Table I.
Selected candidates of identified S-nitrosylated proteins from Arabidopsis cell cultures and leaves
Cell culture extracts treated with GSNO or GSH and leaf extracts of NO-treated or -untreated Arabidopsis plants were subjected to the biotin switch method and analyzed by nanoLC/MS/MS after trypic digestion. The MASCOT search engine was used to parse MS data to identify proteins from primary sequence databases. The best-matching peptide identifying the protein is given. If there were further peptides found, the number of the peptides is given. Hints confirming that the identified protein is a candidate for S-nitrosylation are given in the right column. The results of two separate experiments of each treatment were summarized in the table. Acc. No., Accession number.
| Protein | Acc. No. | Molecular Mass | Identified Peptides (Score) GSNO/NO | Identified Peptides (Score) GSH/Untreated | Hints to S-Nitrosylation |
|---|---|---|---|---|---|
| D | |||||
| Stress-Related Proteins | |||||
| GST, putative | NP_565178 | 25,634 | VTEFVSELR (79) | NPILPSDPYLR (38) | Sies et al. (1998); Ji et al. (2002) |
| Hsp 90, putative | AAL49788 | 80,036 | ADLVNNLGTIAR (50) + 1 | Jaffrey et al. (2001); Fratelli et al. (2002, 2003); Lind et al. (2002); Shenton and Grant (2003) | |
| Cu/Zn-superoxide dismutase | NP_172360 | 15,088 | AVVVHADPDDLGK (55) + 1 | Lawler and Song (2002) | |
| Redox-Related Proteins | |||||
| Glutathione peroxidase, putative | NP_192897 | 25,568 | FAPTTSPLSIEK (65) + 1 | FAPTTSPLSIEK (51) | Koh et al. (2001) |
| Peroxiredoxin-related | AAF66133 | 21,230 | AVNVEEAPSDFK (37) | Motohashi et al. (2001); Fratelli et al. (2002, 2003); Lind et al. (2002) | |
| Type 2 peroxiredoxin-related | NP_176773 | 17,417 | APIAVGDVVPDGTISFFDENDQLQTASVHSLAAGK (51) | ||
| Glutaredoxin, putative | NP_198853 | 11,749 | LVPLLTEAGAIAGK (59) | Klatt et al. (2000); Song and Lee (2003) | |
| Signaling/Regulating Proteins | |||||
| Elongation factor eEF-1α-chain | S08534 | 49,457 | VETGMIKPGMVVTFAPTGLTTEVK (61) + 4 | IGGIGTVPVGR (58) +2 | Fratelli et al. (2002); Shenton and Grant (2003) |
| Elongation factor EF-2 | A96602 | 94,185 | AYLPVVESFGFSSQLR (80) + 4 | LWGENFFDPATR (43) +2 | |
| Elongation factor 1B α-subunit | NP_568375 | 24,186 | TYISGDQLSVDDVK (67) + 1 | ||
| Elongation factor 1B γ, putative | AAK59587 | 46,371 | VPVLETPEGPIFESNAIAR (40) + 1 | ||
| Initiation factor eIF-4A1 | CAC43286 | 41,823 | GLDVIQQAQSGTGK (41) | GLDVIQQAQSGTGK (38) | Lind et al. (2002); Shenton and Grant (2003) |
| Initiation factor5A-4-related | NP_173985 | 17,129 | TYPQSAGNIR (58) | ||
| Cytoskeleton Proteins | |||||
| Tubulin α 6 chain | JQ1597 | 49,506 | AVFVDLEPTVIDEVR 84) + 1 | DVNAAVGTIK (34) +1 | Jaffrey et al. (2001) |
| Tubulin β 4 chain | S68122 | 49,876 | AVLMDLEPGTMDSLR (82) + 2 | GHYTEGAELIDSVLDVVR (71) | Jaffrey et al. (2001); Lind et al. (2002) |
