The Dynamics of the Cell Wall Proteome of Developing Alfalfa Stems
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Material
2.2. Cell Wall Protein Enrichment
2.2.1. Extraction of Cell Wall Proteins
2.2.2. Concentration and Desalting of the Extracts.
2.3. Cell Wall Protein Analysis by 2D-DIGE
2.3.1. Protein Migration
2.3.2. Spot Selection
2.3.3. Spot Picking, Digestion, MS/MS Analysis
2.3.4. Post-Identification Statistical Procedure
3. Results
4. Discussion
4.1. Carbohydrate-Interacting Proteins Accumulate in the Cell Wall of the Apical Region
4.2. β-galactosidases are Abundant in the Apical and Intermediate Stem Part
4.3. Class III Peroxidases MtPrx29, MtPrx41, and MtPrx15
4.4. Enzymes Involved in Protein Degradation/Maturation Accumulate in the Oldest Stem Region
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Cluster | Spot | gi-Number | Name | Loc | Type | Base | Int. | Apex |
---|---|---|---|---|---|---|---|---|
1 | CaCl2-2127 | gi|2951684 | lectin [M. sativa] | Extrac | Sol | 0.37 | −0.20 | −0.39 |
1 | CaCl2-2128 | gi|2951684 | lectin [M. sativa] | Extrac | Sol | 0.25 | −0.30 | −0.27 |
1 | CaCl2-2193 | gi|400180 | RecName: Full=Truncated lectin 2 | Extrac | Sol | 0.34 | −0.14 | −0.14 |
1 | EGTA-1167 | gi|388505450 | Glutelin type-A [M. truncatula] | Cytop | Sol | 0.25 | −0.14 | −0.23 |
1 | EGTA-1390 | gi|400180 | RecName: Full=Truncated lectin 2 | Extrac | Sol | 0.40 | −0.20 | −0.23 |
1 | EGTA-1411 | gi|2951684 | lectin [M. sativa] | Extrac | Sol | 0.20 | −0.29 | −0.30 |
1 | EGTA-1420 | gi|400180 | RecName: Full=Truncated lectin 2 | Extrac | Sol | 0.19 | −0.19 | −0.22 |
1 | LiCl-765 | gi|2951684 | lectin [M. sativa] | Extrac | Sol | 0.21 | −0.25 | −0.23 |
2 | CaCl2-1870 | gi|388505450 | Glutelin type-A [M. truncatula] | Cytop | Sol | 0.20 | −0.20 | −0.26 |
2 | CaCl2-2363 | gi|357468557 | Ferritin-3 [M. truncatula] | Plast | Sol | 0.24 | −0.04 | −0.44 |
2 | CaCl2-2627 | gi|357492793 | Ferritin-2 [M. truncatula] | Plast | Sol | 0.11 | −0.01 | −0.40 |
2 | EGTA-2050 | gi|50320305 | putative defensin 2.1 precursor [M. sativa] | Extrac | Sol | 0.15 | −0.14 | −0.19 |
3 | CaCl2-1013 | gi|922395483 | PNGase A [M. truncatula] | Extrac | Sol | 0.02 | −0.08 | −0.17 |
3 | CaCl2-2165 | gi|228204925 | chitinase class III-1 [M. sativa] | Extrac | Sol | 0.04 | −0.12 | −0.21 |
3 | CaCl2-2426 | gi|357468557 | Ferritin-3 [M. truncatula] | Plast | Sol | 0.09 | −0.08 | −0.14 |
3 | EGTA-1228 | gi|357437719 | Cysteine proteinase [M. truncatula] | Lyso | Sol | 0.16 | −0.12 | −0.14 |
3 | EGTA-1372 | gi|228204925 | chitinase class III-1 [M. sativa] | Extrac | Sol | 0.03 | −0.14 | −0.23 |
3 | EGTA-2117 | gi|3913031 | RecName: Full=Beta-amylase [M. sativa] | Cytop | Sol | 0.12 | −0.11 | −0.20 |
3 | EGTA-570 | gi|3913031 | RecName: Full=Beta-amylase [M. sativa] | Cytop | Sol | 0.11 | −0.10 | −0.22 |
3 | EGTA-573 | gi|3913031 | RecName: Full=Beta-amylase [M. sativa] | Cytop | Sol | 0.09 | −0.06 | −0.19 |
