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Table 3 Abundant proteins in the proteomes of seed-borne strains compared with nodule strains

From: Genomic studies of nitrogen-fixing rhizobial strains from Phaseolus vulgaris seeds and nodules

Proteins of R. phaseoli CCGM1
Spot no. Gene ID Protein Function COG Mascot score Sequence coverage Matched peptides Spot concentrationa Ratio
CIAT652 CCGM1
 24 RLPCCGM1_c3018 SucB Dihydrolipoamide succinyltransferase C 115 27 13/28 - 679.8 -
 41 RLPCCGM1_c0918 PdhA Pyruvate dehydrogenase (acetyl-transferring) protein subunit alpha C 71 25 9/36 503.7 1013.7 2.0
 8 RLPCCGM1_p0657 RepA Plasmid partitioning protein RepAb D 73 28 10/32 21.8 77.3 3.5
 5 RLPCCGM1_c0705 AldA Alanine dehydrogenase E 150 34 13/29 143.1 442.6 3.1
 7 RLPCCGM1_c1335 SufS Cysteine desulfurase E 72 19 7/19 14.5 46.9 3.2
 14 RLPCCGM1_p1587 FdhA Glutathione-independent formaldehyde dehydrogenase E 118 42 16/32 3.3 62.8 19.0
 25 RLPCCGM1_c1870 IlvI Acetolactate synthase 3 catalytic subunit E 73 17 8/30 - 59.4 -
 29 RLPCCGM1_c3812 ArgD Acetylornithine transaminase E 143 49 14/35 - 97.4 -
 6 RLPCCGM1_c0701 CpdB Bifunctional 2′,3′-cyclic nucleotide 2′-phosphodiesterase/3′-nucleotidase periplasmic protein F 96 18 11/27 - 46.5 -
 11 RLPCCGM1_c3249 PurH Bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase F 105 31 11/31 6.7 41.5 6.2
 2 RLPCCGM1_c2616 Pgk Phosphoglycerate kinase G 118 36 11/25 17.5 41.3 2.4
 9 RLPCCGM1_c2662 PykA Pyruvate kinase G 86 29 9/43 9.6 37.6 3.9
 34 RLPCCGM1_c1984 - Family 1 extracellular solute-binding protein G 130 45 13/35 - 127.5 -
 38 RLPCCGM1_c3763 FrcB Fructose ABC transporter substrate-binding protein G 75 25 5/8 - 156 -
 40 RLPCCGM1_c2613 Gap Glyceraldehyde 3-phosphate dehydrogenase G 67 35 8/29 - 191.9 -
 3 RLPCCGM1_c4187 Dxs 1-deoxy-D-xylulose-5-phosphate synthase H 108 26 12/24 9.7 25.8 2.7
 23 RLPCCGM1_c3273 CoaE Dephospho-CoA kinase H 57 23 5/23 - 53 -
 26 RLPCCGM1_c4205 RibA Riboflavin biosynthesis protein H 69 24 7/21 - 75 -
 36 RLPCCGM1_c3299 AhcY S-adenosyl-L-homocysteine hydrolase H 142 34 13/28 - 146.6 -
 39 RLPCCGM1_c2569 SerC Phosphoserine aminotransferase H 113 43 12/39 - 190.4 -
 17 RLPCCGM1_c3650 FadB Enoyl-CoA hydratase I 70 35 8/30 - 20.8 -
 18 RLPCCGM1_c3059 - Oxidoreductase I 87 44 12/55 - 21 -
 35 RLPCCGM1_c3416 FabB 3-oxoacyl-ACP synthase I 89 33 12/49 - 127.6 -
 1 RLPCCGM1_c1345 TyrS Tyrosyl-tRNA synthetase J 101 27 12/37 20.7 44 2.1
 15 RLPCCGM1_c2760 - Acetyltransferase J 40 37 10/44 - 19.1 -
 13 RLPCCGM1_c1935 MurD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase M 139 31 13/26 - 15.2 -
 33 RLPCCGM1_c2681 ExoN UTP--glucose-1-phosphate uridylyltransferase M 162 51 14/40 - 122.2 -
