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. 2006 Aug;173(4):1851–1869. doi: 10.1534/genetics.105.049619

TABLE 1.

Identity of protein spots that differ between the ancestor and evolved clones and two protein spots shown as internal standards for visualization

Protein spot no.a Protein (gene)b Functional groupc Expression lower in:d Quantitatione
M1 AhpC (ahpC) Cell processes, protection 1.060 ± 0.065
0.991 ± 0.034
M2 GapA (gapA) Metabolism, energy metabolism 0.999 ± 0.011
0.993 ± 0.079
1 CirA (cirA)* Transport, outer membrane Evol 0.656 ± 0.011
0.678 ± 0.052
2 FadL (fadL)* Transport, outer membrane Anc 1.956 ± 0.080
2.800 ± 0.195
3 LamB (lamB)* Transport, outer membrane Evol(0) OFF
OFF
4 ArtJ (artJ) Transport, periplasmic space Evol 0.504 ± 0.038
0.536 ± 0.037
5 GlnH (glnH) Transport, periplasmic space Evol(0) OFF
OFF
6–7 MalE (malE)* Transport, periplasmic space Evol(0) OFF
OFF
8–9 MetQ (metQ) Transport, periplasmic space Evol(0) OFF
OFF
10 MglB (mglB)* Transport, periplasmic space Evol 0.736 ± 0.007
0.554 ± 0.007
11 MglB (mglB)* Transport, periplasmic space Evol 0.599 ± 0.036
0.451 ± 0.010
12 ModA (modA)* Transport, periplasmic space Evol 0.433 ± 0.008
0.408 ± 0.034
13 RbsB (rbsB)* Transport, periplasmic space Evol(0) OFF
OFF
14 TolB (tolB) Transport, periplasmic space Evol 0.165 ± 0.020
0.139 ± 0.031
15 TolB (tolB) Transport, periplasmic space Evol 0.206 ± 0.008
0.258 ± 0.044
16 ZnuA (znuA) Transport, periplasmic space Anc(0) ON
ON
17 AroG (aroG) Metabolism, amino-acid biosynthesis Evol 0.127 ± 0.008
0.203 ± 0.014
18 IlvB (ilvB)** Metabolism, amino-acid biosynthesis Anc(0) ON
ON
19 LeuA (leuA)* Metabolism, amino-acid biosynthesis Anc(0) ON
ON
20 LeuA (leuA)* Metabolism, amino-acid biosynthesis Anc(0) ON
ON
21 SerC (serC)* Metabolism, amino-acid biosynthesis Evol 0.320 ± 0.008
0.380 ± 0.012
22 AceB (aceB) Metabolism, central intermediary metabolism Anc 4.959 ± 0.186
6.017 ± 0.285
23 GpmA (gpmA) Metabolism, central intermediary metabolism Evol 0.403 ± 0.071
0.344 ± 0.013
24 NfnB (nfnB) Metabolism, central intermediary metabolism Anc(0) ON
ON
25 ATPF (atpF) Metabolism, energy metabolism Evol 0.461 ± 0.002
0.524 ± 0.025
26 ATPF (atpF) Metabolism, energy metabolism Evol 0.409 ± 0.064
0.492 ± 0.014
27 Mdh (mdh)* Metabolism, energy metabolism Evol 0.532 ± 0.047
0.545 ± 0.024
28 SucC (sucC)* Metabolism, energy metabolism Evol 0.631 ± 0.005
0.742 ± 0.022
29 SucD (sucD)* Metabolism, energy metabolism Evol 0.463 ± 0.014
0.484 ± 0.029
30–31 PflB (pflB)* Metabolism, energy metabolism Evol(0) OFF
OFF
32 FabI (fabI) Metabolism, fatty acid biosynthesis Evol 0.497 ± 0.012
0.424 ± 0.026
33 FklB (fklB) Information transfer, chaperone, folding Evol 0.374 ± 0.017
0.333 ± 0.012
34 GroEL (groL)** Information transfer, chaperone, folding Evol 0.300 ± 0.037
0.399 ± 0.040
35 HtpG (htpG) Information transfer, chaperone, folding Evol 0.447 ± 0.026
0.454 ± 0.044
36 Aat (aat) Information transfer, protein degradation Evol 0.555 ± 0.038
0.564 ± 0.026
37 HslU (hslU) Information transfer, protein degradation Evol 0.468 ± 0.063
0.414 ± 0.020
38 Fur (fur)* Information transfer, transcription Evol(0) OFF
OFF
39 AsnS (asnS)** Information transfer, translation Evol 0.556 ± 0.043
0.653 ± 0.019
40 AsnS (asnS)** Information transfer, translation Evol 0.505 ± 0.032
0.379 ± 0.029
41 GlyS (glyS) Information transfer, translation Evol 0.216 ± 0.039
0.238 ± 0.024
42 GlyS (glyS) Information transfer, translation Evol 0.200 ± 0.019
0.157 ± 0.021
43 Mannosyl-transferasef Cell processes Anc(0) ON
ON
44 MinD (minD) Cell processes, cell division Evol 0.218 ± 0.029
0.292 ± 0.017
45 MinD (minD) Cell processes, cell division Evol 0.272 ± 0.028
0.255 ± 0.019
46 GTP-dependent nucleic acid- binding proteinf GTP-binding protein Evol 0.739 ± 0.043
0.731 ± 0.061
47 BipA (bipA) GTP-binding protein, elongation factor Evol 0.543 ± 0.029
0.442 ± 0.031
48 BipA (bipA) GTP-binding protein, elongation factor Evol 0.542 ± 0.044
0.583 ± 0.040
49 YcdO (ycdO) Hypothetical, unknown Evol 0.559 ± 0.068
0.633 ± 0.027
50 OppA (oppA) Transport, periplasmic space Ara + 1 0.315 ± 0.006
0.975 ± 0.090
51 ArgT (argT) Metabolism, amino-acid biosynthesis Ancg 2.204 ± 0.322
1.054 ± 0.037
52 MetE (metE) Metabolism, amino-acid biosynthesis Ara + 1 0.544 ± 0.048
0.983 ± 0.055
53 MetE (metE) Metabolism, amino-acid biosynthesis Ara + 1 0.409 ± 0.040
0.950 ± 0.039
54 GlpK (glpK)* Metabolism, carbon compound utilization Ara − 1 1.066 ± 0.137
0.256 ± 0.027
55 TktA (tktA) Metabolism, central intermediary metabolism Ara + 1 0.559 ± 0.049
0.996 ± 0.045
56 PykF (pykF) Metabolism, energy metabolism Ara − 1(0) 1.112 ± 0.041
OFF
57 GuaA (guaA)* Metabolism, nucleotide biosynthesis Ara − 1 0.996 ± 0.096
0.274 ± 0.015
58 PurH (purH) Metabolism, nucleotide biosynthesis Ara + 1 0.615 ± 0.060
0.964 ± 0.120
59 EF-Tu (tufAB)** Information transfer, translation Ancg 2.476 ± 0.163
—h
60 SodB (sodB)* Cell processes, adaptation to stress Ara + 1 0.370 ± 0.030
1.000 ± 0.039
a

