TABLE 2.

Proteomic and transcriptomic analyses of proteins of P. gingivalis grown with heme limitation or with heme excess^a

Product no.	TIGR accession no.	Protein and peptide sequence(s) identifiedb	Scorec	nd	ICAT ne	Fold change by proteomicsf	SD	Fold change by transcriptomicsg	Transcriptomic P value
Proteinases
1	PG0026	Hypothetical protein (homology to Arg proteases), C*VVNSPGGQTASMAK	30/14	5	2	0.41	0.1	1.59	0.025
		FSNLPVLGGESC*R	58/14
2	PG0232	Zinc carboxypeptidase, C*QILIENHDKR	21/18	4	2	0.43	0.1	NS
		YPSLC*TTSVIGK	56/19
3	PG2024/PG0506	Arginine-specific protease (RgpACat/RgpB), GQDEMNEILC*EK	51/14	12	2	0.45	0.2	NS
		C*YDPGVTPK	24/14
4	PG2024/PG0506	Arginine-specific protease (RgpA/Kgp adhesins), DAGMSAQSHEYC*VEVK	34/15	25	3	1.1	0.4	NS
		EGLTATTFEEDGVAAGNHEYC*VEVK	44/13
		C*VNVTVNSTQFNPVK	59/15
Invasion related proteins
5	PG0159	Endopeptidase PepO, METELAQIC*YSK	55/13	6	1	2.0	0.5	NS
6	PG0350	Internalin-related protein, FVPYNDDEGGEEENVC*TTEHVEMAK	35/13	14	4	3.6	1.3	1.90	0.035
		IIMELSEADVEC*TIK	46/14
		ILHC*NNNQLTALNLSANTK	23/15
		LDLPANADIETLNC*SK	52/13
7	PG1374	Immunoreactive 47-kDa protein (IrpI), GLSVLVC*HSNQIAGEEMTK	27/15	5	2	6.5	1.8	2.85	7.9 × 10−4
		NPNLTYLAC*PK	61/13
8	PG2130h	FimX						2.11	0.0059
9	PG2131h	PgmA						2.35	0.0021
10	PG2132	Fimbrillin FimA, YDASNELRPTILC*IYGK	45/16	2	1	0.57	0.1	2.65	0.0035
11	PG2133h	Lipoprotein						1.86	0.034
12	PG2134h	FimC						1.58	0.23
13	PG2135	FimD						ND
14	PG2136h	FimE						2.02	0.0028
15	PG1638h	Thioredoxin family protein						1.98	7.0 × 10−4
16	PG1639h	Hypothetical protein						1.86	0.0026
17	PG1640h	DinF, membrane-spanning MATE efflux pump						1.66	0.0021
18	PG1641h	PtpA, protein tyrosine phosphatase						1.89	0.0038
19	PG1642	Cation-translocating ATPase (ZntA)						2.71	7.3 × 10−5
Iron transport and related proteins
20	PG0090	Dps family protein, EEHELVC*AASTLK	36/13	3	1	1.1	0.1	NS
21	PG0616	Thioredoxin/HBP35 (heme binding protein), GATPEDVC*TATFTGK	47/13	6	1	0.48	0.1	0.42	0.0017
22	PG0618	Alkyl hydroperoxide reductase subunit C, AAQYVAAHDGQVC*PAK	36/15	1	1	41.0		2.30	0.0029
23	PG0619h	Alkyl hydroperoxide reductase subunit F						1.73	0.015
24	PG0644h	HtrE (Tla); TonB-linked receptor						2.05	1.5 × 10−4
25	PG0645h	HtrD; no known function						2.07	0.0056
26	PG0646h	HtrC; ABC heme transport system ATP binding protein						1.72	0.0056
27	PG0647h	HtrB; ABC heme transport system permease						1.91	0.0028
28	PG0648h	HtrA; ABC heme transport system solute binding protein						2.20	7.0 × 10−4
29	PG1043h	FeoB2						1.51	0.022
30	PG1551h	HmuY						10.11	4.5 × 10−5
31	PG1552	HmuR, MNSDELFEEITYPGYTIC*R	25/15	1	1	4.0		3.13	0.0026
32	PG1553h	HmuS						4.75	8.9 × 10−5
33	PG1554h	Hypothetical protein						1.13	0.84
34	PG1555h	TolQ						2.36	0.070
35	PG1556h	HmuV						2.28	0.0031
36	PG1019	Hypothetical protein, TYMIDTNDSENDC*IAR	70/14	2	1	25.0		2.57	0.0026
37	PG1020h	Conserved hypothetical protein; possible outer membrane receptor protein						3.36	3.0 × 10−4
38	PG1286	Ferritin, FGSVLEVFQQVYEHEC*K	73/13	2	1	1.2		1.72	0.012
39	PG1858h	Flavodoxin A						15.3	7.5 ×10−6
Others
40	PG0694	Omp40, RPVSC*PECPEPTQPTVTR	26/16	5	1	1.2	0.1	NS
41	PG0695	Omp41, RPVSC*PECPEVTPVTK	39/15	12	1	1.2	0.2	NS
42	PG1874h	Conserved hypothetical protein						1.52	0.047
43	PG1875h	Hemolysin A						1.40	0.049

^aData in bold indicate proteins that are predicted to be encoded in operons.

^bC*, ICAT-modified cysteine.

^cHighest scoring peptide score/threshold score (P = 0.05).

^dTotal number of independent peptide identification events for each protein.

^eNumber of unique ICAT-labeled peptides identified for each protein.

^fAverage ratio for all quantified peptides for each protein (heme limitation/heme excess).

^gNS, no statistically significant change detected; ND, not detected.

^hIdentified only in microarray analysis.