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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0490

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

2204445-2225868

Substrate

capsule polysaccharide

Loci

BF638R_1864-BF638R_1883

Species

Bacteroides fragilis/817

Degradation or Biosynthesis

biosynthesis

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

rfbA BF638R_RS08735 WP_014298681.1 0 - 894 (+) NC_016776.1:2204445-2205339 2.7.7.24
- BF638R_RS08740 WP_032576176.1 1087 - 2371 (+) NC_016776.1:2205532-2206816 -
- BF638R_RS08745 WP_014298683.1 2363 - 3083 (+) NC_016776.1:2206808-2207528 -
aepX BF638R_RS08750 WP_005817134.1 3102 - 4404 (+) NC_016776.1:2207547-2208849 5.4.2.9
aepY BF638R_RS08755 WP_014298685.1 4415 - 5552 (+) NC_016776.1:2208860-2209997 4.1.1.82
- BF638R_RS08760 WP_014298686.1 5548 - 6673 (+) NC_016776.1:2209993-2211118 2.6.1.37
- BF638R_RS08765 WP_014298687.1 6675 - 7785 (+) NC_016776.1:2211120-2212230 -
- BF638R_RS08770 WP_014298688.1 7781 - 8330 (+) NC_016776.1:2212226-2212775 -
- BF638R_RS08775 WP_014298689.1 8316 - 9261 (+) NC_016776.1:2212761-2213706 -
- BF638R_RS08780 WP_014298690.1 9257 - 10424 (+) NC_016776.1:2213702-2214869 -
- BF638R_RS08785 WP_014298691.1 10420 - 11677 (+) NC_016776.1:2214865-2216122 -
- BF638R_RS08790 WP_014298692.1 11663 - 12536 (+) NC_016776.1:2216108-2216981 -
- BF638R_RS08795 WP_014298693.1 12856 - 14194 (+) NC_016776.1:2217301-2218639 -
- BF638R_RS08800 WP_014298694.1 14193 - 15204 (+) NC_016776.1:2218638-2219649 -
- BF638R_RS08805 WP_014298695.1 15207 - 16230 (+) NC_016776.1:2219652-2220675 -
wecB BF638R_RS08810 WP_041161361.1 16217 - 17348 (+) NC_016776.1:2220662-2221793 5.1.3.14
- BF638R_RS08815 WP_014298697.1 17368 - 18232 (+) NC_016776.1:2221813-2222677 -
- BF638R_RS08820 WP_005817165.1 18228 - 19440 (+) NC_016776.1:2222673-2223885 -
- BF638R_RS08825 WP_014298698.1 19462 - 20470 (+) NC_016776.1:2223907-2224915 -
- BF638R_RS08830 WP_014298699.1 20473 - 21424 (+) NC_016776.1:2224918-2225869 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

rfbA 1 - 894 (+) CDS No
- 1088 - 2371 (+) CDS No
- 2364 - 3083 (+) CDS No
aepX 3103 - 4404 (+) CDS No
aepY 4416 - 5552 (+) CDS No
- 5549 - 6673 (+) CDS No
- 6676 - 7785 (+) STP: STP|Aminotran_1_2 No
- 7782 - 8330 (+) CDS No
- 8317 - 9261 (+) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 9258 - 10424 (+) other Yes
- 10421 - 11677 (+) other Yes
- 11664 - 12536 (+) CAZyme: GT11 Yes
- 12857 - 14194 (+) TC: gnl|TC-DB|C6IBZ4|9.A.29.2.1 Yes
- 14194 - 15204 (+) other Yes
- 15208 - 16230 (+) TC: gnl|TC-DB|Q6MMD5|9.B.18.2.1 Yes
wecB 16218 - 17348 (+) CDS No
- 17369 - 18232 (+) CDS No
- 18229 - 19440 (+) CDS No
- 19463 - 20470 (+) CDS No
- 20474 - 21424 (+) CDS No

PUL ID

PUL0490

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.