Table 3. S. meliloti 2011 protein markers differentially overexpressed under continuous cultivation of the rhizobia at extracellular pH 7.0 compared with the expression of the same markers at pH 6.1.

Gel Code (a)	ORF	Protein name (a)	Accession number	Squence Coverage (%)	Score (MASCOT)	Ratio of intensities (pH 7.0/pH 6.1) (b)	M Value (h) (transcriptome)	Predicted/putative function	COG (i)
1	SMa2361	—	Q92XH5	43	162	ON	−3.05	Hypothetical protein.	R
2	SMc00786	DppA1	Q92RW0	18	87	2.21	−1.37	Periplasmic dipeptide transport protein precursor.	E
3	SMc01525	DppA2 (c)	Q92N26	41	201	5.46	−0.77	Periplasmic oligopeptide-binding protein precursor.	E
4		DppA2 (c)		46	156			Periplasmic oligopeptide-binding protein precursor.	E
5		DppA2 (c)		42	220			Periplasmic oligopeptide-binding protein precursor.	E
6		DppA2 (c)		41	168			Periplasmic oligopeptide-binding protein precursor.	E
7	SMb21196	OppA	Q9AKR0	25	72	SVNA	NA	ABC transporter of tetrapeptides and some tripeptides, periplasmic solute-binding protein.	E
8	SMc01946	LivK (d)	Q926C5	47	144	30.25	−2.58	Leucine- isoleucine- valine- threonine- and alanine-binding protein precursor.	E
9		LivK (d)		31	132			Leucine- isoleucine- valine- threonine- and alanine-binding protein precursor.	E
10	SMc00242	—	Q92PR4	27	87	ON	NA	Hypothetical signal peptide protein.	R
11	SMc01827	—	Q92K04	18	57	ON	−2.58	Hypothetical protein.	P
12	SMb20605	—	Q926E2	26	93	ON	−4.80	Aliphatic amidase expression-regulating protein.	E
13	SMb20745	GlnII	Q92TR3	20	58	5.00	−2.71	Glutamine synthetase II (EC 6.3.1.2).	E
14	SMb20964	—	Q9R9R2	38	101	1.44	NA	Peroxidase	P
15	SMc04023	ExoN2	Q92M48	25	110	ON	−0.40	UTP-glucose-1-phosphate uridylyltransferase (EC 2.7.7.9)	M
16	SMa1353	—	Q92YX3	27	70	4.55	−0.58	D-tagatose 3-epimerase (EC 5.3.1.-).	G
17	SMc02896	IlvE1	Q92SX8	23	59	ON	1.12	Probable branched-chain amino acid aminotransferase (EC 2.6.1.42).	E-H
18	SMc03061	AglE	Q9Z3R5	16	88	ON	0.53	Alpha-glucosides-binding periplasmic protein AglE precursor.	G
19	SMb20292	—	Q92WP7	51	143	1.51	−1.42	Hypothetical immunogenic protein.	R
20	SMa1507	—	Q92YP3	33	80	ON	−1.75	Transcriptional activator protein precursor.	R
–	SMc02356	LivA	Q92MNO	25	111	SVNA	−1.57	Putative branched chain amino acid binding periplasmic ABC transporter.	E-T
–	SMc02873	—	Q92SZ7	34	102	SVNA	−0.41	Multiple sugar-binding protein precursor.	G
–	SMc02118	AapJ	Q92Q71	48	187	SVNA	−2.82	General L-amino acid-binding periplasmic protein.	E-T
–	SMc03786	Bfr	Q92LA7	55	110	SVNA	−1.51	Bacterioferritin (BFR).	P
–	SMc02259	—	Q92S63	46	146	SVNA	−1.14	Lysine-arginine-ornithine-binding periplasmic protein precursor.	E-T
–	SMb21144	—	Q926G9	33	233	SVNA	−0.56	Putative choline uptake ABC transporter periplasmic solute-binding protein precursor.	M
–	SMc01605	—	Q92NI5	37	161	SVNA	−1.17	Putative periplasmic binding ABC transporter protein.	P
–	SMb20915	AslA1	Q92UC0	34	161	SVNA	−2.46	Putative arylsulfatase.	P
–	SMc00140	—	Q92PA9	55	125	SVNA	−1.30	Arginine-binding periplasmic protein 2 precursor.	E-T
–	SMc01642	PrbA	Q92NF1	27	97	SVNA	−1.38	Periplasmic dipeptide transportprotein precursor.	E
–	SMc00777	ThrC1	Q92RF5	38	116	SVNA	−0.45	Probable threonine synthase.	S

a: The code numbers (first column) and protein names (third column) correspond to those as in Fig. S3 and Fig. 1B, respectively. The polypeptides from each spot were identified by means of UV-MALDI-TOF MS and the peptide-mass fingerprint as described in Materials and Methods. Bold data corresponds to polypeptides detected as overexpressed both by the ImageMaster 2D™ (GE) software (using 50% volume difference compared to the spot a pH 6.1, and p test lower than 0.05 in a t-test), and by (a priori) comparative visual inspection of the 2D gels (i.e. by the comparison of spots from gels shown in Fig. 1A,B).

b: Ratios of spot intensities (spot intensity at pH 7.0 vs. spot intensity of the homolog spot at pH 6.1) as estimated by the spot volume function of the ImageMaster 2D™ software.

c–g: The same letters correspond to different isoforms and/or modifications or degradation products of a same protein detected at different positions in the 2D gel from Fig. 1B (or its replicates).

h: M values correspond to the log₂ of the relative transcriptional activity of the indicated gene at pH 7.0 compared to the corresponding activity at pH 6.1, as listed in Supplementary Table S1.

i: COG classes as previously defined elsewhere¹⁰³. Cf. consolidated COG analysis from the differential proteome and transcriptome in Fig. 2.

NA: Transcriptome data not available.

SVNA: “Spot volume not available” when using the ImageMaster sofware.

ON: Polypeptides that are present only in the cytoplasm of only rhizobia grown at pH 7.0 (absent in the homologous sample from rhizobia grown at pH 6.1).