| Actin 2/7 | NP_196543 | 41,709 | NYELPDGQVITIGAER (114) + 3 | AGFAGDDAPR (53) +1 | Dalle-Donne et al. (2000, 2003); Jaffrey et al. (2001); Fratelli et al. (2002, 2003); Lind et al. (2002) |
| Actin depolymerizing factor 3-like | NP_851227 | 15,912 | YAIFDFDFVSSEGVPR (54) | ||
| Annexin | CAA67608 | 35,757 | HYNDEDVIR (48) + 2 | DALLANEATK (48) +2 | Liu et al. (2002); Kuncewicz et al. (2003) |
| Metabolic Enzymes | |||||
| Fru 1,6-biphosphate aldolase, putative | NP_190861 | 38,516 | VSPEVIAEHTVR (85) + 4 | LASINVENVETNR (64) +3 | Fratelli et al. (2002); Lind et al. (2002); Ito et al. (2003); Shenton and Grant (2003) |
| Triosephosphate isomerase | T50646 | 27,138 | VASPAQAQEVHDELR (109) + 3 | VASPAQAQEVHDELR (68) +3 | Fratelli et al. (2002); Ito et al. (2003); Shenton and Grant (2003) |
| GAPDH C-subunit | NP_187062 | 36,891 | GILGYTEDDVVSTDFVGDNR (92) + 4 | AASFNIIPSSTGAAK (46) +3 | Mohr et al. (1996, 1999); Klatt et al. (2000); Motohashi et al. (2001); Kuncewicz et al. (2003); Shenton and Grant (2003) |
| 2-Phosphoglycerate hydrolase (enolase) | NP_181192 | 47,689 | VTAAVPSGASTGIYEALELR (86) + 3 | Fratelli et al. (2002); Lind et al. (2002); Shenton and Grant (2003) | |
| Phosphoglycerate kinase | NP_178073 | 42,105 | GVTTIIGGGDSVAAVEK (62) + 2 | Fratelli et al. (2002) | |
| Aconitase | Q8L784 | 108,133 | INPLVPVDLVIDHSVQVDVAR (43) | Navarre et al. (2000) | |
| SAM synthetase, putative | AAO11581 | 42,769 | KPEEVGAGDQGHMFGYATDETPELMPLTHVLATK (70) + 5 | FVIGGPHGDAGLTGR (76) +4 | Ruiz et al. (1998); Perez-Mato et al. (1999) |
| Adenosylhomocysteinase | CAB09795 | 51,447 | LVGVSEETTTGVK (48) | ||
| Met synthase | NP_197294 | 84,304 | IPSSEEIADR (82) + 1 | FALESFWDGK (53) +1 | Yamazaki et al. (2004) |
| Cys synthase | CAA58893 | 33,842 | IDGFVSGIGTGGTITGAGK (59) | LFVAIFPSFGER (35) | |
| ATP synthase CF1 α-chain | NP_051044 | 55,294 | LIESPAPGIISR (49) + 2 | Eaton et al. (2003) | |
| ATP synthase CF1 β-chain | NP_051066 | 53,900 | YKELQDIIAILGLDELSEEDR (96) + 14 | GIYPAVDPLDSTSTMLQPR (108) +6 | |
| Proteins Involved in Photosynthetic Processes | |||||
| GAPDH precursor, chloroplast | JQ1285 | 42,481 | VVDLADIVANNWK (74) + 1 | Mohr et al. (1996, 1999); Klatt et al. (2000); Motohashi et al. (2001); Kuncewicz et al. (2003); Shenton and Grant (2003) | |
| Rubisco large chain | NP_051067 | 52,922 | ESTLGFVDLLR (90) + 6 | LSGGDHIHAGTVVGK (56) +2 | Marcus et al. (2003) |
| Rubisco small chain 1a precursor | RKMUA1 | 20,189 | IIGFDNTR (45) + 1 | IIGFDNTR (58) +1 | Motohashi et al. (2001) |
| Rubisco activase, large subunit | AAA20202 | 51,948 | VPLILGIWGGK (34) | GLAYDTSDDQQDITR (81) +3 | Zhang and Portis (1999); Zhang et al. (2002) |
| PSII P680 47-kD protein | NP_051084 | 56,001 | MPTFFETFPVVLVDGDGIVR (85) | ||
| PSII D2 protein,fragment | AAO13251 | 35,220 | NILLNEGIR (31) | Carlberg et al. (1999) | |
| PSII oxygen-evolving complex 33 | NP_190651 | 34,998 | NTAASVGEITLK (53) + 4 | ||
| Rieske Fe-S protein | CAC03598 | 24,334 | VLFVPWVETDFR (63) |