Table I

Localization of proteins to the ER and Golgi by LOPIT

The 28 proteins identified with known or predicted localizations are shown. A PLS-DA model was built based on the known ER, Golgi, and mitochondrial/plastid proteins. This model was then used to rank the remaining proteins according to how well they fit these three localizations. Values closest to 1 indicate a good fit. Proteins with Golgi values above 0.93 were assigned to the Golgi, and proteins with ER values above 0.88 were assigned to the ER. The highest PLS-DA result for each protein is shown in bold. Asterisks indicate proteins that fall just below the threshold for confident assignment to the Golgi.

NameAccession no.Predicted localization (Ref.)PLS-DA results
GolgiERMit/plastid
Proteins assigned to the Golgi
    Glycosyltransferase family 29 At1g08660 Golgi (36) 1.06 –0.090.03
    Glycosyltransferase family 34 (AtGT5) At1g74380 Golgi (37) 1.19 –0.280.09
    Glycosyltransferase family 8 (quasimodo1) At3g25140 Golgi (38) 1.25 –0.340.09
    Glycosyltransferase family 8 At3g61130 Golgi (36) 0.96 –0.070.11
    Glycosyltransferase family 47 At4g38040 Golgi (36) 1.11 –0.06–0.05
Proteins assigned to the ER
    Obtusifoliol 14-demethylase (CYP51) At1g11680 ER (40)0.04 1.07 –0.11
    β-ketoacyl reductase (glossy8) At1g67730 ER (41)0.11 0.89 0.00
    Cinnamate-4-hydroxylase (AtC4H) At2g30490 ER (43)–0.05 1.08 –0.03
    Protein disulfide isomerase At2g32920 ER (44)–0.48 1.37 0.11
    Serine C-palmitoyltransferase family (LCB1 homolog) At4g36480 ER (45)0.11 0.96 –0.07
Proteins not assigned to the ER or Golgi
    Plasma membrane proton ATPase At2g18960 PM (35)–0.140.53 0.61
    NADH dehydrogenase family (ndb4) At2g20800 Mit. (46)0.16–0.03 0.88
    TOC75 homolog At3g46740 Plastid (47, 48)0.39–0.60 1.22
    Glycosyltransferase family 2 * At3g07330 Golgi (36) 0.78 0.070.15
    Apyrase * At5g18280 Golgi (39) 0.90 –0.010.11
    Ribophorin I At1g76400 ER (42)0.43 0.63 –0.06
Training set of proteins used to build the PLS-DA model
    Fucosyltransferase At1g49710 Golgi (22, 23) 1.06 –0.120.06
    Glycosyltransferase family 34 (gtl-6) At2g22900 Golgi (7) 0.99 0.08–0.07
    N-acetyl glucosaminyltransferase At4g38240 Golgi (23, 24) 0.93 –0.040.11
    ER-type Ca2+-pumping ATPase (ECA1) At1g07810 ER (25)0.11 0.96 –0.08
    AtSec12 At2g01470 ER (26)0.06 0.99 –0.05
    NADH-cytochrome b5 reductase At5g17770 ER (27)–0.17 0.88 0.29
    Calnexin At5g61790 ER (28)0.14 1.00 –0.14
    Mitochondrial ADP,ATP carrier protein 1 (AAC1) At3g08580 Mit. (29)0.17–0.01 0.84
    Mitochondrial phosphate transporter (AT5) At5g14040 Mit. (30, 31)0.18–0.13 0.95
    Dicarboxylate/tricarboxylate carrier (AtDTC) At5g19760 Mit. (32)–0.060.04 1.01
    Long chain acyl-CoA synthetase 9 (LACS9) At1g77590 Plastid (33)0.080.08 0.83
    Chloroplast NAD-de pend ent malate dehydrogenase At3g47520 Plastid (34)0.00–0.10 1.10