Antibiotics and probiotics in chronic pouchitis: A comparative proteomic approach

Table 2 Summary of identification results of protein spots conserved in pouchitis/pouch remission and normal pouch/probiotic-treated pouch groups

Spot ID	Swiss-Prot Acc. No.	Protein name	COG1	Subcellular location	Theoretical Mr/pI	Experimental Mr/pI	Method of identification2
A	Q15365	Poly(rC)-binding protein 1 (PCBP1)	A	Nucleus	37.53/6.66	35.99/7.17	MALDI-TOF MS
B	Q6IBM5	Rho GDP dissociation inhibitor (GDI) α, isoform CRA_a (ARHGDIA)	T	Cytoplasm	23.21/5.03	25.73/4.99	MALDI-TOF MS
C	Q5R8R5	Glutathione S-transferase P (GSTP1)	O	Cytoplasm	23.36/5.93	24.33/5.80	MALDI-TOF MS
D	P61088	Ubiquitin-conjugating enzyme E2 N (UBE2N)	O	Nucleus	17.14/6.13	19.00/6.10	MALDI-TOF MS
E	P68871	Hemoglobin subunit β (HBB)	C	Extracellular	16.00/6.74	13.10/7.70	MALDI-TOF MS
F	Q1HDT5	Hemoglobin α 1-2 hybrid (HBA1)	C	Extracellular	15.27/9.04	12.50/9.55	MALDI-TOF MS

¹A: RNA processing and modification. For other abbreviations see Table 1;

²For each protein spot, the gel matching identification method was also employed. Spots A, B and D were identified by comparison with published 2D proteome patterns[17,18]; spots C, E and F by comparison with Swiss-2D PAGE.

Table 1 Differentially expressed proteins before and after antibiotic/probiotic administration

