TABLE 1.

Proteomic and transcriptomic analyses of gene products involved in glutamate/aspartate catabolism in P. gingivalis during growth under conditions of heme limitation and 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
1	PG032	Formiminotransferase-cyclodeaminase-related protein, IMEC*VPNFSEGR	30/14	2	1	2.9		NS
2	PG0548	Pyruvate ferredoxin/flavodoxin oxidoreductase family protein, IAGELLPC*VFHVSAR	33/15	1	1	2.0		NS
3	PG0687	Succinate-semialdehyde dehydrogenase, AFDNGIIC*SGEQSIIYNEADK	37/18	27	6	4.0	1.6	1.77	0.066
		C*SAHAVR	22/16
		EYQATHNQEAVDNIC*R	18/13
		GVGAEDVIC*K	43/13
		NHGAYFC*DEAEGDR	53/14
		TC*NAIIIAPHPR	66/13
4	PG0689	NAD-dependent 4-hydroxybutyrate dehydrogenase, ELIIVPTTC*GTGSEVTNISIAEIK	35/19	12	3	2.8	0.8	1.93	8.9 × 10−5
		ILNC*QPEYVYPK	41/18
		LDELLGC*LLTK	35/14
5	PG0690h	4-Hydroxybutyrate-CoA transferase						3.31	0.03
6	PG0691h	NifU-like protein						1.60	0.0002
7	PG0692	4-Hydroxybutyryl-CoA dehydratase, AGNYMIDLLLANVC*K	42/15	5	2	2.9	0.7	1.65	0.054
		TASC*FQR	20/15
8	PG1067	Hypothetical protein, TDISESAADVLDEPIVVC*R	64/14	2	1	2.4		NS
9	PG1068	Conserved hypothetical protein, MIITAAIC*GAEVLK	40/12	3	2	1.7	0.1	NS
		AVC*PDVIIQPSTGGAVGMTNDER	38/15
10	PG1075h	Butyrate-acetoacetate CoA transferase						1.4	0.05
11	PG1076	Acyl-CoA dehydrogenase, short-chain specific, LYC*AETAMDMTTK	26/14	3	2	1.8	0.2	NS
		SIAQFQNTQFQLADLQC*R	23/19
12	PG1078	Electron transfer flavoprotein, alpha subunit, VTAILC*GYK	22/15	5	2	2.0	0.4	NS
		TGLTADC*TSLEIGDER	55/15
13	PG1079h	Enoyl-CoA						1.3	0.04
14	PG1081	Acetate kinase, VLVLNC*GSSSVK	42/14	9	3	3.5	0.9	NS
		AC*EILGLDYDK	29/15
		VEEC*IPLAPLHNPANLK	42/14
15	PG1082	Phosphotransacetylase, AAELVENPLYLGC*LIVK	52/15	5	2	4.4	1.6	NS
		GC*SVEDIYR	45/15
16	PG1232	Glutamate dehydrogenase, NAD-specific, C*MLDLR	28/14	10	2	2.3	1.2	NS
		LRPESTGFGAVYFVQNMC*K	54/15
17	PG1271	Ornithine aminotransferase, AVIIVC*DGNFHGR	42/19	3	2	0.09		NS
		YFDFLSAYSAVNQGHC*HPK	32/19
18	PG1417	Fumarate hydratase class I, anaerobic, GQLPFC*QDTGTAIILGK	57/15	3	2	1.0	0.2	NS
		HGASC*PVGMGVSC*SADR	18/16
19	PG1612	Methylmalonyl-CoA decarboxylase, alpha subunit, FNGQSVGIVANQPQVMAGC*LDSNASR	28/14	2	2	2.4		NS
		C*TNFGIDK	21/15
20	PG1614	Fumarate reductase, iron-sulfur protein (FrdB), MDELGFGNC*TNTR	45/15	6	2	0.25	0.1	NS
		APVVFDHDC*R	36/13
21	PG1615	Fumarate reductase, flavoprotein subunit (FrdA), LAEVSNAIIDQC*VAQGVPFAR	29/14	1	1	0.35		NS
22	PG1741	Aspartate ammonia-lyase, C*GLHEFNLPAMQPGSSIMPGK	24/14	4	2	1.0	0.2	NS
		VNPVIPEVMNQIC*YK	20/15
23	PG1810	2-Oxoglutarate oxidoreductase, beta subunit, IADMLALLDGTC*LVTR	54/16	3	1	2.5	0.5	NS
24	PG1949	Malate dehydrogenase, LTPNLC*LYDPFAVGLEGVAEEIR	35/15	3	1	1.0	0.2	NS

^aData shown 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.

^hOnly identified in the microarray analysis.