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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0506

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

1808337-1822427

Substrate

capsule polysaccharide

Loci

BF1551-BF1565

Species

Bacteroides fragilis/817

Degradation or Biosynthesis

biosynthesis

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

rmlA1 BF9343_1475 CAH07256.1 0 - 891 (+) CR626927.1:1808337-1809228 -
rmlC2 BF9343_1476 CAH07257.1 890 - 1466 (+) CR626927.1:1809227-1809803 -
- BF9343_1477 CAH07258.1 1474 - 1876 (+) CR626927.1:1809811-1810213 -
- BF9343_1478 CAH07259.1 1895 - 3212 (+) CR626927.1:1810232-1811549 -
- BF9343_1479 CAH07260.1 3218 - 4163 (+) CR626927.1:1811555-1812500 -
- BF9343_1480 CAH07261.1 4155 - 5595 (+) CR626927.1:1812492-1813932 -
- BF9343_1481 CAH07262.1 5789 - 6716 (+) CR626927.1:1814126-1815053 -
- BF9343_1482 CAH07263.1 6712 - 7627 (+) CR626927.1:1815049-1815964 -
- BF9343_1483 CAH07264.1 7626 - 8580 (+) CR626927.1:1815963-1816917 -
- BF9343_1484 CAH07265.1 8593 - 9391 (+) CR626927.1:1816930-1817728 -
- BF9343_1485 CAH07266.1 9390 - 10527 (+) CR626927.1:1817727-1818864 -
- BF9343_1486 CAH07267.1 10534 - 11314 (+) CR626927.1:1818871-1819651 -
- BF9343_1487 CAH07268.1 11301 - 12120 (+) CR626927.1:1819638-1820457 -
- BF9343_1488 CAH07269.1 12119 - 13028 (+) CR626927.1:1820456-1821365 -
- BF9343_1489 CAH07270.1 13143 - 14091 (+) CR626927.1:1821480-1822428 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

rmlA1 1 - 891 (+) CDS No
rmlC2 891 - 1466 (+) CDS No
- 1475 - 1876 (+) CDS No
- 1896 - 3212 (+) CDS No
- 3219 - 4163 (+) CDS No
- 4156 - 5595 (+) TC: gnl|TC-DB|B0RRI5|2.A.66.2.23 Yes
- 5790 - 6716 (+) CAZyme: GT8 Yes
- 6713 - 7627 (+) other Yes
- 7627 - 8580 (+) other Yes
- 8594 - 9391 (+) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 9391 - 10527 (+) other Yes
- 10535 - 11314 (+) CAZyme: GT2|GT2_Glycos_transf_2 Yes
- 11302 - 12120 (+) other Yes
- 12120 - 13028 (+) other Yes
- 13144 - 14091 (+) TC: gnl|TC-DB|P0AC78|9.B.146.1.7 Yes

PUL ID

PUL0506

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.