A proteomic investigation of Fusobacterium nucleatum alkaline-induced biofilms

Chew, Jactty; Zilm, Peter S; Fuss, Janet M; Gully, Neville J

doi:10.1186/1471-2180-12-189

BMC Microbiology

Table 1 Significantly regulated protein expression in response to growth pH 8.2

From: A proteomic investigation of Fusobacterium nucleatum alkaline-induced biofilms

Function	Protein name	Accession number¹	Gene ID²	Spot number³	Fraction⁴	%Seq MS/MS⁵	Density⁶(×10³)		Mean Ratio⁷	p-value⁸	Pred. MW/pI⁹	Obs. MW/pI¹⁰
							pH 8.2	pH 7.4
Cellular energy
2-oxoglutarate pathway	NAD-specific glutamate dehydrogenase (EC 1.4.1.2)	148324272	1750	5	C	29	18.5	3.9	4.8	0.01	46.6/6.1	48/6.2
				6	C	52	18.8	6.0	3.1	0.01		48/6.6
				7^	C	10	1.6	7.5	0.2	0.02		35/7.9
				8^	C	31	5.9	49.3	0.1	0.01		23/9.5
				9^	C	32	2.7	16.6	0.2	0.01		24/8.0
				10^	C	30	nd	24.4	-	0.01		28/9.0
	Gluaconyl-CoA decarboxylase A subunit (EC 4.1.1.70)	148322789	0224	11	C	40	2.5	1.1	2.3	0.02	64.1/5.1	62/5.3
				12	C	34	1.7	nd	+	0.02		62/5.4
	Glutamate formiminotransferase (EC 2.1.2.5)	148323936	1404	13	C	47	0.6	14.3	0.1	0.01	36.0/5.5	38/5.6
Butanoate synthesis	Butanoate: acetoacetate CoA transferase α subunit (EC 2.8.3.9)	148323516	0970	14^	C	36	nd	3.7	-	0.01	23.3/6.1	23/5.8
				15^	C	50	nd	2.9	-	0.01		23/6.1
	Butyryl-CoA dehydrogenase (EC 1.3.99.2)	148323999	1467	16^	C	31	nd	6.7	-	0.05	41.8/7.8	39/8.1
Acetate synthesis	Phosphate acetyltransferase (EC 2.3.1.8)	148323174	0618	17^	C	7	3.8	nd	+	0.05	36.0/7.6	39/7.6
Pyruvate metabolism	D-lactate dehydrogenase (EC 1.1.1.28)	148324271	1749	18	C	41	1.2	nd	+	0.05	37.8/6.1	36/6.1
	Pyruvate synthase (EC 1.2.7.1)	148324582	2072	19^	C	1	nd	1.3	-	0.05	132.1/6.7	58/7.7
One carbon pool by folate	Methenyltetrahydrofolate cyclohydrolase (EC 3.5.4.9)	148323933	1401	31	M	28	nd	2.0	-	0.01	22.9/4.9	19/4.9
				32	M	12	nd	3.3	-	0.01		19/5.0
Transport
Substrate transport	Di-peptide binding protein DppA	148323000	0440	1	C	8	1.6	nd	+	0.02	56.9/5.3	55/4.6
				2	C	6	5.9	0.7	8.6	0.02		55/4.8
				3	C	5	4.1	nd	+	0.02		55/4.9
				4	C	5	1.8	nd	+	0.02		55/5.0
	Dicarboxylate: Proton (H⁺) TRAP-T (tripartite ATP-independent periplasmic) family transporter binding protein	148323082	0524	33	M	10	100.1	1.7	6	0.01	28.9/5.0	39/4.9
				34	M	13	57.1	0.6	10	0.02		39/5.0
	RND (resistance-nodulation-cell division) superfamily antiporter	148323066	0508	35	M	10	1.0	3.9	0.3	0.01	40.8/5.2	43/5.1
				36		7	1.3	3.2	0.4	0.05		43/5.2
	TTT (tripartite tricarboxylate transporter) family receptor protein	148322550	2414	37	M	21	1.3	3.2	0.1	0.04	35.2/5.5	33/5.2
	ABC (ATP binding cassette) superfamily transporter binding protein	148322870	0306	38	M	24	1.1	nd	-	0.01	32.0/4.7	32/4.6
				39	M	24	1.3	nd	-	0.01		32/4.6
Porin	OmpIP family outer membrane porin	148322338	2196	40	M	8	10.6	27.9	0.4	0.02	78.1/8.8	75/8.8
	Fusobacterial outer membrane protein A (FomA)	148323518	0972	41	M	12	63.6	14.3	4.4	0.03	42.3/8.4	42/7.8
