The Effects of Helicobacter pylori-Derived Outer Membrane Vesicles on Hepatic Stellate Cell Activation and Liver Fibrosis In Vitro

Table 2

Quantification proteomics analysis of OMVs derived from pathogenic clinical strains of H. pylori.

Protein ID	Protein description	LFQ intensity OMV 1	LFQ intensity OMV 2	LFQ intensity OMV 4	LFQ intensity OMV 5	Possible function
Outer membrane proteins (OMP)
WP_000595790.1	Outer membrane beta-barrel protein	504540	3604860	963000	4892000	OMP/colonization/adhesion
WP_000768579.1	Outer membrane beta-barrel protein HofC	0	203850	0	184520	OMP/colonization/adhesion
WP_000395375.1	Hop family outer membrane protein (OMP) HopE	0	245410	693600	304390	OMP/colonization/adhesion/type 4 secretion system assembly
WP_000753173.1	Hop family adhesion BabB (Omp19)	0	0	0	73925	Blood group antigen binding adhesin B (BabB)
WP_000592437.1	Hop family adhesion AlpA (Omp20)	0	0	0	1082800	Adherence-associated lipoprotein A (AlpA)
WP_000812546.1	Hop family adhesion AlpB (Omp21)	0	0	0	277750	Adherence-associated lipoprotein B (AlpB)
WP_000831156.1	Outer membrane protein Omp18	0	1459100	0	429570	OMP/immune stimulator
WP_000751514.1	Hop family adhesion HopQ (Omp27)	0	362580	0	0	OMP27/CagA transporter
WP_000716249.1	Hop family adhesion BabA (Omp28)	0	0	1279040	1267000	Blood group antigen binding adhesin A (BabA)
Protein with unknown functions
WP_001268661.1	Hypothetical protein	0	0	0	50133	Unknown
WP_000725112.1	Hypothetical protein	0	249580	0	196290	Unknown
WP_000446639.1	DUF874 family protein	0	29293	0	0	Unknown
WP_001225999.1	Hypothetical protein	23272	0	0	0	Unknown
WP_001228436.1	Hypothetical protein	0	0	0	189012	Unknown
WP_001202825.1	Hypothetical protein	0	0	0	80665	Unknown
WP_000323695.1	DUF3944 domain-containing protein	0	450110	154830	561010	Unknown
Antibiotic resistance
WP_000912892.1	Leucyl aminopeptidase	24719300	39469000	40399000	40792000	Colonization/metronidazole resistant
WP_000670110.1	NAD(P)H-dependent oxidoreductase	0	0	194590	0	Metronidazole resistant
Colonization factors
WP_000738964.1	Polyisoprenoid-binding protein	0	0	0	1887810	Colonization
WP_001174648.1	Thiol peroxidase	0	0	0	147870	Stress resistance and host colonization
WP_001285084.1	Acetone carboxylase subunit alpha	10039200	2686780	8418600	17540800	Colonization
WP_001862402.1	Acetone carboxylase subunit gamma	0	0	1948520	0	Colonization
WP_000731297.1	Fibronectin type III domain-containing protein	0	229900	0	175690	Colonization/type 3 secretion system
WP_001269995.1	Tol/Pal (colicin-tolerant/peptidoglycan-associated lipoprotein) system protein TolB	0	0	0	53991	TolB
WP_000795978.1	LPP20 lipoprotein	2583170	3121670	4231600	5133700	Colonization
WP_000961643.1	Peroxiredoxin	21375000	20724500	16015000	24932200	Colonization
WP_001215729.1	Aliphatic amidase	1222630	176590	4558450	7925500	Ammonia production/increase colonization
WP_001254471.1	Gamma-glutamyltransferase	0	0	0	48692	Gastric colonization
Acid resistance
WP_000038087.1	Nickel-dependent hydrogenase large subunit	0	422490	0	311320	Urease maturation protein
WP_000709479.1	Polyisoprenoid-binding protein	0	0	353520	0	Acid response protein
WP_000779223.1	Urease subunit alpha	48115000	112113000	321814000	107958000	Urease A
WP_000724295.1	Urease subunit beta	87129000	68324000	274879000	157816000	Urease B
WP_001099471.1	Urease accessory protein UreD	0	761510	988360	334590	Urease D
Potent virulence factors
WP_000846523.1	YbhB/YbcL family Raf kinase inhibitor-like protein	0	0	199250	0	Induce tumorigenesis
WP_001040419.1	Polysaccharide deacetylase	685340	1377940	0	2623860	PG amidase/immune response inducer
WP_001053815.1	Acetyl-CoA carboxylase biotin carboxyl carrier protein	0	0	0	44002	Adenocarcinoma progress
WP_000461024.1	ATP-dependent protease subunit HslV	0	0	0	32755	Protease activity
