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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0496

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

4110041-4125220

Substrate

capsule polysaccharide

Loci

BF638R_3472-BF638R_3487

Species

Bacteroides fragilis/817

Degradation or Biosynthesis

biosynthesis

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BF638R_RS16650 WP_014299315.1 0 - 717 (-) NC_016776.1:4110041-4110758 -
rfbC BF638R_RS16655 WP_005817306.1 713 - 1256 (-) NC_016776.1:4110754-4111297 5.1.3.13
rfbA BF638R_RS16660 WP_014299316.1 1252 - 2140 (-) NC_016776.1:4111293-4112181 2.7.7.24
- BF638R_RS16665 WP_014299317.1 2153 - 2933 (-) NC_016776.1:4112194-4112974 -
- BF638R_RS16670 WP_008657389.1 2893 - 3622 (-) NC_016776.1:4112934-4113663 -
- BF638R_RS16675 WP_014299318.1 3618 - 4662 (-) NC_016776.1:4113659-4114703 -
- BF638R_RS16680 WP_014299319.1 4672 - 5785 (-) NC_016776.1:4114713-4115826 -
- BF638R_RS16685 WP_032563521.1 5848 - 6607 (-) NC_016776.1:4115889-4116648 -
- BF638R_RS16690 WP_014299321.1 6657 - 7566 (-) NC_016776.1:4116698-4117607 -
- BF638R_RS16695 WP_050551121.1 7579 - 8908 (-) NC_016776.1:4117620-4118949 -
- BF638R_RS16700 WP_014299323.1 8907 - 9918 (-) NC_016776.1:4118948-4119959 -
- BF638R_RS16705 WP_009292650.1 9920 - 10820 (-) NC_016776.1:4119961-4120861 -
rfbG BF638R_RS16710 WP_009292649.1 10821 - 11901 (-) NC_016776.1:4120862-4121942 4.2.1.45
rfbF BF638R_RS16715 WP_005781149.1 11906 - 12683 (-) NC_016776.1:4121947-4122724 2.7.7.33
rfbH BF638R_RS16720 WP_009292648.1 12720 - 14064 (-) NC_016776.1:4122761-4124105 -
- BF638R_RS16725 WP_005790532.1 14082 - 15180 (-) NC_016776.1:4124123-4125221 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 717 (-) CDS No
rfbC 714 - 1256 (-) CDS No
rfbA 1253 - 2140 (-) CDS No
- 2154 - 2933 (-) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 2894 - 3622 (-) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 3619 - 4662 (-) other Yes
- 4673 - 5785 (-) other Yes
- 5849 - 6607 (-) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 6658 - 7566 (-) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 7580 - 8908 (-) other Yes
- 8908 - 9918 (-) other Yes
- 9921 - 10820 (-) other Yes
rfbG 10822 - 11901 (-) other Yes
rfbF 11907 - 12683 (-) other Yes
rfbH 12721 - 14064 (-) STP: STP|Aminotran_1_2 Yes
- 14083 - 15180 (-) TC: gnl|TC-DB|R6S968|9.B.146.1.4 Yes

PUL ID

PUL0496

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.