Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pyloriEast Asian genomes

Kawai, Mikihiko; Furuta, Yoshikazu; Yahara, Koji; Tsuru, Takeshi; Oshima, Kenshiro; Handa, Naofumi; Takahashi, Noriko; Yoshida, Masaru; Azuma, Takeshi; Hattori, Masahira; Uchiyama, Ikuo; Kobayashi, Ichizo

doi:10.1186/1471-2180-11-104

Table 2 Characteristic gene contents of East Asian (hspEAsia) H. pylori

From: Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pyloriEast Asian genomes

Population type	Strain	Locus of outer membrane proteins					Periplasmic endonuclease nucG^(d)	Molybdenum- related function
		oipA/oipA-2	hopM/hopN	babA/babB/babC ^(a)	sabA/sabB ^(b)	vacA-2 ^(c)
hspEAsia	F57	A/A^(e)	+/-	A/B/-	A/-	x	x	-
	F32	A/x	+/-	A/B(tr)/-	A/-	x	x	-
	F30	A/A	+/-	A/B/-	A/-	x	x	-
	F16	A/A	+/-	A/B/-	A/-	x	x	-
	51	A/A	+/-	A/B/-	A/-	+	x	-
	52	A/A	+/-	A/B/-	A/A	x	x	-
hspAmerind	Shi470	A/x	+/-	A/B/-	A/-	+	+	+
	v225d	A/x	+/-	A/B/-	A/-	+	+	+
	Cuz20	A/x	+/-	A/B/-	A/-	+	+	+
	Sat464	A/x	+/-	A/B/-	A/-	+	+	+
	PeCan4	A/A	+/-	A/B/-	A/B	+	+	+
hpEurope	26695	A/-	+/+	B/A/C	A/A	+	x	+
	HPAG1	A/-	x/+	A/C/B	A/B	+	+	+
	G27	A/-	+/x	C/B/A	A/B	+	+	+
	P12	A/-	+/+	A/B/B(tr)	B/B	+	+	+?^(f)
	B38	A/-	+/+	A/A(tr)/-	A/-	+	+	+
	B8	A/-	+/+	A/A/-	A/Q^(g)	+	+	+
	SJM180	A/-	+/+	B/C/A	A/B	+	+	+
hspWAfrica	J99	A/-	+/+	A/B(tr)/-	A/B	+	+	+
	908^(h)	A/-	-/-^(h)	A(tr)/B(tr)/-^(h)	-/-^(h)	+	+	+

+, present; x, disrupted (nucleotide sequence partly remained); -, absent. See Additional file 2 (= Table S1) for a detailed list.
a) babA locus corresponds to HP0896; babB locus, HP1243; babC locus, HP0317.
b) sabA locus corresponds to jhp0662; sabB locus, jhp0659.
c) Paralog of vacA (HP0289), but not vacA itself (HP0887). Another paralog vacA-4 (HP0922) is in Table 6.
d) HP1382.
e)/, different loci.
f) One of 12 molybdenum-related genes was truncated.
g) hopQ gene. Two hopQ copies exist, one at sabB locus and the other, as in other strains, at the hopQ locus.
h) From the description of the reference [139], the sequence might not represent a complete genome, although it is deposited as a complete circular genome in GenBank. Hence, care should be taken in interpreting the results.
Relevant information about each family from draft sequence of the Japanese strain 98-10 (NZ_ABSX01000001.1- NZ_ABSX01000051.1) [143] are as follows: oipA/oipA-2, with at least one copy, although the exact copy number cannot be determined because of a short contig encoded only the oipA gene but not the flanking region; hopM locus, +? (partial sequence at an end of the contig); hopN locus, not applicable because it was at an end of contigs (hopN fragment is deposited but the sequence was partial at both ends of the contig, preventing locus assignment); babA/babB/babC, A?/?/? (babA at babA locus but partial at an end of the contig; babB and babC loci, not applicable because they were at ends of contigs; babB sequence was partial at both ends of the contig, preventing locus assignment); sabA/sabB, +/-; vacA-2, x; nucG split as in the other hspEAsia strains; Molybdenum-related function, x.

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ISSN: 1471-2180

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