 10 RLPCCGM1_c3962 FlaC Flagellin C protein N 80 32 8/29 29.6 178.8 6.0
 21 RLPCCGM1_p1412 HtpG Heat shock protein 90 O 103 45 13/35 - 31.3 -
 22 RLPCCGM1_c1051 PpiA Peptidyl-prolyl cis-trans isomerase A O 55 30 4/29 - 38.1 -
 31 RLPCCGM1_p1186 - Glutathione S-transferase YghU O 60 30 6/23 - 113.8 -
 4 RLPCCGM1_p1923 KatG Catalase P 89 23 12/35 26.8 81.6 3.0
 16 RLPCCGM1_c0709 SseA Thiosulfate sulfurtransferase P 138 55 12/34 - 20.7 -
 27 RLPCCGM1_c2174 - Methanol dehydrogenase regulator MoxR-like protein R 108 52 14/48 - 76.8 -
 28 RLPCCGM1_c3573 - Oxidoreductase R 80 37 12/48 - 76.8 -
 30 RLPCCGM1_c2292 IdhA Myo-inositol 2-dehydrogenase R 87 44 12/55 - 102.8 -
 19 RLPCCGM1_c4033 - Isoprenylcysteine carboxyl methyltransferase S 62 35 6/54 - 21.8 -
 37 RLPCCGM1_c2285 - Hypothetical protein S 76 42 9/39 - 153.1 -
 12 RLPCCGM1_p0713 - Sensory box/GGDEF family protein T 54 10 9/29 32.6 314.2 9.6
 20 RLPCCGM1_p2036 CpaC Pilus assembly protein U 135 32 12/47 - 25.2 -
 32 RLPCCGM1_p1459 - Hypothetical protein - 67 22 6/16 23 119.3 5.2
Proteins of R. phaseoli CIAT652
Spot no. Gene ID Protein Function COG Mascot score Sequence coverage Matched peptides Spot concentrationa Ratio
CIAT652 CCGM1
 47 RHECIAT_PC0000173 - Putative oxidoreductase C 132 21 15/27 6.5 - -
 62 RHECIAT_CH0002031 PdhA2 Pyruvate dehydrogenase subunit beta C 114 37 18/39 51.5 - -
 67 RHECIAT_CH0004343 - Aldehyde dehydrogenase C 52 17 6/31 86.1 - -
 69 RHECIAT_CH0001680 NuoE1 NADH dehydrogenase subunit E C 147 51 17/45 119.3 - -
 75 RHECIAT_CH0000039 PckA Phosphoenolpyruvate carboxykinase C 99 33 13/38 400.7 - -
 76 RHECIAT_CH0002032 PdhC Dihydrolipoamide S-acetyltransferase C 101 33 12/25 909.1 - -
 49 RHECIAT_PC0000423 - Putative oligopeptide ABC transporter substrate-binding protein E 56 8 7/23 7.6 2.9 2.6
 50 RHECIAT_CH0003659 PotD Spermidine/putrescine ABC transporter substrate-binding protein E 60 25 7/24 243.5 23.9 10.2
 60 RHECIAT_CH0002150 - Peptide ABC transporter substrate-binding protein E 218 44 22/38 39.9 - -
 72 RHECIAT_CH0001992 MetC Cystathionine beta-lyase E 81 38 9/22 190.4 - -
 73 RHECIAT_CH0000879 GuaB Inosine 5′-monophosphate dehydrogenase F 192 44 21/47 210.1 - -
 51 RHECIAT_CH0003979 LacZ2 Beta-D-galactosidase G 129 18 11/14 16.8 - -
 55 RHECIAT_CH0000213 GpmA Phosphoglyceromutase G 214 84 18/52 23.7 - -
 61 RHECIAT_CH0003393 XylF Xylose ABC transporter substrate-binding protein G 113 32 10/41 46.7 - -
 64 RHECIAT_CH0003248 - Omega amino acid--pyruvate transaminase H 147 47 14/26 67.8 - -
 42 RHECIAT_CH0001955 AccC Acetyl-CoA carboxylase biotin carboxylase subunit I 77 33 9/26 795.2 364.4 2.2
 53 RHECIAT_CH0003282 BdhA D-beta-hydroxybutyrate dehydrogenase I 81 28 6/8 19.3 - -
