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Table 2 Properties of ICE elements in strains with complete genome sequences

From: A comprehensive analysis of Helicobacter pylori plasticity zones reveals that they are integrating conjugative elements with intermediate integration specificity

Strain

ICE type

Integration site (P12)

Pos. LJ

Pos. RJ

Size (kb)14

Complete T4SS?

52

none

     

B38

none2

     

F16

none

     

HPAG1

none

     

Sat464

none

     

v225d

none

     

26695

ICEHptfs33

hpp12_981

1049829

473989

(16.0)

N

26695

ICEHptfs4a/4b3

hpp12_13285

1071598

464996

(18.3)

N

35A

ICEHptfs4a

hpp12_92-91

359215

309788

(10.0)15

N

51

ICEHptfs3/4a3

hpp12_999

none

1034232

(32.2)

N

83

ICEHptfs3

hpp12_65

7908512

106931

(27.8)

N

83

ICEHptfs4b

hpp12_1495

1522267

150317212

(19.1)

N

908, 2017, 2018 1

ICEHptfs4a/b4

hpp12_995-9796

99180112

none

(14.6)

N

B8

ICEHptfs3

hpp12_439-438

487322

526844

39.516

Y

B8

ICEHptfs4a

hpp12_1380-5S-rRNA5,7

52870812

452245

(37.0)

N

Cuz20

ICEHptfs4b

hpp12_210-211

266516

227821

38.5

Y

ELS37

ICEHptfs3

hpp12_511-5128

884907

838572

46.3

Y

ELS37

ICEHptfs4b

hpp12_511-5128

838326

none

(2.0)

N

F30

ICEHptfs4a

hpp12_92-91

1239533

1287710

(10.0)15

N

F32

ICEHptfs3

hpp12_312-313

328469

1058181

(4.1 + 25.5)17

N

F57

ICEHptfs4a

hpp12_92-91

152065

103732

(10.0)15

N

F57

ICEHptfs4b

hpp12_259

323634

284294

39.3

Y

G27

ICEHptfs4b

hpp12_1009-1010

1085072

1045702

39.4

Y

Gambia 94/24

ICEHptfs3

hpp12_15085

1473904

1521243

47.3

Y

Gambia 94/24

ICEHptfs4a/b4

hpp12_994-5S-rRNA

106932212

none

(35.2)

N

HUP-B14

ICEHptfs3

hpp12_1365

135565613

135565613

(10.8)

N

India 7

ICEHptfs3

hpp12_599

752074

798006

45.9

Y

India 7

ICEHptfs4a

hpp12_1391-152810

none

none

(7.3)

N

J99

ICEHptfs33

hpp12_444-445

104487813

104487813

(16.7)

N

J99

ICEHptfs4a/b4

hpp12_994-5S-rRNA

none

none

(25.3)

N

Lithuania 75

ICEHptfs3

hpp12_1508

1516637

none

(34.8)

N

Lithuania 75

ICEHptfs4c

n.a. (plasmid integration)

352813

352813

(10.1)

N

P12

ICEHptfs3

hp1354

1424780

1394778

(30.0)

N

P12

ICEHptfs4a

hp0464

452023

492769

40.7

Y

PeCan4

ICEHptfs3

hpp12_1528-15235

1530039

1536824

(6.8)

N

PeCan4

ICEHptfs4a

hpp12_1528-15235, 11

1578142

1537082

41.1

Y

PeCan18

ICEHptfs3

hpp12_440-439

1015120

1064481

49.416

Y

PeCan18

ICEHptfs4a

hpp12_994-5S-rRNA

1067535

none

(3.1)

N

Puno120

ICEHptfs3

hpp12_994-5S-rRNA

1004976

none

(6.8 + 26.6)18

N

Puno135

ICEHptfs3/4b3

hpp12_994-5S-rRNA

1014870

1059997

(45.1)

Y

Shi112

ICEHptfs3

hpp12_226-225

281418

232869

48.616

Y

Shi112

ICEHptfs4b

hpp12_1380-5S-rRNA

1412827

1451480

38.7

Y

Shi169

ICEHptfs4b

hpp12_211-210

240310

201136

39.2

Y

Shi417

ICEHptfs3

hpp12_1510

1546576

1591512

(44.9)

Y

Shi417

ICEHptfs4b

hpp12_1126-1125

1186887

1147709

39.2

Y

Shi470

ICEHptfs4b

hpp12_495

874710

913872

39.2

Y

SJM180

ICEHptfs3

hpp12_454-453

1413941

none

(23.2)

N

SJM180

ICEHptfs4a

hpp12_1364-13659

1371932

141618012

(24.1)

N

SNT49

ICEHptfs4b

hpp12_65

61216

100646

39.4

Y

South Africa 7

ICEHptfs4c

hpp12_1366

1568674

1527381

41.316

Y

South Africa 7

ICEHptfs4b

hpp12_943-944

934499

973788

39.3

Y

XZ274

ICEHptfs4a

hpp12_92-91

162178

111739

(10.0)15

N

XZ274

ICEHptfs4b

hpp12_776

653446

612019

(41.4)16

Y

  1. 1Strains 908, 2017 and 2018 are sequential isolates from a single patient [17] and do not show major differences in their ICEHptfs4 sequences. However, note that GenBank entries EF195724.1, EF195725.1 and EF195726.1 describe ICEHptfs3 clusters in these strains [17] that are not present in the genome sequences.
  2. 2HELPY0971 is possibly a vestige of hpp12_1321/pz7.
  3. 3resulting from insertions of 2-3 genomic islands and subsequent rearrangements.
  4. 4containing ICEHPtfs4a-type genes close to the left junction, and ICEHptfs4b-type genes close to the right junction.
  5. 5associated with genome rearrangement in comparison to strain P12.
  6. 6associated with deletion of hpp12_980 to hpp12_995 (5’) including one copy of 5S-23S-rRNA.
  7. 7associated with a recombination between the two 5S-23S-rRNA loci (including hpp12_1381-1384).
  8. 8partial duplication of both genes; ICEHptfs3 inserted into truncated ICEHptfs4b.
  9. 9within a restriction-modification system inserted into this region.
  10. 10integrated together with a 0.9 kb fragment of ICEHptfs3 and a putative toxin-antitoxin system.
  11. 11integration of ICEHptfs4a into remnant of ICEHptfs4b, which is in turn integrated into truncated ICEHptfs3.
  12. 12irregular integration, using internal AAGAATG motif.
  13. 13left and right junctions coincide due to irregular integration.
  14. 14numbers in parentheses indicate incomplete ICE elements.
  15. 15disrupted by a chromosomal inversion from hpp12_92 to hpp12_128.
  16. 16size of ICE increased by IS element insertion.
  17. 17interrupted by a chromosomal rearrangement between hpp12_312 and hpp12_1044 (including babC deletion).
  18. 18original integration probably in hpp12_994-5S-rRNA locus; from there, relocation of 26.6 kb fragment via internal AAGAATG motifs into hpp12_1510; 1.4 kb duplication (containing xerT) in both loci.
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BMC Genomics

ISSN: 1471-2164

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