Comparison of Helicobacter bilis-Associated Protein Expression in Huh7 Cells Harbouring HCV Replicon and in Replicon-Cured Cells

Table 1

Proteins of transfected and cured Huh7 cells where expression was modulated in cocultures with H. bilis and identified by LC/MS-MS.

	n-Ffold (±SEM)^b		Gene symbol	Function^c	Spot no.		Matching score^d
Protein^a	T-Huh7^e	C-Huh7^f			T-Huh7	C-Huh7	T-Huh7	C-Huh7
				Regulation of cell proliferation and structure
Vimentin^*	5 ± 0.01	3.6 ± 0.02	VIM		17	11	2228	1827
Vimentin^*	3 ± 0.03	2.3 ± 0.1	VIM		18	12	2166	1490
Tubulin beta	0.4 ± 0.3	2.7 ± 0.3	TUBB		14	21	112	962
Tubulin beta^*	NI	2.4 ± 0.5	TUBB		—	45	—	341
Transmembrane protein 4	4.5 ± 0.04	NI	CNPY2		51	—	338	—
Stomatin-like 2	NI	2.4 ± 0.3	SLP2	Cytoskeleton and structural organization	—	10	—	1272
Beta actin	NI	2.35 ± 0.04	ACTB		—	24	—	560
Mutant beta-actin^*	2.7 ± 0.01	NI	ACTB		20	—	166	—
Mutant beta-actin^*	2.1 ± 0.3	NI	ACTB		38	—	161	—
Actin related protein 2/3 complex, subunit 5-like	2.2 ± 0.1	0.4 ± 0.1	ARPC5		47	40	181	422
Stathmin 1	0.3 ± 0.1	3.2 ± 0.02	STMN1		46	39	536	322
Integrin beta 4 binding protein isoform a	0.3 ± 0.01	NI	ITGB4	Cell-matrix adhesion	33	—	139	—
Ran-binding protein 1	0.4 ± 0.1	NI	RAN-BP1		31	—	147	—
				Metabolism and Biosynthesis enzymes
Malate dehydrogenase	0.4 ± 0.1	NI	MDHA		10	—	451	—
Enolase^*	2.1 ± 0.3	NI	ENO		23	—	782	—
Enolase^*	4.2 ± 0.02	NI	ENO	Energy metabolism	53	—	800	—
Triosephosphate isomerase 1	2.1 ± 0.3	2.6 ± 0.3	TIM		26	34	1115	1210
ATP synthase beta sub unit	3.5 ± 0.2	2.4 ± 0.2	ATP5B		9	36	75	423
ATP synthase, H^+ transporting mitochondrial F0 complex sub unit d isoform a	2.1 ± 0.3	NI	ATP5H		35	—	139	—
UV excision repair protein RAD23 homolog B	2.1 ± 0.1	NI	RAD23B	Nucleic acid metabolism (DNA repair)	16	—	889	—
Enoyl coenzyme A hydratase 1, peroxisomal	4.8 ± 0.01	NI	ECH1	Fatty acid metabolism	24	—	549	—
Tryptophan 5-monooxygenase activation protein	NI	2.7 ± 0.3	YWHAQ	Amino acid metabolism	—	27	—	609
Selenophosphate synthetase	NI	4.3 ± 0.02	SEPHS1		—	8	—	584
Pyrophosphatase 1	NI	3.7 ± 0.01	PPA1	Nucleotide metabolism	—	22	—	201
				Protein translation, Modification, and Degredation
Heterogeneous nuclear ribonucleoprotein	NI	3.4 ± 0.03	HNRP	RNA processing	—	6	—	870
Valosin-containing protein^*	0.4 ± 0.1	NI	VCP		1	—	3218	—
Valosin-containing protein^*	0.2 ± 0.1	NI	VCP		2	—	2178	—
Valosin-containing protein^*	0.4 ± 0.1	NI	VCP		3	—	1318	—
Prefoldin subunit 2	3.8 ± 0.02	2.9 ± 0.1	PFDN2		43	38	378	299
Cathepsin D preprotein	2.7 ± 0.3	2.2 ± 0.3	CTSD		27	9	370	615
Ubiquitin-conjugating enzyme E2N	0.4 ± 0.3	NI	UBE2N		44	—	230	—
Ubiquilin 1^*	2.4 ± 0.01	NI	UBQLN1		12	—	116	—
Ubiquilin 1^*	2.1 ± 0.3	NI	UBQLN1	Protein degradation	13	—	602	—
Ubiquitin carboxy-terminal hydrolase L1	0.3 ± 0.1	NI	UCHL1		30	—	230	—
Ubiquitin carboxyl-terminal esterase L3	NI	2.5 ± 0.06	UCHL3		—	29	—	320
S-phase kinase-associated protein 1A isoform b	3.2 ± 0.05	NI	SKP1		42	—	124	—
Proteasome alpha 3 subunit isoform 1	2.1 ± 0.3	4.1 ± 0.01	PSMA3		52	26	63	71
Proteasome 26S non-ATPase subunit 4	2.5 ± 0.1	NI	PSMA4		15	—	599	—
Prolyl 4-hydroxylase, alpha 1 subunit isoform 2 precursor	NI	2.5 ± 0.03	P4HA1		—	5	—	888
Heme binding protein 2	2.8 ± 0.01	NI	HEBP2		32	—	107	—
Small glutamine-rich tetratricopeptide	NI	0.1 ± 0.01	SGTA		—	20	—	403
Eukaryotic translation initiation factor 3	3.0 ± 0.02	NI	EIF3A		22	—	994	—
Eukaryotic translation initiation factor 5A^*	2.7 ± 0.1	2.3 ± 0.05	EIF5A		49	44	542	253
Eukaryotic translation initiation factor 5A^*	2.8 ± 0.1	NI	EIF5A	Protein translation, modification, and; elongation activity	50	—	147	—
