Table I. Protein induction in Mtvector and MtROP9i transgenic roots after microbial infections.

Proteins are sorted beginning with the proteins of highest relative in-gel intensities, followed by those with steadily decreasing intensities. Protein induction is compared with that of infected Mtwt roots as investigated previously (Schenkluhn et al., 2010).

Spot No.a	TC No.b	Best Matching Gene Productc	Molecular Weightd	pId	Regulation in Mtwt Rootse	Protein Regulationf
						Regulation in Mtvector/MtROP9i	3 hpi	24 hpi
Protein induction in Mtvector transgenic roots
10	132039	Class 10 -1 PR protein	16.8	4.3	Ae	Mtvector (Ae, Gi)	3.24 (0.3) Ae	3.82 (0.4)
							2.33 (0.2) Gi	1.63 (0.1)
71	129282	Peroxidase precursor	63.5	4.1	Ae	Mtvector (Ae, Sm, Gi)	3.48 (0.2) Ae	2.5 (0.3)
							2.42 (0.4) Sm	2.26 (0.2)
2.37 (0.3) Gi	2.13 (0.2)
72	129282	Peroxidase precursor	64.0	4.1	Ae	Mtvector (Ae, Sm, Gi)	3.37 (0.4) Ae	2.23 (0.3)
							1.82 (0.2) Sm	2.46 (0.2)
2.14 (0.2) Gi	2.31 (0.3)
22	127667	Peroxidase	26.5	6.8	Sm, Sm + Ae	Mtvector (Sm, Gi, Ae)	2.82 (0.2) Sm	2.50 (0.3)
							2.44 (0.2) Gi	2.41 (0.1)
1.77 (0.4) Ae	2.04 (0.3)
48	132014	Proteasome subunit β type-1	32.0	7.9	Gi, Gi + Ae	Mtvector (Sm, Gi, Ae)	2.75 (0.3) Sm	2.47 (0.4)
							2.32 (0.2) Gi	2.36 (0.3)
2.19 (0.2) Ae	1.67 (0.3)
26	130855	Proteasome subunit α type-5	28.4	4.4	Ae	Mtvector (Ae, Gi)	2.24 (0.3) Ae	3.42 (0.2)
							2.25 (0.3) Gi	2.33 (0.4)
39	116053	Proteasome subunit α type	31.5	5.0	Ae	Mtvector (Ae)	2.4 (0.3) Ae	2.67 (0.2)
4	130380	Superoxide dismutase (copper-zinc)	16.0	5.4	Ae, Sm + Ae	Mtvector (Ae, Sm, Gi)	2.27 (0.4) Ae	2.34 (0.2)
							1.80 (0.2) Sm	1.76 (0.3)
1.54 (0.2) Gi	1.50 (0.1)
49	119714	Guanine nucleotide-binding protein (β)	36.0	7.0	Ae	Mtvector (Ae, Sm, Gi)	2.41 (0.2) Ae	2.38 (0.2)
							1.62 (0.3) Sm	1.56 (0.2)
1.49 (0.1) Gi	1.57 (0.3)
51	127667	Peroxidase	39.0	10.4	Ae, Gi + Ae	Mtvector (Ae, Gi)	2.48 (0.3) Ae	2.12 (0.2)
							2.06 (0.5) Gi	1.96 (0.3)
5	116948	Putative ripening-related protein	17.5	5.6	Ae, Con, Sm + Ae	Mtvector (Sm, Ae)	2.33 (0.1) Sm	1.84 (0.3)
							1.56 (0.3) Ae	1.67 (0.1)
59	116827	Glyceraldehyde 3-phosphate dehydrogenase	45.4	7.3	Ae	Mtvector (Sm, Gi, Ae)	2.45 (0.2) Sm	1.55 (0.4)
							1.72 (0.2) Gi	1.86 (0.3)
30	114090	Ran-binding protein	32.0	4.4	Sm	Mtvector (Sm)	1.54 (0.3) Sm	2.37 (0.3)
