6589 - 7678 (+) NC_006347.1:1784344-1785433 4.2.1.45
- BF_RS07225 WP_011202466.1 7677 - 8568 (+) NC_006347.1:1785432-1786323 -
- BF_RS07230 WP_005816696.1 8581 - 9769 (+) NC_006347.1:1786336-1787524 -
- BF_RS07235 WP_005816698.1 9775 - 10672 (+) NC_006347.1:1787530-1788427 -
- BF_RS07240 WP_005816700.1 10668 - 11568 (+) NC_006347.1:1788423-1789323 -
- BF_RS07245 WP_011202468.1 11564 - 12782 (+) NC_006347.1:1789319-1790537 -
- BF_RS07250 WP_011202469.1 12884 - 14030 (+) NC_006347.1:1790639-1791785 -
- BF_RS07255 WP_005816707.1 14013 - 15015 (+) NC_006347.1:1791768-1792770 -
- BF_RS07260 WP_005816709.1 15456 - 16419 (+) NC_006347.1:1793211-1794174 -
- BF_RS07265 WP_005816711.1 17242 - 18502 (+) NC_006347.1:1794997-1796257 -
- BF_RS07270 WP_011202470.1 18443 - 19256 (+) NC_006347.1:1796198-1797011 -
- BF_RS07275 WP_011202471.1 19260 - 20358 (+) NC_006347.1:1797015-1798113 -
- BF_RS07280 WP_011202472.1 20404 - 21439 (+) NC_006347.1:1798159-1799194 -
- BF_RS07285 WP_011202473.1 21443 - 22934 (+) NC_006347.1:1799198-1800689 -
- BF_RS07290 WP_011202474.1 22951 - 23848 (+) NC_006347.1:1800706-1801603 -
- BF_RS07295 WP_005816723.1 23966 - 24914 (+) NC_006347.1:1801721-1802669 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1824 (+) STP: STP|Fer4 No
- 1830 - 3557 (+) CDS No
- 3577 - 3819 (+) CDS No
- 3865 - 5352 (+) CDS No
rfbF 5387 - 6199 (+) CDS No
- 6138 - 6593 (+) CDS No
rfbG 6590 - 7678 (+) CDS No
- 7678 - 8568 (+) CDS No
- 8582 - 9769 (+) CDS No
- 9776 - 10672 (+) CDS No
- 10669 - 11568 (+) CDS No
- 11565 - 12782 (+) CDS No
- 12885 - 14030 (+) CDS No
- 14014 - 15015 (+) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 15457 - 16419 (+) other Yes
- 17243 - 18502 (+) other Yes
- 18444 - 19256 (+) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 19261 - 20358 (+) CAZyme: GT4 Yes
- 20405 - 21439 (+) CAZyme: GT4 Yes
- 21444 - 22934 (+) other Yes
- 22952 - 23848 (+) other Yes
- 23967 - 24914 (+) TC: gnl|TC-DB|P0AC78|9.B.146.1.7 Yes

PUL ID

PUL0518

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.