Table I.
Putative novel proteins of Arabidopsis leaf peroxisomes identified by 1-D LC-MS/MS and classified into functional groups
Listed are 85 proteins, among which 30 had also been independently identified by previous proteome analyses (indicated in the Proteome Evidence column) but had not been confirmed to be peroxisomal by alternative methods. Functional categories 1 to 6 refer to β-oxidation (auxiliary), ROS metabolism, other metabolic enzymes, nucleotide and nucleic acid metabolism, chaperones and proteases, and other proteins, respectively. PTSs in parentheses, such as (SRF>) for At5g02240, indicate PTS-related peptides; SKV> in At4g16566.1 and SLM> in At5g65400.1 were later proven to be functional PTS1s in this study. Detailed biophysical and MS data on all these proteins are provided in Supplemental Table S3. Reu07, Reumann et al. (2007); Eub08, Eubel et al. (2008); Fukao03, Fukao et al. (2003); chpt, chloroplast; cyt, cytosol; nuc, nucleus; perox, peroxisome; pm, plasma membrane; n.d., not determined.
| Gene Locus | Acronym | Annotation | Functional Category | PTS1/2 | NSAF (×10−3) | Proteome Evidence | EYFP Localization |
|---|---|---|---|---|---|---|---|
| At1g02920.1 | GSTF7 | Glutathione transferase | 2 | Unknown | 0.54 | This study | cyt |
| At1g04290.1 | sT4 | Small thioesterase isoform 4 | 1 | SNL> | 1.46 | Reu07; this study | n.d. |
| At1g11840.1 | GLX1 | Glyoxalase I homolog | 2 | Unknown | 0.40 | This study | n.d. |
| At1g16730.1 | UP6 | Unknown protein | 6 | SKL> | 0.70 | This study | n.d. |
| At1g19570.1 | DHAR1 | Dehydroascorbate reductase | 2 | Unknown | 0.53 | This study | perox |
| At1g20010.1 | TUB5 | Tubulin β-5 chain | 6 | Unknown | 0.13 | This study | n.d. |
| At1g20560.1 | AAE1 | Acyl-activating enzyme 1 | 1 | SKL> | 0.31 | Eub08; this study | perox |
| At1g26340.1 | B5 #6 | Cytochrome b5, putative | 6 | Unknown | 0.84 | This study | n.d. |
| At1g45145.1 | TRX-H-5 | Thioredoxin H-type 5 | 6 | Unknown | 1.20 | This study | n.d. |
| At1g48320.1 | sT1 | Small thioesterase 1 | 1 | AKL> | 2.54 | This study | perox |
| At1g49240.1 | Actin 8 | 6 | Unknown | 0.25 | This study | n.d. | |
| At1g50510.1 | IndA | Indigoidine synthase A | 3 | RIx5HL | 2.58 | Eub08; this study | perox |
| At1g52400.1 | BGL1 | β-Glucosidase 1 | 2 | Unknown | 1.13 | Reu07; this study | n.d. |
| At1g52410.2 | UP1/TSA1 | Unknown protein 1/TSK-ASSOCIATING PROTEIN1 | 6 | SSL> | 0.97 | Reu07; this study | n.d. |
| At1g64850.1 | Calcium-binding EF-hand family protein | 6 | Unknown | 0.35 | This study | n.d. | |
| At1g75750.1 | GASA1 | GA-responsive GAST1 protein homolog | 6 | Unknown | 1.16 | This study | n.d. |
| At1g77540.1 | ATF2 | Acetyltransferase | 6 | SSI> | 0.50 | This study | perox |
| At1g78300.1 | GRF2 | General regulatory factor 2, G-box-binding factor GF14 ω (14-3-3 protein) | 6 | Unknown | 0.44 | This study | n.d. |
| At1g78370.1 | GSTU20 | Glutathione transferase | 2 | Unknown | 0.78 | This study | n.d. |
| At1g78380.1 | GSTU19 | Glutathione transferase | 2 | Unknown | 1.16 | This study | n.d. |
| At2g05380.1 | GRP3S | Gly-rich protein 3 short isoform | 4 | Unknown | n.d. | This study | n.d. |
| At2g16600.1 | CYP19-1/ROC3 | Cyclophilin 19-1 | 5 | Unknown | 0.98 | This study | n.d. |
