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 6 Genes diverged between East Asian and European H. pylori

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

Gene	Description	Representative of the gene family^(a,b,c)	Distance d_a^(d)	Distance d_b^(e)	d_bzone	Reference
hpaA-2	HpaA paralog	HP0492^(f)	0.1608	0.0253	3	[68]
cagA	Cag pathogenicity island protein	HP0547^(f)	0.1009	0.0285	3	[11]
	Bacterial SH3 domain	HP1250	0.0901	0.0615	3
futA, futB	α-(1,3)-fucosyltransferase	HP0379, HP0651	0.0553	0.0436	3	[15]
sotB	Sugar efflux transporter	HP1185	0.0441	0.0095	2
vacA	Vacuolating cytotoxin A	HP0887	0.0420	0.0137	2	[67]
miaA	tRNA delta(2)-isopentenylpyrophosphate transferase	mHP1415	0.0373	0.0241	3	[64, 144]
	Hypothetical protein	HPAG1_0619	0.0366	0.0540	3
hcpD	Cysteine-rich protein, SLR (Sel1-like repeat) protein	HP0160	0.0363	0.0323	3	[16]
yajC	Preprotein translocase subunit YajC	HP1551	0.0353	0.0268	3	[81]
agt	β-1,3-N-acetyl-glucosaminyl transferase	HP1105	0.0338	0.0228	2
rnhB	Ribonuclease HII	mHP1323^(f)	0.0337	0.0398	3	[103, 104]
fliK	Flagellar hook length control	HP0906	0.0328	0.0382	3	[85]
homC	Putative outer membrane protein	HP0373	0.0325	0.1207	3
hopJ,hopK	Outer membrane protein	HP0477, HP0923	0.0313	0.0357	3	[27]
frxA	NAD(P)H-flavin oxidoreductase	HP0642	0.0306	0.0212	2	[120]
secG	Preprotein translocase subunit SecG	mHP1255	0.0300	0.0226	2	[80]
	Hypothetical protein	HP0384	0.0296	0.0302	3
tipα	Tumor necrosis factor alpha-inducing protein	HP0596	0.0293	0.0145	2	[66]
hydE	Membrane-bound, nickel containing, hydrogen uptake hydrogenase	HP0635	0.0288	0.0252	3	[92]
tilS	tRNA(Ile) lysidine synthase	HP0728	0.0286	0.0193	2	[96, 97]
comH	Periplasmic competence protein	HP1527	0.0285	0.0194	2	[82]
def	Peptide deformylase	HP0793	0.0285	0.0065	2	[98]
vacA-4	Putative vacuolating cytotoxin-like protein	HP0922	0.0284	0.0222	2
hypD	Hydrogenase expression/formation protein	HP0898	0.0284	0.0169	2	[91, 145, 146]
addA	Helicase	HP1553	0.0283	0.0308	3	[100]
hsdR	Type I restriction enzyme, R protein	mHP1402	0.0282	0.0245	3
	Hypothetical protein	mHP0174	0.0268	0.0203	2
oipA,oipA-2	Outer membrane protein OipA	HP0638	0.0267	0.0097	2	[70]
prmA	Ribosomal protein L11 methyltransferase	HP1068	0.0261	0.0118	2	[99]
maf	Maf family (motility accessory family of flagellin-associated proteins) homolog	HP0465	0.0259	0.0214	2	[86]
	Hypothetical protein	HP0097	0.0257	0.0207	2
	Hypothetical protein	HP1143	0.0254	0.0146	2
cvpA	Membrane protein required for colicin V production and secretion	mHP0181	0.0252	0.0169	2	[83]
pgl	6-phosphogluconolactonase	HP1102	0.0250	0.0130	2
horI	Outer membrane protein Horl	HP1113	0.0248	0.0348	3
fixQ	cbb3-type cytochrome c oxidase subunit Q	mHP0146	0.0248	0.0023	1
	Hypothetical protein	HP0150	0.0248	0.0154	2
cheY	Chemotaxis effector	HP1067	0.0248	0.0014	1	[84]
fliT	Flagellar chaperone	HP0754	0.0245	0.0138	2	[84]
ftsA	Cell division protein	HP0978	0.0244	0.0071	2	[105, 106]
rnhA	Ribonuclease H	HP0661	0.0243	0.0217	2	[103, 104]
ilvE	Branched-chain amino acid aminotransferase	HP1468	0.0239	0.0136	2
fixS	Cation transport subunit for cbb3-type oxidase	HP1163	0.0237	0.0250	3	[87]
nuoF	NADH-ubiquinone oxidoreductase chain F	HP1265	0.0236	0.0202	2
	Putative thiol:disulfide interchange protein	HP0861	0.0234	0.0185	2
	Hypothetical protein	HP0806	0.0233	0.0233	3

(a) m, different assignment of start codon from the RefSeq entry in the GenBank database
(b) All paralogous genes in each orthologous group are counted.
(c) Assignments to gene families are in Additional file 5 (= Table S4).
(d) Distance between the last common ancestor of hspEAsia and the last common ancestor of hpEurope.
(e) Average of distances between the last common ancestor of hspEAsia and each hspEAsia strain.
(f) A homolog in the draft genome sequence of another East Asian strain 98-10 has been reported to be diverged from four Western strains [143]. The other genes listed as diverged in 98-10 [143], HP0806, HP0061, HP1524, HP0519 and HP1322, did not meet the criteria of this study. HP0806 was below the d_athreshold; for the others, the hspEAsia genes did not form a separate sub tree from hpEurope.

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ISSN: 1471-2180

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