3 | EGTA-586 | gi|3913031 | RecName: Full=Beta-amylase [M. sativa] | Cytop | Sol | 0.12 | −0.09 | −0.18 |
3 | EGTA-587 | gi|3913031 | RecName: Full=Beta-amylase [M. sativa] | Cytop | Sol | 0.07 | −0.05 | −0.14 |
3 | EGTA-593 | gi|3913031 | RecName: Full=Beta-amylase [M. sativa] | Cytop | Sol | 0.08 | −0.13 | −0.22 |
3 | EGTA-595 | gi|3913031 | RecName: Full=Beta-amylase [M. sativa] | Cytop | Sol | 0.05 | −0.11 | −0.16 |
3 | EGTA-610 | gi|3913031 | RecName: Full=Beta-amylase [M. sativa] | Cytop | Sol | 0.12 | −0.09 | −0.28 |
3 | EGTA-615 | gi|3913031 | RecName: Full=Beta-amylase [M. sativa] | Cytop | Sol | 0.10 | −0.15 | −0.23 |
3 | EGTA-640 | gi|3913032 | RecName: Full=Beta-amylase [M. sativa] | Cytop | Sol | 0.13 | −0.07 | −0.14 |
4 | CaCl2-1716 | gi|388518933 | Endochitinase [M. truncatula] | Extrac | Sol | 0.26 | 0.10 | −0.12 |
4 | CaCl2-1880 | gi|357448991 | endo-1,3-beta-glucosidase [M. truncatula] | Extrac | Sol | 0.19 | 0.06 | −0.08 |
4 | CaCl2-2356 | gi|357468557 | Ferritin-3 [M. truncatula] | Plast | Sol | 0.14 | 0.08 | −0.20 |
4 | CaCl2-2425 | gi|357468557 | Ferritin-3 [M. truncatula] | Plast | Sol | 0.23 | 0.06 | −0.32 |
4 | CaCl2-2439 | gi|357468557 | Ferritin-3 [M. truncatula] | Plast | Sol | 0.28 | 0.04 | −0.21 |
4 | CaCl2-2553 | gi|357468557 | Ferritin-3 [M. truncatula] | Plast | Sol | 0.24 | −0.04 | −0.18 |
4 | CaCl2-2827 | gi|22901738 | high FW vegetative storage protein | Extrac | Sol | 0.21 | −0.03 | −0.23 |
4 | CaCl2-2828 | gi|357437721 | Cysteine proteinase [M. truncatula] | Lyso | Sol | 0.09 | 0.05 | −0.13 |
4 | EGTA-1111 | gi|71534882 | serine carboxypeptidase S10 [M. sativa] | Extrac | Sol | 0.21 | 0.00 | −0.16 |
4 | EGTA-1114 | gi|3913031 | RecName: Full=Beta-amylase [M. sativa] | Cytop | Sol | 0.18 | 0.06 | −0.08 |
4 | EGTA-1119 | gi|50317234 | Aspartic proteinase Asp1 [M. truncatula] | Extrac | Sol | 0.17 | 0.00 | −0.12 |
4 | EGTA-1143 | gi|357448997 | endo-1,3-beta-glucosidase [M. truncatula] | Extrac | Sol | 0.15 | −0.02 | −0.10 |
4 | EGTA-1166 | gi|298364452 | chitinase [M. sativa] | Extrac | Sol | 0.11 | 0.03 | −0.17 |
4 | EGTA-1168 | gi|657377089 | peroxidase family protein [M. truncatula] | Extrac | Sol | 0.16 | −0.03 | −0.12 |
4 | EGTA-1233 | gi|357437719 | Cysteine proteinase [M. truncatula] | Extrac | Sol | 0.12 | 0.03 | −0.14 |
4 | EGTA-1461 | gi|169147017 | putative thaumatin-like protein | Extrac | Sol | 0.19 | 0.05 | −0.04 |
4 | EGTA-1922 | gi|71534922 | thioredoxin h [M. sativa] | Cytop | Sol | 0.12 | −0.01 | −0.15 |
4 | EGTA-914 | gi|657371151 | eukaryotic aspartyl protease | Extrac | Sol | 0.19 | −0.02 | −0.17 |
4 | LiCl-1068 | gi|23049900 | put early nodulin-like 2 [T pratense] | CM | Memb | 0.10 | 0.09 | −0.08 |
5 | CaCl2-1769 | gi|357491415 | Peroxidase [M. truncatula] | Extrac | Sol | 0.40 | 0.29 | 0.11 |
