Table I. List of proteins with significantly different abundances consistently found in fra2 and ktn1-2 mutants as compared with wild type (Col-0). NA = not applicable.

Accession no.	Description	Sample	Normalized intensity average in Col-0 roots	Normalized intensity average in fra2 roots	Normalized intensity average in ktn1-2 roots	Fold change		p value
						fra2 vs Col-0	ktn1-2 vs Col-0	fra2 vs Col-0	ktn1-2 vs Col-0
Amino acid metabolism
gi15233111	Cysteine synthase C1	Roots	52115.82	185447.46	136112.56	3.56	2.61	0.05	0.01
gi15223910	Aspartate semialdehyde dehydrogenase	Roots	55508.12	230059.47	125986.93	4.14	2.27	0.05	0.05
Proteolysis
gi18402225	Granulin repeat cysteine protease family protein	Roots	75658.44	343248.11	448897.32	4.54	5.93	0.01	0.00
Protein synthesis and translation
gi18410833	50S ribosomal protein L31	Aerial parts	6417292.09	2295801.19	4254452.45	0.36	0.66	0.007	0.023
gi18399100	40S ribosomal protein S18	Roots	113741.22	227944.46	394848.67	2.00	3.47	0.00	0.00
gi15221798	60S ribosomal protein L6-1	Roots	123564.32	196333.48	383764.34	1.59	3.11	0.00	0.01
gi79324564	40S ribosomal protein S5-1	Roots	219962.29	82575.80	94830.59	0.38	0.43	0.01	0.01
gi79317147	50S ribosomal protein L4	Aerial parts	7808895.67	1985714.83	2279779.83	0.25	0.29	0.005	0.003
gi30692346	Small subunit ribosomal protein S1	Aerial parts	8943813.19	5884181.99	5048811.79	0.66	0.56	0.055	0.005
gi15232603	60S acidic ribosomal protein P0-2	Aerial parts	9543945.84	4587130.63	4871300.09	0.48	0.51	0.001	0.009
Energy, metabolism, and photosynthesis
gi26557005	ATPase subunit 1	Aerial parts	2793480.24	7217395.44	5089236.13	2.58	1.82	0.007	0.030
gi18412632	ATP synthase γ chain 1	Aerial parts	24872995.56	16236642.88	17444031.98	0.65	0.70	0.022	0.030
gi15230595	phosphoglycerate kinase 1	Aerial parts	99022520.01	73663523.69	28363047.45	0.74	0.29	0.026	0.003
gi79313434	γ-Hydroxybutyrate dehydrogenase	Roots	14385.25	0	0	Unique in Col-0		NA	NA
gi145329204	Triose-phosphate isomerase	Roots	148158.00	366354.23	305748.27	2.47	2.06	0.00	0.00
gi15235029	chlorophyll a-b binding protein CP26	Aerial parts	4581201.95	9236218.52	6837980.22	2.02	1.49	0.05	0.033
gi15228194	Sedoheptulose-1,7-bisphosphatase	Aerial parts	8304146.35	13526281.91	13754753.35	1.63	1.66	0.010	0.045
gi15230358	Adenylosuccinate synthetase	Roots	61378.48	0	0	Unique in Col-0		NA	NA
gi7525041	Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit	Aerial parts	411927407.76	294914235.63	277266195.81	0.72	0.66	0.019	0.019
gi30684767	ATP-dependent zinc metalloprotease FTSH 2 (VAR2)	Aerial parts	10406900.99	5403906.75	6122905.04	0.52	0.59	0.027	0.052
gi15217918	DNA-damage resistance protein DRT112	Aerial parts	13493270.03	2986221.23	4416446.13	0.22	0.33	0.011	0.007
gi15242465	Soluble inorganic pyrophosphatase 1	aerial parts	11022571.57	5807403.25	5763606.13	0.53	0.52	0.044	0.027
gi238479213	Ribulose bisphosphate carboxylase large chain, catalytic domain	Aerial parts	15069515.17	10777815.24	9451326.29	0.72	0.63	0.021	0.021
Stress response and redox regulation
gi15236014	Lipase/lipooxygenase, PLAT/LH2 family protein	Roots	38041.31	0	0	Unique in Col-0		NA	NA
gi18413214	Nucleoside diphosphate kinase 1	Roots	226388.99	380425.14	393491.58	1.68	1.74	0.02	0.39
gi15235401	Glutathione S-transferase F2	Roots	644121.71	1578139.78	2106336.43	2.45	3.27	0.00	0.01
gi15230982	Peroxiredoxin Q	Aerial parts	9363992.23	5543512.31	3980676.95	0.59	0.43	0.042	0.005
gi79313261	PYK10-binding protein 1	Roots	1166764.61	630062.78	644475.44	0.54	0.55	0.01	0.01
gi18415805	Ferredoxin/thioredoxin reductase subunit A (variable subunit) 2	Aerial parts	2441812.37	895399.11	1305568.55	0.37	0.53	0.011	0.053
gi15236386	Selenium-binding protein 2	Aerial parts	1289730.38	0	0	Unique in Col-0		NA	NA
gi15234648	Peroxidase 45	Roots	447213.47	690524.52	951861.94	1.54	2.13	0.05	0.02
Signaling
gi18413181	14-3-3-like protein GF14 chi	Roots	797937.21	0	0	Unique in Col-0		NA	NA
Hormonal homeostasis
gi42570831	S-Alkyl-thiohydroximate lyase SUR1	Roots	6362.74	0	0	Unique in Col-0		NA	NA
gi15221692	Pyruvate dehydrogenase E1 component subunit α-2 (IAR4)	Roots	253127.82	55389.52	66337.07	0.22	0.26	0.01	0.02
Protein folding, chaperones
gi334185828	Clp ATPase	Roots	107823.61	37454.35	48712.02	0.35	0.45	0.02	0.03
gi18415982	Tetratricopeptide repeat protein	Roots	222702.14	427357.63	486498.43	1.92	2.18	0.03	0.02
gi15237739	Cyclophilin ROC7	Aerial parts	10957142.37	3657898.57	3546535.06	0.33	0.32	0.002	0.004
Unknown function
gi18404496	NAD(P)-binding Rossmann-fold-containing protein	Aerial parts	8607872.32	5447058.47	5603099.42	0.63	0.65	0.008	0.007
gi15237739gi15224648	Membrane-associated progesterone binding protein 2	Roots	203330.29	371469.14	439583.49	1.83	2.16	0.03	0.02
gi15237739gi30682601	Vacuolar calcium-binding protein-like protein	Roots	57633.53	242968.33	103128.61	4.22	1.79	0.01	0.05
gi15237739gi334187997	Uncharacterized protein	Aerial parts	739698.22	0	0	Unique in Col-0		NA	NA
Membrane transport
gi15237739gi18397991	MD-2-related lipid recognition domain-containing protein	Roots	102011.46	0	0	Unique in Col-0		NA	NA