 48 RHECIAT_PA0000110 FusAa Elongation factor G J 55 16 8/27 6.8 - -
 54 RHECIAT_CH0004024 PrfA Peptide chain release factor 1 J 119 41 14/40 19.9 - -
 58 RHECIAT_CH0001897 ValS Valyl-tRNA synthetase J 85 12 8/12 26.5 - -
 59 RHECIAT_CH0002285 ThrS Threonyl-tRNA synthetase J 124 23 16/34 31.3 - -
 65 RHECIAT_CH0000980 GlyS Glycyl-tRNA synthetase subunit beta J 192 38 23/37 71.6 - -
 66 RHECIAT_CH0002242 MetS Methionyl-tRNA synthetase J 105 26 10/22 72.1 - -
 57 RHECIAT_CH0001733 - Nucleoside-diphosphate-sugar epimerase M 57 19 5/22 26.4 - -
 74 RHECIAT_CH0003488 NoeJ Mannose-1-phosphate guanylyltransferase (GDP) protein M 145 48 18/52 243.4 - -
 46 RHECIAT_CH0001879 - Peroxidase O 67 35 8/29 119.2 23.7 5.0
 52 RHECIAT_CH0001895 Pcm1 Protein-L-isoaspartate(D-aspartate) O-methyltransferase O 93 38 6/16 19 - -
 63 RHECIAT_CH0002260 PpiD1 Peptidyl-prolyl cis-trans isomerase D signal peptide protein O 57 16 6/14 67.7 - -
 70 RHECIAT_CH0004147 - Nitrate/sulfonate/bicarbonate ABC transporter substrate-binding protein P 106 42 11/29 127.6 - -
 71 RHECIAT_CH0002820 - Ferrichrome ABC transporter substrate-binding protein P 135 52 12/23 146.6 - -
 56 RHECIAT_PC0000681 VbsO L-lysine 6-monooxygenase (NADPH) protein Q 105 32 11/23 25.5 - -
 43 RHECIAT_CH0004212 - ABC transporter substrate-binding protein R 99 36 9/29 360.8 - -
 44 RHECIAT_CH0004405 - Hypothetical protein S 89 33 8/38 253.5 111.4 2.3
 68 RHECIAT_CH0002473 - Hypothetical protein S 109 31 14/38 94.5 - -
 45 RHECIAT_CH0004199 TypA GTP-binding protein TypA/BipA T 151 34 21/42 215.3 - -
Proteins of S. americanum CCGM7
Spot no. Gene ID Protein Function COG Mascot score Sequence coverage Matched peptides Spot concentrationa Ratio
CFNEI73 CCGM7
 2 SAMCCGM7_Ch3507 AcnA Aconitate hydratase C 69 17 11/31 - 185.6 -
 3 SAMCCGM7_Ch3374 SucB Dihydrolipoamide succinyltransferase C 99 25 11/21 - 127 -
 4 SAMCCGM7_Ch1973 FumC Fumarate hydratase class II C 100 21 10/20 - 105.8 -
 8 SAMCCGM7_pC0039 TctC Tricarboxylate transport protein C 64 30 6/11 - 45.4 -
 11 SAMCCGM7_Ch0047 PckA Phosphoenolpyruvate carboxykinase C 88 20 11/30 6.5 143.9 22.1
 12 SAMCCGM7_Ch2624 Ald Aldehyde dehydrogenase C 65 17 7/18 - 17.3 -
 20 SAMCCGM7_Ch3356 AtpD ATP synthase subunit beta C 111 38 13/34 41.4 407.9 9.9
 28 SAMCCGM7_Ch1381 NuoG NADH-quinone oxidoreductase subunit G C 111 23 13/27 9.3 52.4 5.6
 29 SAMCCGM7_Ch2523 AcoD Acetaldehyde dehydrogenase 2 C 133 27 14/33 65.9 259.8 3.9
 31 SAMCCGM7_Ch3358 AtpA ATP synthase subunit alpha C 97 29 14/41 78.5 290.4 3.7
 16 SAMCCGM7_Ch1849 CarB Carbamoyl-phosphate synthase large subunit E 74 10 11/20 7.5 103.4 13.8
 17 SAMCCGM7_Ch2552 LeuA 2-isopropylmalate synthase E 118 27 13/23 - 11.4 -