The protein spots M1 and M2 show similar intensities across all genotypes and serve as internal standards for visualization only (Figure 1). Protein spots 1–49 show significant and parallel changes in the two independently evolved clones compared to their ancestor (○ in Figure 1). Protein spots 50–60 show significant changes in only one of the two evolved clones (▵ and ▿ in Figure 1). Some proteins were identified in two different spots; this pattern corresponds to post-translational modifications or to degradation products (in each case, both protein spots showed the same changes in the evolved clones).

b

Regulation by cAMP–CRP and ppGpp is indicated by “*” and “**,” respectively, for the functionally characterized genes (Cashel et al. 1996 and Salgado et al. 2004 for the table; Man et al. 1997 for serC; Zhang et al. 2005 for sodB; Zheng et al. 2004 for modA, kbl, and leuA; Traxler et al. 2006 for asnS).

c

Functional groupings of the proteins are shown according to the data from GenProtEC (http://genprotec.mbl.edu).

d

Anc, expression lower in the ancestor clone; Anc(0), proteins absent from the ancestor but appearing in both evolved clones; Evol, expression lower in both evolved clones; Evol(0), proteins disappearing in both evolved clones; Ara + 1, expression lower than in the ancestor only in the Ara + 1 evolved clone; Ara − 1, expression lower than in the ancestor only in the Ara − 1 evolved clone; Ara − 1(0), protein spot disappearing in the Ara-1 evolved clone.

e

Quantitative gel analysis was performed using the Melanie II software (Genebio). For every spot, the protein expression of each evolved clone was standardized using the ancestral strain as a reference, after first standardizing for total protein volume over all spots (see materials and methods). For example, a value of 2.0 indicates that the relative abundance of a particular protein spot is twice as high in an evolved clone as in the ancestor, whereas a value of 0.5 indicates that the relative abundance of a protein in the evolved clone is only half that measured in the ancestor. The upper and lower entries for each protein are relative abundances measured in the Ara + 1 and Ara − 1 evolved clones, respectively. Mean values are shown along with standard deviations based on the three independent sets of gels. OFF, protein spots absent in the evolved clones, but present in the ancestor. ON, protein spots absent in the ancestor, but present in the evolved clones.

f

Based on protein sequence comparisons. A gene name could not be assigned.

g

ArgT and EF-Tu are significantly higher only in the Ara + 1 evolved clone.

h

The Melanie II software was unable to quantify the EF-Tu protein spot in the Ara − 1 evolved clone because the spot was fuzzy and precise delineation was impossible for two of the three replicate gels.