Screening Helicobacter pylori genes induced during infection of mouse stomachs

Table 1 Strains and plasmids used in this study

Strains or phenotype	Relevant genotype or plasmids	Source or reference
Helicobacter pylori
SS1		Lee et al[11]
HP1061		Goodwin et al[12]
Escherichia coli
DH5αλpir+	λpir, supE44, ΔlacU169(φ80lacZΔM15), hsdR17, recA1, endA1, gyrA96, thi-1, relA1	Stanley Maloy, San Diego State University
TAM1 λpir+	Λpir, mcrA, ∆(mrrhsdRMSmcrBC), φ80lacZΔM15, ∆lacX74, recA1, ara∆139(ara-leu)7697, galU, rpsL, endA1, nupG	Active Motif, Inc., Carlsbad, CA 92008
Plasmids
pIVET8		Slauch et al[52]
pIVET9		This study
pIVET10		“
pIVET11		“
pIVET12		“

SS1: Sydney strain 1.

Table 2 Primers used in this study

Genes	Primer sequences 5’-3’
HP1	CTGGAGAGACTAAGCCCTCC
HP2A	AACATTACTGACGCTGATTG
Kan AatII F	GATTTAGACGTCTCAGGGCGCAAGGGCT
Kan AatIIR	TTCCTTTGACGTCTCAGAAGAACTCGTCAA
Kan BglII F (Mut)	AGG GGA TCA AGG TCA GAT CAA GAG A
Kan BglII R (Mut)	TCT CTT GAT CTG ACC TTG ATC CCC T
MCS BamHI F (Mut)	GTC GAC CGA CCC CAA GCT TCT AGA GGT ACC G
MCS BamHI R (Mut)	CGG TAC CTC TAG AAG CTT GGG GTC GGT CGA C
Kan BamHI F (pIVET12)	GAT TTA GGA TCC TCA GGG CGC AAG GGC T
Kan BamHI R (pIVET12)	TTC CTT TGG ATC CTC AGA AGA ACT CGT CAA
CAT	CAA CGG TGG TAT ATC CAG
MCAT	GCC ATT GGG ATA TAT CAA CGG TGG TAT ATC C
NMCAT	CTC CAT TTT AGC TTC CTT AGC TCC TGA AAA TCT CG
CagA F	GATGGCGTGATGTTTGTTGATT
CagA R	CGTAGCACCCACACCCTTATC
CysS F	TGTTATTCCCCCACCATGAAA
CysS R	GCAAGCTCCACGCCAAAG
Flhf F	TGTTGCCCTGAAGATTTGAATTT
Flhf R	TAGCGCGCGGCTAATTTAG
FliA F	AAGCAACAACACCACCATCAAG
FliA R	GCTGGGCAAGCGCTCTT
FliM F	CGCCAGGTGATGCAAATTT
FliM R	AGCGACGATTTGGACCACAT
FucT F	TGAATGTGCATGATTTCAACAACT
FucT R	GCTTTCCCATCAAGGGTGTTT
HsdM F	CTGGGACATTCAAATCAATTATGG
HsdM R	CGTCTTGCAAGCGTTTAAGATCT
InfB F	GAGTCGCTCACACGGAAGCT
InfB R	CAATGAAAGACACCCATTTGTCA
LpxC F	CAAGCCCATCATTTTGTCTTTAGTAA
LpxC R	CAAGTAATTCACTTCTTGCAAAAACC
MinC F	TGCGCAAACACCAGCTTTT
MinC R	ATGGCGCTCATAAATCGTTGT
MurC F	GGCTCATGGAAAGAGCAGTATCA
MurC R	GCCCCAATAATCGCTCCAA
MurD F	GCGGCACTAACGGGAAAA
MurD R	CCCACTCACAGCCTTAAAATCTTC
MurI F	AAAAGCGACGATTCAATCCAA
MurI R	AAGTAGCTAAATGCGAAATGTTCAAA
Nth F	TGAATTATTGGTGGCGACCAT
Nth R	TTGGGCGTTATTTGATTCACTCT
Omp26 F	CAAATCGGCACCGTTACCA
Omp26 R	CATGAAATCCCGCTAGAAGCA
Pgi F	AGCCCACCACAGGGTGTTT
Pgi R	CTCCAATATTGCTTGGTGAAATCTT
PriA F	GGAGGAGCGCTAGGCAAAT
PriA R	AGTTCGCACCTTTCTTGCAATT
RbfA F	GCGAGTTGAATTCTTTAAGCGTTAC
RbfA R	GACCCTCAGCTTTTTTCAATTTAGA
RecG F	GCGATCAACAAAACGCCATTA
RecG R	GCACCCCACATCGCCTATAA
SodB F	TGCTAAAGACAGCATGGGAGATT
SodB R	TTCACATAAGTTTGATGGTGTTTCC
TlpC F	TGGTTAGCGCGATTTATACGAA
TlpC R	GGGTAGGCGATTTTTGAATCC
TnpB F	TTGGTGTTTAGAATGCGGGTATAG
TnpB R	TTTCCTACCCCAAAAAGACTTAACC
TrxB F	CGCCATTGCTTTGTGCAA
TrxB R	TGATGCGGCTGAATTCTTTTT
Type II R / M F	TTCTATAACAGCACCGCTGACATT
Type II R / M R	CGCGTATATTTGTTAGAAGTGATGAAA
VacA F	GGGTTATGCCAGACAAATGATTG
VacA R	TCTTATGCTCTAAACTGGCTATGTTGTT
VirB4 F	GACCATAGCCCTTATTTGTTTAATTTTC
VirB4 R	CTCCTATAATCATGGTATGTCCCACTAC
Ycf5 F	AGCGCTATCAATGAAATGAGCAT
Ycf5 R	CCACACCCCGCCTAAGAAA
HP0423 F	TCGCTCCTTAAGGTTACACGATT
HP0423 R	TCAAAGCCACCATCAATAACAAA
HP0424 F	CGCTGTTTTTAGTTTTAGAGGCTTTC
HP0424 R	GGCTAGGGAAGTGGCTCAAA
HP0426 F	TGCGGTATAGGCTTTCATGAACT
HP0426 R	AAGGTGTTCAAAGACAGCAAAAAA
HP0427 F	TTGCGGTGTGGGTTAATGAA
HP0427 R	GCAACGCTACCATACTTTTATCACTT