Eukaryotic translation elongation factor 1 delta isoform 2	NI	2.2 ± 0.4	EEF2D		—	18	—	627
Eukaryotic translation elongation factor 1 delta isoform 1	NI	0.4 ± 0.1	EEF1D		—	19	—	565
Human pre-mRNA splicing factor	NI	2.1 ± 0.2	SF2		—	37	—	61
Mitochondrial ribosomal protein L7L12^*	NI	2.1 ± 0.4	MRPL17	Ribosomal structure, and biogenesis	—	42	—	164
Mitochondrial ribosomal protein L7L12^*	NI	2.4 ± 0.1	MRPL17		—	43	—	86
				Regulation of transcription
Basic transcription factor 3-like 4	0.4 ± 0.5	NI	BTF3L4	DNA binding	36	—	106	—
WD repeat domin 77	NI	2.5 ± 0.03	WDR	Coordination of multiprotein complex; assemblies	—	14	—	166
				Stress response
Mitochondria heat shock protein 75^*	2.3 ± 0.2	2.7 ± 0.1	DnaK		4	1	1817	3016
Mitochondria heat shock protein 75^*	2.7 ± 0.5	3.1 ± 0.1	DnaK		5	2	1817	2383
Heat shock 70 kDa protein 8 isoform 1^*	2.9 ± 0.1	2.3 ± 0.3	HSPA8	Heat shock proteins and chaperones	6	3	2463	2383
Heat shock 70 kDa protein 8 isoform 1^*	2.6 ± 0.1	2.7 ± 0.1	HSPA8		7	4	1822	1792
Chaperonin	2.3 ± 0.2	NI	Cpn60		21	—	1361	—
T-complex polypeptide 1 (chaperonin)	0.15 ± 0.01	NI	TCP1		8	—	336	—
Superoxide dismutase copper chaperone	0.35 ± 0.2	NI	HMA	Oxidative stress response	25	—	203	—
Cu/Zn superoxide dismutase	0.2 ± 0.03	NI	CuZnSOD		37	—	69	—
Peroxiredoxin 2 isoform a	2.4 ± 0.05	2.7 ± 0.2	PRDX2		34	35	564	78
Peroxiredoxin 3 isoform a precursor	NI	2.5 ± 0.1	PRDX3	Thio-specific antioxidant protein	—	31	—	179
Peroxiredoxin 4	NI	3.2 ± 0.05	PRDX4		—	30	—	782
Thioredoxin-like 1	NI	0.37 ± 0.1	TXNL1	Oxidoreductase activity	—	—	17	758
Endoplasmic reticulum thioredoxin superfamily member	4.7 ± 0.01	NI	TXNDC12		48	—	112	—
CGI-150 protein	NI	2.1 ± 0.1	CGI	Response to toxin	—	23	—	521
				Signal transduction and transport
Progesterone receptor membrane component 1^*	0.3 ± 0.2	NI	PGRMC1		40	—	322	—
Progesterone receptor membrane component 1^*	0.35 ± 0.4	NI		Signal transduction	41	—	294	—
Phospholipase C-alpha	0.3 ± 0.03	NI	PLCα		19	—	227	—
Glia maturation factor, beta	NI	2.8 ± 0.01	GMFB		—	41	—	233
Sorcine isoform a	3.1 ± 0.01	NI	SRI	Transmembrane transporter protein	39	—	320	—
Calcium-binding mitochondrial carrier	NI	0.2 ± 0.01	EFH		—	7	—	242
				Tumour-related
Tumor protein D52-like 2 isoform f	3.7 ± 0.03	NI	TPD52	Tumorigenesis	29	—	63	—
Hepatoma-derived growth factor	NI	2.9 ± 0.01	HDGF	Cellular proliferation and differentiation	—	13	—	65
Transformation upregulated nuclear protein	4.2 ± 0.01	NI	HNRNP-K		54	—	116	—
Rho GDP dissociation inhibitor alpha	NI	2.3 ± 0.2	GDI		—	28	—	412
C-myc binding protein	0.3 ± 0.03	NI	MM1		45	—	159	—
RAS related protein	NI	3.1 ± 0.1	RAB33		—	33	—	147
Immunity-related GTPase	3.0 ± 0.3	NI	IRGQ	Oncogene related	11	—	125	—
B23 nucleophosmin^*	NI	2.9 ± 0.1	NPM		—	15	—	1065
B23 nucleophosmin^*	NI	3.2 ± 0.1	NPM		—	16	—	1091
DJ-1 protein	NI	0.2 ± 0.01	DJ-1		—	32	—	429
Prohibitin	NI	3.2 ± 0.1	PHB	Negative regulator of apoptosis	—	25	—	59

^a Proteins were identified by LC-MS/MS and MASCOT searches of the NCBI nr database. ^bDifferential expression by at least 2-fold level of proteins of transfected or cured Huh7 cells exposed to sublethal concentration of H. bilis initial inoculum density of 10³ cfu/mL; an n-fold value of >2 indicates upregulation, while a value of <0.5 indicates downregulation. ^cProteins were classified into functional categories based on the PANTHER, KEGG, Swiss-Prot and NCBI databases, and by reference to the published literature. ^dProteins with peptide matching score of >49 were considered significant for identification. ^*Protein isoforms. ^eTransfected Huh7 cells; ^fCured Huh7 cells.