2	128617	Profilin-1	14.8	4.5	Ae, Sm + Ae	Mtvector (Gi)	1.75 (0.2) Gi	1.77 (0.3)
14	136600	Putative ripening-related protein	18.0	5.4	Ae, Gi	Mtvector (Gi)	1.65 (0.3) Gi	1.54 (0.1)
23	118388	Fru-bisP aldolase	29.5	7.4	Ae	Mtvector (Sm)	1.59 (0.3) Sm	1.81 (0.1)
29	139326	Translational elongation factor 1, subunit B	32.5	4.3	Sm	Mtvector (Sm)	1.64 (0.2) Sm	1.45 (0.4)
36	124173	Short-chain dehydrogenase/reductase	30.0	6.6	Ae	Mtvector (Sm)	1.52 (0.3) Sm	1.51 (0.2)
44	139960	Stromal ascorbate peroxidase	37.5	6.1	Sm, Sm + Ae	Mtvector (Ae)	1.69 (0.3) Ae	1.48 (0.2)
74	118164	Cationic peroxidase 1 (precursor)	68.0	4.8	Sm, Sm + Ae	Mtvector (Gi)	1.67 (0.3) Gi	1.55 (0.3)
76	136030	Stress-induced protein ST1-like protein	67.8	5.9	Ae	Mtvector (Ae)	1.50 (0.1) Ae	1.58 (0.1)
82	140211	β-Glucosidase G1	62.0	7.4	Sm, Gi + Ae	Mtvector (Sm)	1.63 (0.2) Sm	1.20 (0.4)
Protein induction in MtROP9i transgenic roots
9	134736	Calmodulin 2	17.4	4.1	Gi	MtROP9i (Gi, Sm, Ae)	3.23 (0.4) Gi	2.49 (0.3)
							1.96 (0.4) Sm	2.23 (0.1)
2.21 (0.3) Ae	2.04 (0.2)
27	119667	Triosephosphate isomerase	30.0	6.2	Gi	MtROP9i (Gi)	2.47 (0.1) Gi	2.50 (0.3)
35	115931	Vegetative Gal-binding lectin	30.0	5.6	Ae	MtROP9i (Ae, Sm)	2.44 (0.2) Ae	2.36 (0.1)
							1.72 (0.3) Sm	1.56 (0.1)
33	132148	14-3-3-like protein	33.0	4.8	Gi, Sm, Gi + Ae, Sm + Ae	MtROP9i (Gi, Ae)	2.40 (0.1) Gi	2.46 (0.1)
					1.70 (0.2) Ae		1.58 (0.2)
42	117071	Auxin-induced protein	37.5	5.3	Gi, Sm, Gi + Ae, Sm + Ae	MtROP9i (Gi, Ae, Sm)	2.23 (0.1) Gi	2.41 (0.1)
							1.53 (0.3) Ae	2.04 (0.2)
1.46 (0.2) Sm	0.23 (0.1)
89	121437	Osmotin/thaumatin-like protein	27.0	7.1	Ae	MtROP9i (Gi, Ae)	2.24 (0.3) Gi	2.47 (0.1)
							2.25 (0.3) Ae	2.36 (0.4)
54	126275	Putative adenosine kinase 2 (fragment)	42.5	4.9	Gi, Sm	MtROP9i (Gi)	2.50 (0.3) Gi	2.34 (0.1)
16	125444	Putative ripening-related protein	16.5	7.3	Ae	MtROP9i (Ae)	2.48 (0.2) Ae	2.50 (0.2)
56	136010	Putative narbonin	42.0	5.2	Ae, Gi + Ae, Gi	MtROP9i (Ae)	2.41 (0.3) Ae	1.67 (0.4)
57	122880	Transaldolase	48.0	5.4	Ae	MtROP9i (Ae)	2.43 (0.3) Ae	1.60 (0.1)
62	116147	Pyruvate dehydrogenase E1 component α	45.0	7.8	Ae	MtROP9i (Ae)	2.31 (0.1) Ae	1.53 (0.2)
65	113679	Putative ankyrin-repeat protein	33.0	4.8	Sm, Gi, Sm + Ae	MtROP9i (Sm, Gi, Ae)	2.45 (0.2) Sm	1.55 (0.4)
							1.78 (0.1) Gi	1.88 (0.2)
1.59 (0.1) Ae	1.70 (0.5)