Spot ID	Swiss-ProtAcc. No.	Protein name	COG1	Subcellular location	Theoretical Mr/pI	ExperimentalMr/pI	Method of identification2	Change in protein expression with AB/PB treatment3
Pouchitis/antibiotic-induced remission
1	P27797	Calreticulin (CALR)	O	Endoplasmic reticulum	48.14/4.29	68.52/4.35	GM (Swiss-2D PAGE)	Up
2	P11021	78 kDa glucose-regulated protein (GRP78)	O	Endoplasmic reticulum	72.33/5.07	73.88/4.95	GM (Swiss-2D PAGE)	Down
3	P10809	60 kDa heat shock protein, mitochondrial precursor (HSP60)	O	Mitochondrial matrix	61.05/5.70	60.20/5.32	GM (Swiss-2D PAGE)	Up
4	P11142	Heat shock cognate 71 kDa protein (HSPA8)	O	Nucleolus	70.90/5.37	69.20/5.18	GM[20]	Up
5	P38646	Stress-70 protein, mitochondrial precursor (75 kDa glucose-regulated protein) (GRP75)	O	Mitochondrion	73.68/5.87	71.41/5.70	GM (Swiss-2D PAGE)	Down
6	Q9BU08	Putative uncharacterized protein, fragment (CCT5)	S	Undefined	59.47/5.45	60.46/5.58	GM[21]	Up
7	P02787	Serotransferrin precursor (TF)	P	Extracellular	77.05/6.81	79.49/7.09	GM (Swiss-2D PAGE)	Down
8	Q16822	Phosphoenolpyruvate carboxykinase (GTP), mitochondrial precursor (PCK2)	C	Mitochondrion	70.73/7.56	71.67/7.62	GM[19]	Up
9	P68371	Tubulin β-2C chain (TUBB)	Z	Cytoplasm	49.83/4.79	52.44/4.79	MALDI-TOF MS	Up
10	P06576	ATP synthase subunit β, mitochondrial precursor (ATP5B)	C	Mitochondrion	56.56/5.26	48.675.01	MALDI-TOF MS	Up
11	Q8NBS9	Thioredoxin domain-containing protein 5, precursor (TXNDC5)	R	Endoplasmic reticulum	47.63/5.63	49.43/5.09	GM[20]	Down
12	P35900	Keratin, type I cytoskeletal 20 (KRT20)	W	Cytoplasm	48.49/5.52	48.15/5.54	GM[19]	Down
13	P06733	α-enolase (ENO1)	G	Cytoplasm	47.17/7.01	46.80/7.57	MALDI-TOF MS	Down
14	P11177	Pyruvate dehydrogenase E1 component subunit β, mitochondrial precursor (PDHB)	C	Mitochondrion	39.25/6.20	32.96/5.64	MALDI-TOF MS	Down
15	P17707	S-adenosylmethionine decarboxylase proenzyme (AMD1)	T	Cytoplasm	38.34/5.71	31.91/5.74	MALDI-TOF MS	Up
16	P13804	Electron transfer flavoprotein subunit α, mitochondrial precursor (ETFA)	C	Mitochondrion	35.08/8.62	34.01/7.91	GM[20]	Up
17	P21796	Voltage-dependent anion-selective channel protein 1 (VDAC1)	P	Mitochondrion	30.77/8.62	30.60/9.20	GM[19]	Down
18	P07339	Cathepsin D, precursor (CTSD)	O	Lysosome	44.55/6.10	28.02/5.70	GM (Swiss-2D PAGE)	Down
19	Q99439	Calponin-2 (CNN2)	Z	Cytoplasm	33.70/6.94	29.64/7.55	MALDI-TOF MS	Up
20	P00915	Carbonic anhydrase I (CA1)	R	Cytoplasm	28.87/6.59	27.52/7.45	GM[19]	Down
21	P62937	Peptidyl-prolyl cis-trans isomerase A (PPIA)	O	Cytoplasm	18.01/7.68	16.42/8.09	GM[19]	Up
22	P12104	Fatty acid-binding protein, intestinal (FABP2)	I	Cytoplasm	15.21/6.62	14.07/6.99	MALDI-TOF MS	Up
23	P51161	Ileal lipid binding protein (FABP6)	I	Cytoplasm	14.37/6.29	13.58/7.22	MALDI-TOF MS	Up
24	P09382	Galectin-1 (LGALS1)	W	Extracellular	14.72/5.33	13.25/5.26	MALDI-TOF MS	Down
25	P07148	Fatty acid-binding protein, liver (FABP1)	I	Cytoplasm	14.21/6.60	12.13/6.80	MALDI-TOF MS	Up
26	Q5T1C5	Protein S100-A10 (S100A10)	R	Plasma membrane	11.20/6.82	10.52/7.25	MALDI-TOF MS	Up
Non-inflamed pouch/probiotic-treated pouch
1	P18206	Vinculin (VCL)	Z	Cytoplasm	123.80/5.50	114.44/5.81	GM (Swiss-2D PAGE)	Up
2	P27797	CALR	O	Endoplasmic reticulum	48.14/4.29	68.52/4.35	GM (Swiss-2D PAGE)	Down
3	P28331	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial precursor (NDUFS1)	C	Mitochondrion	79.47/5.89	77.54/5.52	GM[21]	Down
4	P11142	HSPA8	O	Nucleolus	70.90/5.37	69.20/5.18	GM[20]	Up
5	P38646	GRP75	O	Mitochondrion	73.68/5.87	71.41/5.70	GM (Swiss-2D PAGE)	Down
6	P02787	TF	P	Extracellular	77.05/6.81	79.49/7.09	GM (Swiss-2D PAGE)	Down
7	Q16822	PCK2	C	Mitochondrion	70.73/7.56	71.67/7.62	GM[19]	Up
8	Q71U36	Tubulin α-1A chain (TUBA1A)	Z	Cytoplasm	50.15/4.94	56.47/4.82	GM[17]	Down
9	Q8NBS9	TXNDC5	R	Endoplasmic reticulum	47.63/5.63	49.43/5.09	GM[20]	Down
10	P35900	KRT20	W	Cytoplasm	48.49/5.52	48.15/5.54	GM[19]	Down
11	P06733	ENO1	G	Cytoplasm	47.17/7.01	46.80/7.57	MALDI-TOF MS	Down
12	P12532	Creatine kinase, ubiquitous mitochondrial precursor (CKMT1B)	C	Mitochondrion	47.04/8.60	43.16/8.48	GM[20]	Down
13	P22695	Cytochrome b-c1 complex subunit 2, mitochondrial precursor (UQCRC2)	C	Mitochondrion	48.44/8.74	44.10/8.83	GM[21]	Up
14	P11177	PDHB	C	Mitochondrion	39.25/6.20	32.96/5.64	MALDI-TOF MS	Up
15	P17707	AMD1	T	Cytoplasm	38.34/5.71	31.91/5.74	MALDI-TOF MS	Up
16	P00918	Carbonic anhydrase II (CA2)	R	Cytoplasm	29.25/6.87	30.75/7.69	MALDI-TOF MS	Down
17	P60174	Triosephosphate isomerase (TPI1)	G	Cytoplasm	26.67/6.45	26.14/7.32	MALDI-TOF MS	Up

¹Abbreviation of cellular role categories. Categories were taken from Cluster of Orthologous Groups (COG) (http://www.ncbi.nlm.nih.gov/COG/), and the abbreviation was used to mark the categories. C: Energy production and conversion; G: Carbohydrate transport and metabolism; I: Lipid transport and metabolism; O: Posttranslational modification, protein turnover, chaperones; P: Inorganic ion transport and metabolism; R: General function prediction only; S: Function unknown; T: Signal transduction mechanisms; W: Extracellular structures; Z: Cytoskeleton;

²GM: Gel matching;

³AB: Antibiotic; PB: Probiotic.