				42	M	12	58.1	2.3	25.8	0.03		42/8.1
				43	M	14	18.3	nd	+	0.01		42/8.6
				44	M	5	23.3	1.6	7.7	0.01		40/9.2
Electron acceptor	Electron transfer flavoprotein subunit A	148324001	1469	20	C	9	0.1	3.2	0.0	0.01	42.5/5.5	25/5.2
				21	C	19	nd	1.1	-	0.01		25/5.4
	Electron transfer flavoprotein subunit B	148324000	1468	45	M	15	nd	5.1	-	0.01	28.6/4.7	27/4.7
	NADH dehydrogenase (ubiquinones), RnfG subunit	148322329	2186	46	M	10	0.9	nd	+	0.05	19.0/4.6	18/4.6
Stress response
Heat shock proteins (HSP)	60 kDa chaperonin (GroEL)	29839341	1329	22	C	*	0.9	0.3	3.2	0.05	57.5/5.0	57/4.7
				23	C	*	3.9	0.8	4.9	0.01		57/4.7
				24	C	*	3.8	nd	+	0.05		57/4.9
	70 kDa chaperone protein (DnaK)	40643393	1258	25	C	*	0.7	3.2	0.2	0.01	65.3/5.0	65/4.7
				26	C	*	0.2	2.5	0.1	0.05		65/4.7
	Peptidyl-prolyl cis-trans isomerase	148322857	0293	27	C	55	0.8	nd	+	0.01	26.7/5.0	27/4.6
DNA repair	Recombination protein RecA	148324333	1811	28	C	59	3.4	nd	+	0.05	35.2/5.6	35/5.5
Protein synthesis
Translation	Elongation factor EF-Ts	148323585	1043	29	C	*	0.2	2.0	0.1	0.02	33.0/5.3	35/5.1
				30	C	*	0.7	2.8	0.1	0.03		35/5.3
				54	M	29	nd	2.6	-			38/5.2
	Elongation factor EF-Tu	148322297	2153	47	M	9	nd	5.5	-	0.01	43.4/5.1	45/5.5
				48	M	10	nd	6.2	-	0.01		45/5.6
	Ribosomal protein S2	148323584	1042	49	M	9	nd	3.0	-	0.01	27.9/5.3	30/5.5
				50	M	13	nd	3.2	-	0.01		29/5.7
Hypothetical protein	Hypothetical protein FNP_1008	148323554	1008	51	M	6	20.0	6.6	3.0	0.01	45.5/4.9	45/4.9
	Hypothetical protein FNP_0594	148323151	0594	52	M	12	0.8	2.9	0.3	0.04	9.9/4.7	11/5.2
	Hypothetical protein FNP_0283	148322501	0238	53	M	6	6.6	16.6	0.4	0.01	18.0/5.0	10/5.0

All proteins were identified using MALDI MS/MS except those marked with ‘^’ were identified using LC-ESI MS/MS.
¹Protein accession number on National Centre for Biotechnology Information (NCBI).
²Annotated gene ID on Oralgen Database (http://www.oralgen.lanl.gov/_index.html).
³Spot number as shown in Figure 1.
⁴Protein present in either cytoplasmic (C) or membrane (M) fraction.
⁵Percentage of sequenced peptides from MS/MS analysis found to match the identified protein.
⁶The average protein density of biofilm cells (pH 8.2) compared to planktonic cells (pH 7.4) on gel images determined by PD-Quest software V. 7.2.
⁷Mean ratio of biofilm cell protein quantity against planktonic cell protein quantity; calculation based on 3–5 replicate gels.
⁸p-value^, Student t-test.
⁹Predicted molecular weight (MW) and isoelectric point (pI) of protein determined from Oralgen Databases.
¹⁰Observed MW and pI of protein determined from 2DE gels (Figure 1).
⁺Proteins that were only resolved in biofilm cells.
^-Proteins that were only resolved in planktonic cells.
nd – not detected on 2DE gels.

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ISSN: 1471-2180

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