21	114909	ATP synthase subunit d, mitochondrial	21.0	5.3	Gi, Sm	MtROP9i (Gi)	1.75 (0.2) Gi	2.35 (0.2)
28	131709	Acid phosphatase	30.5	6.8	Sm	MtROP9i (Gi, Sm)	1.62 (0.2) Gi	2.46 (0.3)
							1.69 (0.1) Sm	2.27 (0.1)
58	139129	Ribulose bisphosphate carboxylase/oxygenase activase large protein isoform	53.5	5.4	Ae, Sm, Sm + Ae	MtROP9i (Ae)	1.67 (0.1) Ae	2.03 (0.2)
60	121355	Formate dehydrogenase, mitochondrial	44.0	7.6	Ae, Gi + Ae	MtROP9i (Ae)	1.49 (0.3) Ae	2.16 (0.1)
32	132148	14-3-3-like protein	33.0	4.7	Gi, Sm, Gi + Ae, Sm + Ae	MtROP9i (Gi, Ae)	1.77 (0.1) Gi	1.84 (0.2)
					1.59 (0.2) Ae		0.57 (0.2)
50	124940	Glycoside hydrolase, family 17	34.0	8.3	Ae	MtROP9i (Sm, Ae)	1.59 (0.2) Sm	1.58 (0.2)
							1.53 (0.2) Ae	1.65 (0.3)
61	117244	Fru-bisP aldolase	43.5	7.3	Ae	MtROP9i (Ae)	1.79 (0.1) Ae	1.53 (0.2)
66	120756	Phosphoglycerate kinase	55.0	5.3	Gi, Gi + Ae	MtROP9i (Gi)	1.75 (0.1) Gi	1.50 (0.3)
53	116888	F2E2.4	45.5	4.4	Sm, Sm + Ae	MtROP9i (Gi, Ae)	1.76 (0.2) Gi	0.85 (0.2)
63	118388	Fru-bisP aldolase	43.0	8.1	Ae, Sm + Ae	MtROP9i (Ae)	0.49 (0.1) Ae	1.56 (0.2)
Protein induction in both MtROP9i and Mtvector transgenic roots
11	117333	Disease resistance response protein Pi49	17.0	4.4	Ae	MtROP9i (Ae)	2.84 (0.3) Ae	2.76 (0.7)
						Mtvector (Gi)	1.83 (0.2) Gi	1.92 (0.2)
12	106314	Abscisic acid-responsive protein ABR17	16.9	5.5	Ae	MtROP9i (Ae)	2.80 (0.2) Ae	2.93 (0.1)
						Mtvector (Sm)	1.64 (0.3) Sm	1.81 (0.2)
40	136734	Isoflavone reductase	40.0	5.3	Ae	MtROP9i (Ae)	2.56 (0.1) Ae	2.30 (0.2)
						Mtvector (Sm)	2.61 (0.2) Sm	1.67 (0.1)
46	126900	Isoflavone reductase-like NAD(P)H-dependent oxidoreductase	37.5	7.2	Ae, Gi, Gi + Ae	MtROP9i (Ae, Gi)	2.32 (0.2) Ae	2.5 (0.3)
						2.46 (0.1) Gi	2.31 (0.1)
Mtvector (Sm)	1.73 (0.4) Sm	2.64 (0.3)
77	121513	Mitochondrial processing peptidase	65.0	6.6	Gi, Gi + Ae	MtROP9i (Gi)	2.42 (0.2) Gi	2.76 (0.3)
						Mtvector (Sm)	2.20 (0.3) Sm	2.06 (0.2)
17	140281	Chalcone-flavonone isomerase 1	27.0	5.4	Ae, Gi, Gi+ Ae	MtROP9i (Gi) Mtvector (Sm)	2.21 (0.2) Gi	2.16 (0.3)
							1.63 (0.3) Sm	2.46 (0.6)
18	117480	Trypsin protein inhibitor 3	24.0	4.8	Ae, Gi + Ae	MtROP9i (Ae, Gi)	2.42 (0.2) Ae	2.40 (0.3)
						2.47 (0.2) Gi	2.06 (0.2)
Mtvector (Sm)	1.84 (0.2) Sm	0.61 (0.4)
43	118248	NAD(P)H-dependent 6′-deoxychalcone synthase	40.5	6.3	Gi, Ae, Gi + Ae	MtROP9i (Gi, Ae)	2.12 (0.2) Gi	2.24 (0.3)