| At2g21660.1 | GRP7 | Gly-rich protein isoform 7 | 4 | Unknown | 1.29 | Reu07; this study | n.d. |
| At2g27490.1 | COAE | Dephospho-CoA kinase | 3 | Unknown | 0.24 | This study | perox |
| At2g28760.1 | UXS6 | UDP-Xyl synthase 6 | 3 | Unknown | 0.17 | This study | n.d. |
| At2g29590.1 | sT5 | Small thioesterase 5 | 1 | SKL> | 0.72 | This study | perox |
| At2g30870.1 | GSTF10/ERD13 | Glutathione transferase | 2 | Unknown | 0.53 | This study | cyt |
| At2g31670.1 | UP3 | Unknown protein 3 | 6 | SSL> | 1.83 | Reu07; this study | n.d. |
| At2g36530.1 | LOS2 | Low expression of osmotically responsive genes 1 | 6 | Unknown | 0.38 | This study | n.d. |
| At2g38540.1 | LTP1 | Nonspecific lipid transfer protein 1 | 1 | Unknown | 0.72 | This study | cyt/pm |
| At2g41790.1 | P-M16 | Peptidase family M16 | 5 | PKL> | 0.85 | Eub08; this study | n.d. |
| At2g42490.1 | CuAO | Copper amine oxidase | 3 | SKL> | 1.75 | Eub08; this study | perox |
| At2g42520.1 | RH37 | DEAD-box RNA helicase 37 | 4 | Unknown | 0.18 | Reu07; this study | n.d. |
| At2g42590.1 | GRF9 | General regulatory factor 9, G-box-binding factor GF14 μ (14-3-3 protein) | 6 | Unknown | 0.22 | This study | cyt/pm |
| At2g43940.1 | Thiol methyltransferase | 3 | (STL>) | 1.38 | This study | n.d. | |
| At2g47390.1 | Ser-type endopeptidase | 5 | (SLL>) | 0.03 | This study | n.d. | |
| At3g01980.1 | SDRc | Short-chain dehydrogenase/reductase isoform c | 1 | (SYM>) | 0.85 | Reu07; this study | n.d. |
| At3g02360.1 | 6PGDH | Phosphogluconate dehydrogenase | 1 | SKI> | 1.46 | Reu07; this study | n.d. |
| At3g14150.1 | HAOX1 | Hydroxy-acid oxidase isoform 1 | 1 | SML> | 1.87 | This study | peroxa |
| At3g15950.1 | UP2/NAI2 | Unknown protein 2 | 6 | (SLN>) | 0.04 | Reu07; this study | n.d. |
| At3g24170.1 | GR | Glutathione reductase | 2 | (TNL>) | 0.45 | Reu07; this study | n.d. |
| At3g25530.1 | GHBDH | γ-Hydroxybutyrate dehydrogenase | 1 | Unknown | 0.29 | This study | n.d. |
| At3g26420.1 | ATRZ-1A | Gly-rich RNA-binding protein | 4 | Unknown | 0.58 | This study | nuc |
| At3g48140.1 | B12D1 | Senescence-associated protein/B12D-related protein | 6 | Unknown | 0.64 | This study | perox |
| At3g48170.1 | BADH | Betaine aldehyde dehydrogenase | 3 | SKL> | 4.90 | Reu07; this study | n.d. |
| At3g51600.1 | LTP5 | Nonspecific lipid transfer protein 5 | 1 | Unknown | 0.24 | This study | n.d. |
| At3g51660.1 | MIF | Macrophage migration inhibitory factor | 2 | SKL> | 4.05 | Reu07; this study | n.d. |
| At3g55290.1 | SDRd | Short-chain dehydrogenase/reductase isoform d | 1 | SSL> | 1.82 | Reu07; this study | n.d. |
| At3g56240.1 | CCH | Copper homeostasis factor (copper chaperone) | 5 | (SQV>) | 1.17 | This study | cyt |
| At3g56460.1 | ZnDH | Zinc-binding dehydrogenase | 3 | SKL> | 6.84 | Eub08; this study | perox |
| At3g56490.1 | HIT3 | His triad family protein 3 | 4 | (RVx5HF) | 1.35 | This study | perox/chpt |
| At3g61200.1 | sT3 | Small thioesterase 3 | 1 | SKL> | 0.90 | Fukao03; this study | perox |
| At4g04320.1 | MCD | Malonyl-CoA decarboxylase | 1 | SRL> | 0.88 | Eub08; this study | perox |
| At4g09320.1 | NDPK1 | Nucleoside diphosphate kinase type 1 | 3 | Unknown | 2.18 | This study | perox/nuc/cyt |
| At4g14880.1 | OASS A1 | O-Acetylserine sulfhydrylase isoform A1 | 3 | Unknown | 0.26 | Reu07; this study | n.d. |