 18 SAMCCGM7_pA0276 - Homoserine dehydrogenase E 72 22 9/28 - 11.2 -
 26 SAMCCGM7_Ch1267 GlyA Pyridoxal-phosphate-dependent serine hydroxymethyltransferase E 85 21 9/22 11.9 75.8 6.4
 19 SAMCCGM7_Ch3100 - 5′-nucleotidase F 122 22 12/19 11.1 120.3 10.8
 35 SAMCCGM7_Ch3605 PurH Bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase F 80 23 10/31 140.6 278.9 2.0
 24 SAMCCGM7_Ch3149 Pgm Phosphoglucomutase Pgm G 61 12 5/7 6.4 - -
 30 SAMCCGM7_Ch2630 ChvE Multiple sugar-binding periplasmic receptor G 55 24 6/25 34.2 127.5 3.7
 32 SAMCCGM7_Ch3057 FbaB Fructose-bisphosphate aldolase G 70 32 9/34 27.2 95.8 3.5
 33 SAMCCGM7_Ch3054 Gap Glyceraldehyde-3-phosphate dehydrogenase G 80 29 7/15 33.7 109.3 3.2
 21 SAMCCGM7_Ch0041 AhcY S-adenosyl-L-homocysteine hydrolase H 81 26 10/29 21.2 169 8.0
 14 SAMCCGM7_Ch1196 FabF 3-oxoacyl-ACP synthase I 66 16 7/17 - 16.8 -
 1 SAMCCGM7_Ch2527 RplY 50S ribosomal protein L25 J 199 72 17/32 - 498.9 -
 7 SAMCCGM7_Ch1428 GatB Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B J 72 18 7/19 - 59.6 -
 23 SAMCCGM7_Ch0231 Pnp Polyribonucleotide nucleotidyltransferase J 122 29 17/38 35.5 270.8 7.6
 9 SAMCCGM7_Ch0831 GroEL Chaperonin O 95 28 14/36 12.8 380.2 29.7
 25 SAMCCGM7_pC0433 ClpV Protease O 63 15 10/32 - 7 -
 5 SAMCCGM7_Ch0999 CysN Sulfate adenylyltransferase subunit 1 P 121 45 15/44 - 65.2 -
 13 SAMCCGM7_pC1570 - Iron ABC transport system, solute-binding protein P 89 19 17/11 - 17.1 -
 22 SAMCCGM7_pC1145 - Ferrichrome-iron receptor P 149 19 13/16 - 7.8 -
 27 SAMCCGM7_pC1571 - Iron ABC transport system, solute-binding protein P 105 26 11/23 20.6 123.5 6.0
 34 SAMCCGM7_pC1766 Fct Ferrichrysobactin receptor P 174 35 18/31 2.6 7.4 2.8
 6 SAMCCGM7_Ch2381 - ABC transporter ATP-binding protein R 126 31 17/30 - 60.4 -
 10 SAMCCGM7_pA0100 VirB10 Type IV secretion system protein U 150 32 12/19 - 23.8 -
 15 SAMCCGM7_pC0430 ImpC Type VI secretion system protein U 96 23 10/21 14 206 14.7
Proteins of S. americanum CFNEI73
Spot no. Gene ID Protein Function COG Mascot score Sequence coverage Mached peptides Spot concentrationa Ratio
CFNEI73 CCGM7
 37 SAMCFNEI73_Ch3492 LpdA Dihydrolipoamide dehydrogenase C 134 37 13/23 48.2 - -
 44 SAMCFNEI73_Ch3194 - Hypothetical protein C 93 44 9/22 21.6 - -
 47 SAMCFNEI73_Ch0872 AtpF ATP synthase subunit B’ C 94 35 7/18 51 3.4 15.0
 53 SAMCFNEI73_Ch1106 - Electron transfer flavoprotein-ubiquinone oxidoreductase C 105 24 11/22 10.4 - -
 54 SAMCFNEI73_Ch0062 GlcB Malate synthase G C 156 27 14/19 15.1 1.7 8.9
 57 SAMCFNEI73_Ch0755 MmsA Methylmalonate-semialdehyde dehydrogenase C 132 33 17/29 66.6 12.8 5.2
 70 SAMCFNEI73_Ch1382 NuoD NADH-quinone oxidoreductase subunit D C 135 42 20/54 45.7 21 2.2