						2.06 (0.1) Ae	2.32 (0.2)
Mtvector (Sm)	1.73 (0.2) Sm	2.14 (0.2)
45	113451	Chalcone reductase	38.0	6.3	Ae, Gi	MtROP9i (Gi, Ae)	2.26 (0.1) Gi	2.20 (0.2)
							2.00 (0.3) Ae	2.23 (0.2)
						Mtvector (Sm)	1.66 (0.3) Sm	1.54 (0.1)
24	121437	Osmotin/thaumatin-like protein	20.0	7.2	Ae	MtROP9i (Ae)	2.06 (0.3) Ae	2.32 (0.2)
						Mtvector (Sm)	2.12 (0.2) Sm	0.31 (0.1)
7	128250	Nucleoside diphosphate kinase	15.8	7.3	Sm	Mtvector (Sm, Ae)	2.45 (0.2) Sm	2.5 (0.3)
							1.72 (0.2) Ae	0.58 (0.2)
MtROP9i (Gi)	1.61 (0.2) Gi	1.76 (0.3)
47	130358	Malate dehydrogenase	38.5	7.4	Gi	MtROP9i (Gi, Ae)	2.10 (0.2) Gi	1.64 (0.2)
						2.06 (0.3) Ae	0.52 (0.4)
Mtvector (Sm)	1.78 (0.2) Sm	2.01 (0.2)
38	114090	Ran-binding protein	36.0	4.3	Gi	MtROP9i (Gi) Mtvector (Sm)	2.07 (0.3) Gi	1.63 (0.2)
							1.54 (0.2) Sm	1.71 (0.3)
6	126924	Actin-depolymerizing factor 2	15.9	5.8	Ae, Sm + Ae	MtROP9i (Ae) Mtvector (Gi)	1.70 (0.1) Ae	1.65 (0.2)
							2.14 (0.3) Gi	1.52 (0.1)
19	122640	Kunitz proteinase inhibitor ST1-like	20.5	5.5	Ae	MtROP9i (Ae, Sm)	1.56 (0.3) Ae	1.72 (0.2)
							0.54 (0.3) Sm	1.50 (0.3)
03	114386	Major latex protein homolog	16.0	5.2	Ae, Sm, Con, Gi	Mtvector (Sm, Gi) MtROP9i (Ae)	2.06 (0.1) Sm	1.53 (0.3)
							1.58 (0.3) Gi	0.32 (0.2)
79	135749	Δ-1-Pyrroline-5-carboxylate dehydrogenase 12A1, mitochondrial	64.5	6.9	Sm, Gi	Mtvector (Sm)	1.59 (0.2) Sm	1.71 (0.3)
						MtROP9i (Gi)	1.49 (0.2) Gi	0.21 (0.1)

^aProtein number. ^bBest matching tentative consensus (TC) sequence identifier in the MtGI. ^cProtein encoded by the best matching gene. ^dCalculated from the position on the two-dimensional electrophoresis gel. ^ePredominant protein induction in Mtwt roots following microbial infection as investigated previously (Schenkluhn et al., 2010). Ae, A. euteiches induced; Gi, G. intraradices induced; Sm, S. meliloti induced; Gi + Ae and Sm + Ae, induced in mycorrhized or nodulated roots secondarily infected with A. euteiches; Con, induced in control roots. ^fProtein regulation in the Mtvector and MtROP9i transgenic roots at 3 and 24 hpi. Specific induction is indicated with the abbreviations of the microbes as described above. Abundances represent relative in-gel abundances (±sd): greater than 2.5-fold, abundance is highly increased; 2- to 2.5-fold, increased abundance; 1.5- to 2-fold, abundance is slightly increased.