| At4g16566.1 | NBP/HIT1 | Nucleotide-binding protein/His triad family protein 1 | 4 | (SKV>) | 3.11 | Reu07; this study | perox |
| At4g17530.1 | RAB1c | Ras-related small GTP-binding protein | 6 | Unknown | 0.28 | This study | nuc |
| At4g30010.1 | UP8 | Unknown protein | 6 | Unknown | 0.63 | This study | n.d. |
| At4g34870.1 | CYP18-4/ROC5 | Cyclophilin 18-4 | 5 | Unknown | 1.98 | This study | nuc/cyt/pm |
| At4g38740.1 | CYP18-3/ROC1 | Cyclophilin 18-3 | 5 | Unknown | 0.66 | This study | cyt |
| At4g39260.1 | GRP8 | Gly-rich repeat protein 8 | 4 | Unknown | 0.67 | Reu07; this study | n.d. |
| At5g02240.1 | Catalytic/coenzyme binding | 3 | (SRF>) | 0.11 | This study | nuc | |
| At5g02500.1 | Hsp70-1/HSC70-1 | Heat shock protein 70 | 5 | Unknown | 0.61 | This study | n.d. |
| At5g10450.1 | GRF6 | General regulatory factor 6, G-box-binding factor GF14 λ (14-3-3 protein) | 6 | Unknown | 1.14 | This study | n.d. |
| At5g11910.1 | ELT1 | Esterase/lipase/thioesterase family isoform 1 | 1 | SRI> | 1.24 | This study | perox |
| At5g15970.1 | COR6.6 | Cold-regulated protein (stress-induced protein KIN2) | 6 | Unknown | 1.72 | This study | n.d. |
| At5g16370.1 | AAE5 | Acyl-activating enzyme 5 | 1 | SRM> | 2.26 | Reu07; this study | n.d. |
| At5g17920.1 | METE1 | Cobalamin-independent Met synthase | 3 | (SAK>) | 0.78 | Reu07; this study | n.d. |
| At5g20010.1 | GTP-binding nuclear protein (RAN-1) | 6 | Unknown | 0.26 | This study | nuc | |
| At5g23050.1 | AAE17 | Acyl-activating enzyme 17 | 1 | SKL> | 1.30 | Eub08; this study | n.d. |
| At5g25980.1 | TGG2 | Myrosinase, thioglucosidase 2 | 2 | Unknown | 0.30 | Reu07; this study | n.d. |
| At5g26000.1 | TGG1 | Myrosinase, thioglucosidase 1 | 2 | Unknown | 0.84 | Reu07; this study | n.d. |
| At5g38480.1 | GRF3 | General regulatory factor 3, G-box-binding factor GF14 ψ (14-3-3 protein) | 6 | Unknown | 0.56 | This study | cyt/pm |
| At5g42980.1 | TRX-H-3 | Thioredoxin H-type 3 | 6 | Unknown | 1.20 | This study | cyt |
| At5g43940.1 | HMGDH | S-(Hydroxymethyl)glutathione dehydrogenase (GSH-FDH) | 2 | Unknown | 0.37 | Reu07; this study | n.d. |
| At5g44020.1 | Acid phosphatase class B family protein | 6 | Unknown | 0.94 | This study | n.d. | |
| At5g44250.1 | UP5 | Unknown protein | 6 | SRL> | 0.63 | This study | perox |
| At5g47040.1 | Lon2 | Lon protease homolog 2 | 5 | SKL> | 2.07 | This study | peroxb |
| At5g47210.1 | Nuclear RNA-binding protein, putative | 4 | Unknown | 0.08 | This study | cyt/nonperox dots | |
| At5g48230.1 | ACAT2 | Acetoacetyl-CoA thiolase 2 | 1 | Unknown | 2.11 | Reu07; this study | n.d. |
| At5g48545.1 | HIT2 | His triad family protein 2 | 4 | RLx5HL | 0.72 | This study | perox |
| At5g54500.1 | FQR1 | Quinone reductase | 3 | (STA>) | 0.28 | This study | n.d. |
| At5g56030.1 | Hsp90-2/HSP81-2/ERD8 | Heat shock protein 81-2 (early responsive to dehydration 8) | 5 | Unknown | 0.24 | This study | n.d. |
| At5g59950.1 | RNA and export factor-binding protein | 4 | Unknown | 0.46 | This study | n.d. | |
| At5g65400.1 | UP7 | Unknown protein | 6 | (SLM>) | 0.67 | This study | perox |
a
C. Mayer and S. Reumann (unpublished data).
b
T. Johnson and L.J. Olsen (unpublished data; in vitro protein import assay and subcellular fractionation).