WP_000890837.1	Tumor necrosis factor alpha-inducing protein	0	1332180	0	319850	Accelerate inflammation and cancer development
WP_000467802.1	Methyl-accepting chemotaxis protein	2200500	4482860	3225630	3047290	Chemotaxis
	Periplasmic serine endoprotease DegP-like	0	657760	909990	770250	Protease high temperature requirement A (HtrA)
WP_000034151.1	Acyl-ACP--UDP-N-acetylglucosamine O-acyltransferase	0	93066	0	0	LPS assembly
WP_000846461.1	DNA starvation/stationary phase protection protein	7560800	6572800	16870200	11009900	Accumulation of neutrophils and monocytes at the site of infection
WP_000858181.1	3-Deoxy-8-phosphooctulonate synthase	0	50028	0	0	3-Deoxy-d-manno-octulosonic acid (KDO)
WP_000739470.1	Peptidylprolyl isomerase CBF2	0	0	0	358410	TH17 inflammation inducer
WP_000540573.1	ATP-dependent Clp endopeptidase proteolytic subunit ClpP	0	264590	0	563180	ATP-dependent caseinolytic proteases (ClpP)
Metabolism and vital functions
WP_000506216.1	Enoyl-ACP reductase FabI	112930	0	0	0	Lipid metabolism
WP_000866624.1	Peptide-methionine (R)-S-oxide reductase MsrB	0	0	1182160	0	Repair enzyme for proteins that have been inactivated by oxidation
WP_000422563.1	DEAD/DEAH box helicase	0	0	0	45347	Helicase
WP_001207734.1	Ketol-acid reductoisomerase	0	1747020	1312860	186410	Amino acid synthesis enzyme
WP_001204347.1	Menaquinone biosynthesis decarboxylase	0	0	0	33451	Respiratory mechanism
WP_000662799.1	M3 family oligoendopeptidase	214060	52823	759950	0	Peptidoglycan endopeptidase
WP_000524601.1	Redox-regulated ATPase YchF	0	84152	0	0	Regulator protein
WP_000608576.1	2,3,4,5-Tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase	0	173380	0	0	Amino acid synthesis enzyme/unknown function
WP_001006979.1	Acetyl-CoA C-acetyltransferase	463830	0	0	0	Metabolic enzyme
WP_000650637.1	Hydantoinase/oxoprolinase family protein	9456000	3187340	7925600	17515000	Metabolic enzyme
WP_000862222.1	GMP reductase	0	0	32786	0	Nucleic acid catabolic enzyme
WP_001268933.1	ADP-glyceromanno-heptose 6-epimerase	0	0	0	227002	Catabolic enzyme
WP_001126584.1	Carbamoyl-phosphate synthase large subunit	0	0	402270	0	Nitrogen metabolism
WP_001159546.1	4-Hydroxy-tetrahydrodipicolinate synthase	0	0	0	370800	Metabolic enzyme
WP_000060246.1	AAA family ATPase	0	0	0	612130	ATPases
WP_000062669.1	3-Methyl-2-oxobutanoate hydroxymethyltransferase	246880	1145910	0	559400	Metabolic enzyme
WP_000037869.1	DNA-directed RNA polymerase subunit beta/beta	464440	1495780	0	1015630	RNA polymerase
WP_000534771.1	Formamidase	0	0	0	856430	Nitrogen metabolism
WP_001160526.1	Class II fumarate hydratase	0	0	1094120	0	Nitrogen metabolism
WP_001862586.1	S41 family peptidase	0	0	565030	0	Endopeptidase
WP_000438056.1	3-Hydroxyacyl-ACP dehydratase FabZ	0	0	97338	0	Catabolic enzyme
WP_000780126.1	UbiX family flavin prenyltransferase	0	127650	0	256960	Catabolic enzyme
WP_000616334.1	Transcription-repair coupling factor	0	0	0	310300	Repair enzyme
WP_000963128.1	Recombinase RecA	170880	0	0	0	RecA
	Superoxide dismutase [Fe]	0	0	0	749400	Superoxide dismutase
WP_000955673.1	Phosphopyruvate hydratase	0	56407	0	0	Enolase
WP_000412947.1	Peroxiredoxin	1152900	0	0	0	Catabolic enzyme
WP_000080506.1	F0F1 ATP synthase subunit alpha	6236520	12373400	3033330	3668760	ATPase
WP_001863096.1	F0F1 ATP synthase subunit beta	1873140	2158280	2582800	1605730	ATPase
WP_000289187.1	NADP-specific glutamate dehydrogenase	0	496220	8149800	2938760	Metabolic enzyme
WP_000864547.1	DNA-directed RNA polymerase subunit alpha	0	0	0	22302	RNA polymerase
WP_001040579.1	Elongation factor Tu	2547840	2607030	1626200	1537060	Elongation factor
WP_000117507.1	Citrate synthase	2217840	4356700	3076740	2120940	Metabolic enzyme
WP_000323988.1	Isocitrate dehydrogenase (NADP(+))	0	555280	0	331560	Metabolic enzyme
WP_001242837.1	Cystathionine gamma-synthase	0	0	873810	0	Metabolic enzyme
