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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0495

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

946722-971045

Substrate

capsule polysaccharide

Loci

BF638R_0778-BF638R_0810

Species

Bacteroides fragilis/817

Degradation or Biosynthesis

biosynthesis

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BF638R_RS03715 WP_005784919.1 0 - 1320 (+) NC_016776.1:946722-948042 -
rfbF BF638R_RS03720 WP_005784921.1 1646 - 2459 (+) NC_016776.1:948368-949181 2.7.7.33
rfbG BF638R_RS03725 WP_005784923.1 2481 - 3582 (+) NC_016776.1:949203-950304 4.2.1.45
- BF638R_RS03730 WP_005784925.1 3578 - 4019 (+) NC_016776.1:950300-950741 -
- BF638R_RS03735 WP_005784927.1 4031 - 4943 (+) NC_016776.1:950753-951665 -
- BF638R_RS24290 WP_005784929.1 5036 - 5186 (+) NC_016776.1:951758-951908 -
- BF638R_RS03740 WP_032578882.1 5336 - 5948 (+) NC_016776.1:952058-952670 -
- BF638R_RS03745 WP_014298262.1 5958 - 6921 (+) NC_016776.1:952680-953643 -
- BF638R_RS03750 WP_005784936.1 6920 - 8390 (+) NC_016776.1:953642-955112 -
- BF638R_RS03755 WP_014298263.1 8411 - 9386 (+) NC_016776.1:955133-956108 -
- BF638R_RS03760 WP_005784941.1 9391 - 10600 (+) NC_016776.1:956113-957322 -
- BF638R_RS03765 WP_014298264.1 10605 - 11754 (+) NC_016776.1:957327-958476 -
- BF638R_RS03770 WP_005784947.1 11775 - 12840 (+) NC_016776.1:958497-959562 -
- BF638R_RS03775 WP_014298265.1 12841 - 14014 (+) NC_016776.1:959563-960736 -
- BF638R_RS03780 WP_014298266.1 14010 - 15099 (+) NC_016776.1:960732-961821 -
- BF638R_RS03785 WP_005784955.1 15110 - 16100 (+) NC_016776.1:961832-962822 -
- BF638R_RS03790 WP_005784957.1 16101 - 17241 (+) NC_016776.1:962823-963963 -
- BF638R_RS03795 - 17234 - 18691 (+) NC_016776.1:963956-965413 -
- BF638R_RS03800 WP_005784961.1 18696 - 19602 (+) NC_016776.1:965418-966324 -
- BF638R_RS24165 - 19996 - 20701 (+) NC_016776.1:966718-967423 -
- BF638R_RS03810 WP_005784969.1 20706 - 21459 (+) NC_016776.1:967428-968181 -
- BF638R_RS03815 WP_005784971.1 21462 - 21978 (+) NC_016776.1:968184-968700 -
- BF638R_RS03820 WP_005784973.1 21991 - 22582 (+) NC_016776.1:968713-969304 -
- BF638R_RS03825 - 22702 - 23082 (+) NC_016776.1:969424-969804 -
- BF638R_RS03830 WP_014298269.1 23190 - 24324 (+) NC_016776.1:969912-971046 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1320 (+) CDS No
rfbF 1647 - 2459 (+) CDS No
rfbG 2482 - 3582 (+) CDS No
- 3579 - 4019 (+) CDS No
- 4032 - 4943 (+) CDS No
- 5037 - 5186 (+) CDS No
- 5337 - 5948 (+) CDS No
- 5959 - 6921 (+) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 6921 - 8390 (+) other Yes
- 8412 - 9386 (+) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 9392 - 10600 (+) other Yes
- 10606 - 11754 (+) other Yes
- 11776 - 12840 (+) other Yes
- 12842 - 14014 (+) other Yes
- 14011 - 15099 (+) other Yes
- 15111 - 16100 (+) other Yes
- 16102 - 17241 (+) CAZyme: GT4|GT94 Yes
- 18697 - 19602 (+) other Yes
- 20707 - 21459 (+) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 21463 - 21978 (+) other Yes
- 21992 - 22582 (+) TC: gnl|TC-DB|H8E4X1|9.B.18.1.2 Yes
- 23191 - 24324 (+) CDS No

PUL ID

PUL0495

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.