Table 3 Helicobacter pylori in vivo induced genes

	Locus	Function or enzyme	Role in virulence
ivi-232	flhF	Regulation of flagella biosynthesis	Motility
ivi-122	fliA	Flagellar motor switch protein
ivi-121	fliM	Flagella motor switch protein
ivi-364	tlpc	Methyl-accepting chemotaxis protein
ivi-11	trxB	Thioredoxin reductase	Oxidative stress protection
ivi-134	nth1	Endonuclease III
ivi-322	ycf5	Cytochrome C biogenesis protein
ivi-352	sodB	Iron-dependent superoxide dismutase	Acid resistance
ivi-161	hsdM	DNA methyltransferase	Nucleic acid metabolism
ivi-162	hsdM/R	Type II restriction enzyme R and M protein
ivi-123	recG	ATP-dependent DNA helicase
ivi-351	priA	Primosome protein replication factor
ivi-361	tnpB	IS606 Transposase
ivi-171	lpxC	UDP-3-O-acyl N- acetylglucosamine deacetylase	Cell envelope structures
ivi-172	minC	Septum site directing protein
ivi-1722	murD	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthase
ivi-1721	murC	UDP-N-acetylmuramoyl alanine-D-glutamate ligase
ivi-363	murI	Glutamate racemase
ivi-321	fucT	Alpha 1, 3-fucosyltransferase
ivi-351	omp26	Outer membrane protein
ivi-112	pgi	Glucose-6-phosphate isomerase	Sugar metabolism
ivi-1132	rbfA	Ribosome binding factor A	Translation and regulation
ivi-1131	infB	Translation initiation factor IF-2
ivi-2721	cysS	Cysteinyl-tRNA synthetase	Protein and peptide synthesis
ivi-110	vacA	Vacuolating toxin	Virulence factors
ivi-362	cagA	Cytotoxin-associated gene
ivi-192	virB4	Type IV secretion system	Transport cagA protein
ivi-241		Predicted coding region HP0426	H. pylori hypothetical protein
ivi-242		Predicted coding region HP0427	H. pylori hypothetical protein
ivi-3101		Predicted coding region HP0423	H. pylori hypothetical protein
ivi-3102		Predicted coding region HP0424	H. pylori hypothetical protein

H. pylori: Helicobacter pylori.