 72 SAMCFNEI73_Ch3505 SdhA Succinate dehydrogenase flavoprotein subunit C 96 20 10/15 42.5 19.9 2.1
 36 SAMCFNEI73_pC0436 FliY Cystine-binding periplasmic protein E 63 26 6/17 63.4 - -
 43 SAMCFNEI73_Ch1350 ArgC N-acetyl-gamma-glutamyl-phosphate reductase E 66 29 7/27 23.5 - -
 49 SAMCFNEI73_pC0934 HutU Urocanate hydratase E 93 21 13/34 13.2 - -
 51 SAMCFNEI73_Ch2492 IlvB Acetolactate synthase large subunit E 82 14 7/10 12.1 - -
 52 SAMCFNEI73_Ch0061 - Hydantoinase/oxoprolinase family protein E 71 17 7/16 10.5 - -
 59 SAMCFNEI73_Ch3399 MetH Methionine synthase E 208 25 24/29 4.6 - -
 63 SAMCFNEI73_Ch0442 DapD 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase E 55 20 7/42 38.3 10.6 3.6
 65 SAMCFNEI73_Ch2207 MetH2 Methionine synthase E 79 28 8/37 25.4 7.9 3.2
 69 SAMCFNEI73_Ch0208 - Extracellular solute-binding protein, family 5 E 74 21 12/47 30 11 2.7
 71 SAMCFNEI73_Ch1748 - Peptide ABC transporter substrate-binding protein E 93 24 13/34 32.5 15.1 2.2
 62 SAMCFNEI73_Ch3182 Pgk Phosphoglycerate kinase G 113 41 12/26 146.7 39.3 3.7
 66 SAMCFNEI73_Ch3273 GlgX Glycogen debranching protein G 131 23 12/18 6.7 2.1 3.2
 58 SAMCFNEI73_pC1978 ThiC Phosphomethylpyrimidine synthase H 113 33 17/37 23.9 5 4.8
 64 SAMCFNEI73_Ch1162 NadB L-aspartate oxidase H 156 31 15/23 33.7 9.7 3.5
 48 SAMCFNEI73_pC0946 MmgC Acyl-CoA dehydrogenase I 83 32 13/40 13.9 - -
 46 SAMCFNEI73_Ch1475 FusA Elongation factor G J 93 22 12/24 15.8 - -
 42 SAMCFNEI73_Ch1028 - ATPase component BioM of energizing module of biotin ECF transporter L 136 40 15/36 23.8 - -
 39 SAMCFNEI73_pC1683 RkpQ N-acylneuraminate-9-phosphate synthase M 202 55 16/39 25.6 - -
 50 SAMCFNEI73_Ch1571 KdsA 2-dehydro-3-deoxyphosphooctonate aldolase M 106 43 16/54 12.4 - -
 67 SAMCFNEI73_Ch2467 MurE UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase M 166 34 13/19 26.3 8.7 3.0
 40 SAMCFNEI73_Ch1644 Pcm Protein-L-isoaspartate O-methyltransferase O 140 57 11/20 24.9 - -
 61 SAMCFNEI73_Ch1368 LonA Endopeptidase La O 62 12 9/20 55 14.3 3.8
 68 SAMCFNEI73_pC1783 - Phosphate ABC transporter substrate-binding protein P 78 27 7/24 104.4 36.3 2.9
 45 SAMCFNEI73_Ch3296 - Cobalamin synthesis protein/P47K family protein R 69 25 9/37 17.9 - -
 55 SAMCFNEI73_Ch3670 - Hypothetical protein R 72 16 8/19 8.2 - -
 38 SAMCFNEI73_pB0529 TraI Autoinducer synthesis protein T 157 75 15/39 30.5 - -
 60 SAMCFNEI73_Ch1589 NtrC Nitrogen assimilation regulatory protein T 63 19 7/20 26.2 6 4.4
 56 SAMCFNEI73_pB0525 TrbE Conjugal transfer protein U 177 27 20/32 7.9 - -
 41 SAMCFNEI73_pC1268 - Peroxiredoxin V 95 37 8/22 24.8 - -
  1. aIn OD units. No value means the spot concentration was under the level of detection
  2. For COG class definition, see legend of Fig. 3