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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0492

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

4414951-4441284

Substrate

capsule polysaccharide

Loci

BF638R_3750-BF638R_3775

Species

Bacteroides fragilis/817

Degradation or Biosynthesis

biosynthesis

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BF638R_RS18025 WP_014299414.1 0 - 954 (-) NC_016776.1:4414951-4415905 -
- BF638R_RS18030 WP_005791042.1 978 - 1992 (-) NC_016776.1:4415929-4416943 -
- BF638R_RS18035 WP_005791043.1 1997 - 2990 (-) NC_016776.1:4416948-4417941 -
- BF638R_RS18040 WP_005791044.1 2993 - 3848 (-) NC_016776.1:4417944-4418799 -
- BF638R_RS18045 WP_005791046.1 3861 - 4983 (-) NC_016776.1:4418812-4419934 -
wecB BF638R_RS18050 WP_014299415.1 4986 - 6156 (-) NC_016776.1:4419937-4421107 5.1.3.14
- BF638R_RS18055 WP_005791050.1 6178 - 7405 (-) NC_016776.1:4421129-4422356 -
- BF638R_RS18060 WP_005791053.1 7391 - 8675 (-) NC_016776.1:4422342-4423626 -
- BF638R_RS18065 WP_014299416.1 8679 - 10524 (-) NC_016776.1:4423630-4425475 -
- BF638R_RS18070 WP_014299417.1 10526 - 11615 (-) NC_016776.1:4425477-4426566 -
- BF638R_RS18075 WP_014299418.1 11618 - 12890 (-) NC_016776.1:4426569-4427841 -
- BF638R_RS18080 WP_014299419.1 12891 - 13875 (-) NC_016776.1:4427842-4428826 -
pseI BF638R_RS18085 WP_014299420.1 13876 - 14905 (-) NC_016776.1:4428827-4429856 2.5.1.97
pseG BF638R_RS18090 WP_005791064.1 14904 - 16311 (-) NC_016776.1:4429855-4431262 3.6.1.57
- BF638R_RS23710 WP_012389005.1 16322 - 18422 (-) NC_016776.1:4431273-4433373 -
- BF638R_RS18105 WP_014299421.1 18426 - 19260 (-) NC_016776.1:4433377-4434211 -
pseC BF638R_RS18110 WP_005791071.1 19260 - 20424 (-) NC_016776.1:4434211-4435375 2.6.1.92
pseB BF638R_RS18115 WP_014299422.1 20430 - 21456 (-) NC_016776.1:4435381-4436407 4.2.1.115
- BF638R_RS18120 WP_005791074.1 21460 - 22591 (-) NC_016776.1:4436411-4437542 -
- BF638R_RS18125 WP_005791076.1 22606 - 23701 (-) NC_016776.1:4437557-4438652 -
- BF638R_RS23715 WP_008998565.1 23973 - 24682 (-) NC_016776.1:4438924-4439633 -
- BF638R_RS24555 WP_008998567.1 24693 - 25044 (-) NC_016776.1:4439644-4439995 -
- BF638R_RS18140 WP_014299426.1 25253 - 25736 (-) NC_016776.1:4440204-4440687 -
updY BF638R_RS18145 WP_010993533.1 25794 - 26334 (-) NC_016776.1:4440745-4441285 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 954 (-) CDS No
- 979 - 1992 (-) CDS No
- 1998 - 2990 (-) CDS No
- 2994 - 3848 (-) CDS No
- 3862 - 4983 (-) CDS No
wecB 4987 - 6156 (-) CDS No
- 6179 - 7405 (-) CDS No
- 7392 - 8675 (-) TC: gnl|TC-DB|A0XZ57|2.A.66.2.13 Yes
- 8680 - 10524 (-) other Yes
- 10527 - 11615 (-) other Yes
- 11619 - 12890 (-) other Yes
- 12892 - 13875 (-) CAZyme: GT2|GT2_Glycos_transf_2 Yes
pseI 13877 - 14905 (-) other Yes
pseG 14905 - 16311 (-) CAZyme: GT0 Yes
- 18427 - 19260 (-) other Yes
pseC 19261 - 20424 (-) STP: STP|Aminotran_1_2 Yes
pseB 20431 - 21456 (-) TC: gnl|TC-DB|Q6MMD5|9.B.18.2.1 Yes
- 21461 - 22591 (-) other Yes
- 22607 - 23701 (-) TC: gnl|TC-DB|Q6MMD5|9.B.18.2.1 Yes
- 25254 - 25736 (-) CDS No
updY 25795 - 26334 (-) CDS No

PUL ID

PUL0492

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.