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. 2016 Jul 11;6:29278. doi: 10.1038/srep29278

Table 2. S. meliloti 2011 protein markers differentially overexpressed under continuous cultivation of the rhizobia at extracellular pH 6.1 compared with the expression of the same markers at pH 7.0.

Gel Code (a) ORF Protein name (a) Accession number Sequence coverage (%) Score (MASCOT) Ratio of intensities (pH 6.1/pH 7.0) (b) M Value (h) (transcriptome) Predicted/putative function COG (i)
1 SMc02365 DegP1 (c) Q52894 41 154 4.80 1.97 Probable serine protease do-like precursor (EC 3.4.21.-). O
2 SMc02365 DegP1 (c) 34 148
3 SMc02365 DegP1 (c) 38 181
4 SMc02050 Tig (d) Q92Q12 46 181 1.49 1.55 Trigger factor (TF). O
5 SMc02050 Tig (d) 47 193
6 SMc02782 GyrB (e) Q92TE4 24 136 ON 0.59 DNA gyrase subunit B (EC 5.99.1.3). L
7 SMc02782 GyrB (e) 10 81
8 SMc03157 – Q92LX5 39 155 2.78 1.23 Outer membrane lipoprotein 3 precursor (PLP3). P
9 SMb20724 – Q92TR9 30 84 2.00 0.65 Hypothetical protein. S
10 SMc01312 FusA (f) Q92QH2 25 116 1.43 0.61 Elongation factor G (EF-G). J
11 SMc01312 FusA (f) 41 192
12 SMc01312 FusA (f) 17 109
13 SMc00324 Pnp (g) Q92SW0 35 180 1.37 1.97 Polyribonucleotide nucleotidyltransferase (EC 2.7.7.8). J
14 SMc00324 Pnp (g) 18 111    
15 SMc00324 Pnp (g) 20 129    
16 SMc00324 Pnp (g) 30 210 4.98 5.36
17 SMc00324 Pnp (g) 20 111 4.98 5.40
18 SMc03978 Tkt2 Q92M82 18 118 2.25 1.11 Transketolase (EC 2.2.1.1). G
19 SMc00043 SodB Q9XD74 48 82 1.60 0.28 Superoxide dismutase [Mn] (EC 1.15.1.1). P
20 SMc02560 ChvI P50350 32 68 1.86 1.23 Transcriptional regulatory protein ChvI. T-K
21 SMc01126 Tme O30808 27 132 2.28 −0.27 NADP-dependent malic enzyme (EC 1.1.1.40). C
22 SMc00861 – Q92KK7 14 62 2.00 0.40 Putative signal peptide protein. R
23 SMc01326 TufB Q925Y6 30 1,82 1.82 0.88 Elongation factor Tu (EF-Tu). J
24 SMc02692 RplY Q92N68 55 200 1.73 1.87 Probable 50S ribosomal protein L25. J
25 SMc00565 RplI Q92QZ9 29 68 1.74 NA Probable 50S ribosomal protein L9. J
26 SMc01333 PrfB Q92QJ2 16 59 3.47 1.21 Peptide chain release factor 2 (RF-2). J
27 SMc00357 Efp Q92ST6 33 65 1.90 0.40 Elongation factor P (EF-P). J
28 SMc01917 NuoE1 P56909 29 80 1.59 0.97 NADH-quinone oxidoreductase chain E 1 (EC 1.6.99.5). C
29 SMc01845 – Q92NK3 18 86 1.51 1.23 Membrane-bound lytic mureintransglycosylase B precursor (EC 3.2.1.-). M
– SMc01285 RpoA Q925Z2 31 93 SVNA 0.55 DNA-directed RNA polymerase alpha chain (EC 2.7.7.6). K
– SMc01318 RplL Q92QH8 66 88 SVNA 0.47 50S ribosomal protein L7/L12. J
– SMc00335 RpsA P14129 43 233 SVNA 1.86 30S ribosomal protein S1. J
– SMc01934 ProS Q92QN2 53 168 SVNA 0.77 Putativeprolyl-tRNAsynthetase (EC 6.1.1.15). J
– SMc00480 Icd Q92PG6 37 148 SVNA 0.49 Isocitrate dehydrogenase [NADP] (EC 1.1.1.42). C
– SMc01270 AdhC1 Q92QD7 37 144 SVNA 0.48 Alcohol dehydrogenase class III (EC 1.1.1.1). C
– SMc03826 ArgG Q92L73 46 189 1.24 1.46 Argininosuccinatesynthase (EC 6.3.4.5). E
– SMc00643 PurA Q92MA5 40 175 SVNA 1 Adenylosuccinatesynthetase (EC 6.3.4.4). F
– SMc02064 SerS Q92Q22 41 150 SVNA 0.48 Seryl-tRNAsynthetase (EC 6.1.1.11). J
– SMc00641 SerA Q92MA3 25 86 SVNA 0.71 D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) (PGDH). E
– SMc01192 MetS Q92PX0 28 109 SVNA 0.26 Methionyl-tRNAsynthetase (EC 6.1.1.10). J
– SMc04461 TolB Q926C2 42 162 SVNA 0.75 TolB protein precursor. U
– SMc02686 PrsA Q92N73 24 55 SVNA NA Probable ribose-phosphate pyrophosphokinase. F
– SMc00153 — Q92PB9 56 95 SVNA 1.80 Probable ATP synthase delta chain (EC 3.6.3.14). S
– SMc00595 NdK Q92QX9 25 82 SVNA 0.88 Nucleoside diphosphatekinase (EC 2.7.4.6). F
– SMc01288 Adk Q93FE6 55 124 SVNA NA Probable adenylatekinase. F
– SMc03242 TypA Q92LG8 27 140 SVNA 3.39 GTP-binding protein typA/BipA. T
– SMc03925 Pgm Q92M12 31 81 SVNA 1.39 Phosphoglucomutase (EC 5.4.2.2). G
– SMc02100 Tsf Q92Q54 62 174 SVNA −0.19 Elongation factor Ts (EF-Ts). J
– SMc02163 Pgi Q92SC4 28 101 SVNA 1.43 Glucose-6-phosphate isomerase (EC 5.3.1.9). G
– SMc02495 Tal Q92LK3 38 80 SVNA 1.70 Probable transaldolase (EC 2.2.1.2). G
– SMc00040 — Q92RC9 27 67 SVNA 1.04 Hypothetical protein. O
– SMc01233 Ssb P56898 64 189 SVNA NA Probable single-strand binding protein. L
– SMc01345 AccC Q92QK1 30 117 SVNA 0.25 Biotin carboxylase (EC 6.3.4.14). I

a: The code numbers (first column) and protein names (third column) correspond to those as in Fig. S2 and Fig. 1A, 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. The 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 7.0, 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 6.1 vs. spot intensity of the homolog spot at pH 7.0) 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. 1A (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 rhizobia grown at pH 6.1 (absent in the homologous sample from rhizobia grown at pH 7.0).