Table 2.
List of 22 identified ionically bound cell wall proteins by the in-gel method coupled with LC-MS/MS in stems of Arabidopsis at the late growth stage.
| Locus IDs | Proteins (putative or function confirmed) | CBM, GH or CE family | SP | |
|---|---|---|---|---|
| SignalP | UniprotKB | |||
| GHs (7) | ||||
| AT5G26000 | Myrosinase 1 (thioglucoside glucohydrolase, TGG1) | GH1 | 1–19 | 1–19 |
| *AT5G49360 | Bifunctional XYL 1/α-L-arabinofuranosidase | GH3 | 1–30 | 1–30 |
| *AT4G30270 | Xyloglucan endotransferase | GH16 | 1–21 | 1–21 |
| AT3G57260 | β-1,3-glucanase 2 | GH17 | 1–30 | 1–22 |
| *AT1G68560 | Bifunctional α-l-arabinofuranosidase/XYL | GH31 | 1–27 | 1–27 |
| AT1G12240 | β-fructofuranosidase (i.e., invertase) | GH32 | None | 1–67 |
| *,^ AT2G28470 | β-galactosidase 8 | GH35 | 1–23 | 1–29 |
| CEs (3) | ||||
| ^ AT1G11580 | Pectin methylesterase (PME) | CE8 | None | 1–34 |
| ^ AT3G14310 | Pectin methylesterase 3 (PME3) | CE8 | None | 1–35 |
| AT1G29670 | GDSL esterase/lipase | 1–24 | 1–24 | |
| OXIDO-REDUCTASE INCLUDING PEROXIDASE (3) | ||||
| AT3G49120 | Peroxidase 34 | 1–30 | 1–30 | |
| AT3G52960 | Thioredoxin-dependent peroxidase | None | None | |
| AT1G76160 | Sks5 (SKU5 Similar 5); copper ion binding/oxidoreductase | 1–23 | n/a | |
| PROTEASES AND PROTEASES INHIBITORS (3) | ||||
| AT1G47128 | Cysteine proteinase/dehydration stress-responsive gene (RD21) | 1–21 | 1–21 | |
| AT3G14067 | Subtilase family protein (proteinase inhibitor) | 1–25 | n/a | |
| AT4G21650 | Serine-type protease | 1–21 | n/a | |
| AT4G26690 | MRH5 (glycerophosphoryl diester phosphodiesterase) | 1–27 | 1–27 | |
| PROTEINS WITH PROTEIN-PROTEIN INTERACTION DOMAINS (3) | ||||
| AT1G33590 | Leucine-rich repeat (LRR) protein | none | n/a | |
| AT1G53070 | Legume lectin family protein | 1–23 | 1–23 | |
| AT1G78830 | Curculin-like (mannose-binding) lectin family protein | 1–22 | n/a | |
| STRESS RESPONSIVE AND DEFENSE PROTEINS (2) | ||||
| AT2G45470 | Fasciclin-like arabinogalactan protein 8 (FLA8) | 1–25 | 1–25 | |
| AT1G75040 | Pathogenesis-related gene 5 (PR5) | 1–23 | 1–23 | |
| MISCELLANEOUS (1) | ||||
| AT4G27520 | Early nodulin-like protein 2 (ENODL2) | 1–28 | 1–28 | |
The protein categories are arranged by the number of proteins identified in each category. Proteins acting on xylan and pectin are indicated by * and ^ symbols, respectively. Note that the full list of identified 236 total stem proteins using the protein gel method was provided in Supplemental Table S2. Note that for AT3G14067, it was formally counted as one of the 22 identified ionically bound cell wall proteins by the in-gel method; however, because of its being identified with five and one peptides in the two biological replicate analyses of the in-gel method, respectively, as well as its being identified by in-solution method (see Table 1), thus still included in this table. The signal peptides (SP) for the proteins were predicted by using the SignalP 4.1 program and the annotation in UniProtKB, as described in the Materials and Methods as well as the Results sections. none, predicted to be without SP; n/a, the prediction annotation for SP is not available.