WP_000476591.1	Porphobilinogen synthase	0	0	0	74893	Metabolic enzyme
WP_000002194.1	F0F1 ATP synthase subunit gamma	0	0	65433	0	ATPase
WP_001221712.1	IMP dehydrogenase	806320	1544980	0	1451060	Metabolic enzyme
WP_001124018.1	Phosphogluconate dehydratase	158780	161430	197580	608640	Metabolic enzyme
WP_001217520.1	Aspartate ammonia-lyase	1172670	826180	924680	303884	Nitrogen metabolism
WP_000131629.1	Ribonuclease J	0	0	0	127260	Ribonuclease
WP_000774319.1	Excinuclease ABC subunit (UvrC)	0	158820	0	0	UvrC
WP_000564420.1	Thioredoxin-disulfide reductase	0	0	304110	0	Metabolic enzyme
WP_000187711.1	Purine-nucleoside phosphorylase	0	0	0	233580	Metabolic enzyme
WP_010875529.1	Excinuclease ABC subunit UvrA	0	121980	0	0	UvrA
WP_000020199.1	Thioredoxin	0	0	918110	1172960	Metabolic enzyme
WP_000247370.1	Catalase	39582000	69503000	262561000	94226000	Catalase
WP_000637150.1	Type I glutamate--ammonia ligase	0	0	3351300	0	Metabolic enzyme
WP_000053246.1	Glutamate--tRNA ligase	0	0	0	154360	Metabolic enzyme
WP_000699284.1	Type II 3-dehydroquinate dehydratase	0	4075540	0	8030600	Catabolic enzyme
Motility
WP_000885496.1	Flagellin A	798030	3071800	50265700	2449870	Flagellin A
WP_000010001.1	Flagellin B	0	132380	0	0	Flagellin B
WP_000646667.1	Flagellar sheath lipoprotein HpaA	0	766340	0	1061070	N-Acetylneuraminyllactose-binding hemagglutinin
Ribosomal proteins
WP_001018245.1	50S ribosomal protein L7/L12	3165000	0	0	0	L7/L12
WP_000529962.1	30S ribosomal protein S3	0	0	134180	0	S3
WP_001862443.1	50S ribosomal protein L9	0	0	111940	0	L9
Iron-related proteins
WP_000934548.1	HugZ family heme oxygenase	0	0	3413400	0	Iron acquisition
WP_000949202.1	Nonheme ferritin	5908500	9860700	9396400	14801600	Ferritin like protein
Others
WP_000342347.1	Hybrid sensor histidine kinase/response regulator	0	192370	0	0	Response protein
WP_000785752.1	Cag pathogenicity island protein Cag1	0	203798	0	0	Membrane apparatus of T4SS
WP_000714010.1	Insulinase family protein	0	0	0	105420	Insulinase/unknown activity
WP_001265981.1	NAD(P)-dependent alcohol dehydrogenase	0	0	0	439940	Sensor protein
WP_000855958.1	Transporter substrate-binding domain-containing protein	2392480	3797000	4192600	2420660	Transporter
WP_029671489.1	Outer membrane beta-barrel protein	0	0	0	64626	Transporter
WP_001862559.1	ABC transporter substrate-binding protein	0	0	0	948250	Transporter
WP_001210849.1	Pyridoxine 5-phosphate synthase	3573670	8087900	1476140	2574090	Transferase
WP_000671934.1	Cochaperone GroES	2343300	3182200	2711900	3589100	Chaperone
WP_001040293.1	Chaperonin GroEL	64544000	136783000	55262000	109558000	Chaperone
WP_000664941.1	Copper-translocating P-type ATPase CopA	781570	0	0	0	Chemotaxis/heat-shock response

OMV1: OMVs derived from H. pylori strain 1; OMV2: OMVs derived from H. pylori strain 2; OMV4: OMVs derived from H. pylori strain 4, OMV5: OMVs derived from H. pylori strain 5. Abbreviations: H. pylori outer membrane protein family C: HofC, Helicobacter outer membrane proteins: Hop, nicotinamide adenine dinucleotide: NAD, Lpp20: lipoprotein 20, heat-shock locus V: hslV, lipopolysaccharides: LPS, protease high temperature requirement A: HtrA, deoxyribonucleic acid: DNA, 3-deoxy-d-manno-octulosonic acid: KDO, cell binding factor 2: CBF2, ATP-dependent caseinolytic proteases: ClpP, fatty acid biosynthesis I: FabI, methionine sulfoxide reductase B: MsrB, guanosine monophosphate: GMP, adenosine diphosphate: ADP, ATPases associated with diverse cellular activities: AAA, adenosine triphosphatase: ATPases, recombinase A: RecA, nicotinamide adenine dinucleotide phosphate: NADP, thermal unstable: Tu, inosine monophosphate: IMP, ultraviolet radiation: Uvr, Helicobacter pylori adhesion A: HpaA, heme utilization gene: Hug, cytotoxic associated gene: cag, copper-translocating P-type ATPase: CopA.