Table 2.

Comparison of FtsH12 and TIC complex protein abundance in FTSH12 mutants. Protein abundance in FtsH12 knock-down plants (mi12-3), overexpressors (ox12-1) and wild type (WT) was determined by label-free mass spectrometry. Listed are protein names with gene loci and associated Uniprot IDs, number of unique peptides supporting the identification, and average iBAQ values as a measure of protein abundance. Significance between FTSH mutants and wild type was determined by a two-tailed Student’s t-test (P<0.05)

Protein name	Gene loci	UniProt IDs	Unique peptides	Average iBAQ mi12-3	Average iBAQ WT	Average iBAQ ox12-1	Significant WT/mi12-3	Significant ox12-1/mi12-3	Significant ox12-1/WT
FtsH12 motor complex subunits
FTSH12	At1g79560	Q9SAJ3	14	0	3110	87 893	+	+	+
FtsHi1	At4g23940	O22993	6	0	2134	8014	+	+	+
FtsHi2	At3g16290	A8MPR5	4	0	3824	8437	+	+	+
FtsHi4	At5g64580	F4KF14	3	0	3992	6308	+	+	+
FtsHi5	At3g04340	F4J3N2	2	0	659	2509		+	+
YCF2	AtCg00860;AtCg01280	P56786	5	1433	2470	1453	+
pdNAD-MDH	At3g47520	Q9SN86	13	1 270 450	1 093 783	1 718 300		+	+
1MD TIC complex
TIC214 / YCF1	AtCg01000;AtCg01130	P56785	14	20 821	5097	19 452	+		+
TIC100	At5g22640	Q8LPR8	7	16 646	3752	33 105	+		+
TIC56	At5g01590	Q7Y1W1	6	19 101	7802	46 503			+
Other TIC subunits
TIC110	At1g06950	Q8LPR9	43	568 540	396 450	667 520			+
TIC40	At5g16620	Q9FMD5	6	105 910	83 516	123 841			+
TIC62	At3g18890	Q8H0U5	6	0	0	23 804		+	+
TIC55	At2g24820	Q9SK50	8	10 723	8683	40 684		+	+
TIC22-IV	At4g33350	Q9SZB2	5	29 746	24 446	49 074		+	+
TIC22-III	At3g23710	F4J469	2	20 041	5375	10 095	+	+
Chloroplast chaperones with suggested motor function
cpHsc70-1	At4g24280	Q9STW6	9	1 728 700	1 531 400	2 821 950		+	+
cpHsc70-2	At5g49910	Q9LTX9	9	188 855	207 958	395 635		+	+
HSP93-III/ CLPC2	At3g48870	F4JF64;Q9SXJ7	12	176 430	168 343	250 565		+	+
CLPC1	At5g50920	Q9FI56	13	1 257 550	1 220 073	2 193 150		+	+