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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0509

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

CR626927.1

Nucelotide position range

4076793-4090314

Substrate

capsule polysaccharide

Loci

BF3451-BF3464

Species

Bacteroides fragilis/817

Degradation or Biosynthesis

biosynthesis

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BF9343_3361 CAH09142.1 0 - 717 (-) CR626927.1:4076793-4077510 -
rfbC1 BF9343_3362 CAH09143.1 713 - 1256 (-) CR626927.1:4077506-4078049 5.1.3.13
rffH1 BF9343_3363 CAH09144.1 1252 - 2140 (-) CR626927.1:4078045-4078933 2.7.7.24
- BF9343_3364 CAH09145.1 2164 - 2977 (-) CR626927.1:4078957-4079770 -
- BF9343_3365 CAH09146.1 2963 - 4019 (-) CR626927.1:4079756-4080812 -
- BF9343_3366 CAH09147.1 4018 - 5095 (-) CR626927.1:4080811-4081888 -
- BF9343_3367 CAH09148.1 5049 - 5889 (-) CR626927.1:4081842-4082682 -
- BF9343_3368 CAH09149.1 5858 - 6845 (-) CR626927.1:4082651-4083638 -
- BF9343_3369 CAH09150.1 6844 - 7771 (-) CR626927.1:4083637-4084564 -
- BF9343_3370 CAH09151.1 7799 - 8795 (-) CR626927.1:4084592-4085588 -
- BF9343_3371 CAH09152.1 8802 - 10023 (-) CR626927.1:4085595-4086816 -
- BF9343_3372 CAH09153.1 10023 - 11010 (-) CR626927.1:4086816-4087803 -
- BF9343_3373 CAH09154.1 11035 - 12385 (-) CR626927.1:4087828-4089178 -
- BF9343_3374 CAH09155.1 12430 - 12508 (-) CR626927.1:4089223-4089301 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 717 (-) CDS No
rfbC1 714 - 1256 (-) CDS No
rffH1 1253 - 2140 (-) CDS No
- 2165 - 2977 (-) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 2964 - 4019 (-) CAZyme: GT4 Yes
- 4019 - 5095 (-) other Yes
- 5050 - 5889 (-) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 5859 - 6845 (-) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 6845 - 7771 (-) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 7800 - 8795 (-) CAZyme: GT10 Yes
- 8803 - 10023 (-) other Yes
- 10024 - 11010 (-) STP: STP|Nitroreductase Yes
- 11036 - 12385 (-) other Yes
- 12431 - 12508 (-) TC: gnl|TC-DB|R6S968|9.B.146.1.4 Yes

PUL ID

PUL0509

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.