5 | CaCl2-2269 | gi|3688528 | pre-pro-TPE4A protein [Pisum sativum] | Lyso | Sol | −0.01 | 0.17 | 0.05 |
5 | EGTA-1052 | gi|357517805 | Endochitinase [M. truncatula] | Lyso | Sol | 0.18 | 0.07 | 0.01 |
5 | EGTA-1057 | gi|388494834 | Endochitinase [M. truncatula] | Lyso | Sol | 0.23 | 0.09 | −0.01 |
5 | EGTA-1450 | gi|3688528 | cysteine proteinase [Vicia sativa] | Lyso | Sol | 0.00 | 0.21 | 0.06 |
5 | EGTA-1451 | gi|571536058 | PREDICTED: vignain-like [Glycine max] | Lyso | Sol | −0.02 | 0.15 | 0.00 |
5 | EGTA-1452 | gi|30141021 | cysteine protease-2 [Helianthus annuus] | Lyso | Sol | −0.04 | 0.14 | −0.01 |
5 | EGTA-2122 | gi|357448991 | endo-1,3-beta-glucosidase [M. truncatula] | Extrac | Sol | 0.26 | 0.10 | −0.03 |
6 | LiCl-885 | gi|357513969 | Germin-like protein [M. truncatula] | Extrac | Sol | −0.40 | −0.28 | −0.08 |
6 | LiCl-935 | gi|388502800 | Germin-like protein [Pisum sativum] | Extrac | Sol | −0.31 | −0.25 | −0.14 |
7 | CaCl2-1593 | gi|593701343 | Cyclophilin 38 isoform 1 [T. cacao] | Plast | Memb | −0.15 | −0.06 | 0.13 |
7 | EGTA-1388 | gi|357480321 | Lactoylglutathione lyase [M. truncatula] | Cytop | Sol | −0.15 | −0.02 | 0.04 |
7 | EGTA-1480 | gi|357512271 | Ribose-5-phosphate isomer. [M. truncatula] | Plast | Sol | −0.18 | 0.01 | 0.18 |
7 | EGTA-1586 | gi|388502800 | Germin-like protein [Pisum sativum] | Extrac | Sol | −0.23 | −0.07 | −0.01 |
7 | EGTA-196 | gi|357437609 | Beta-galactosidase [M. truncatula] | Extrac | Sol | −0.18 | 0.04 | 0.01 |
7 | EGTA-197 | gi|357437609 | Beta-galactosidase [M. truncatula] | Extrac | Sol | −0.19 | 0.03 | 0.03 |
7 | EGTA-201 | gi|357437609 | Beta-galactosidase [M. truncatula] | Extrac | Sol | −0.24 | 0.02 | 0.03 |
7 | EGTA-203 | gi|357437609 | Beta-galactosidase [M. truncatula] | Extrac | Sol | −0.23 | 0.05 | 0.05 |
7 | EGTA-205 | gi|357437609 | Beta-galactosidase [M. truncatula] | Extrac | Sol | −0.19 | 0.01 | 0.02 |
7 | EGTA-206 | gi|357437609 | Beta-galactosidase [M. truncatula] | Extrac | Sol | −0.19 | 0.02 | 0.03 |
7 | EGTA-2120 | gi|357437609 | Beta-galactosidase [M. truncatula] | Extrac | Sol | −0.16 | 0.05 | 0.03 |
7 | EGTA-214 | gi|357437609 | Beta-galactosidase [M. truncatula] | Extrac | Sol | −0.24 | 0.04 | 0.03 |
7 | EGTA-215 | gi|357437609 | Beta-galactosidase [M. truncatula] | Extrac | Sol | −0.23 | 0.05 | 0.05 |
7 | EGTA-216 | gi|357437609 | Beta-galactosidase [M. truncatula] | Extrac | Sol | −0.18 | 0.02 | 0.01 |
7 | EGTA-220 | gi|357437609 | Beta-galactosidase [M. truncatula] | Extrac | Sol | −0.21 | 0.06 | 0.06 |
7 | EGTA-221 | gi|357437609 | Beta-galactosidase [M. truncatula] | Extrac | Sol | −0.18 | 0.06 | 0.06 |
7 | EGTA-222 | gi|657400954 | beta-like galactosidase [M. truncatula] | Extrac | Sol | −0.23 | 0.00 | 0.04 |
7 | EGTA-240 | gi|357437609 | Beta-galactosidase [M. truncatula] | Extrac | Sol | −0.23 | 0.02 | 0.01 |
7 | EGTA-272 | gi|87241408 | Protease-associated PA [M. truncatula] | Extrac | Sol | −0.08 | −0.01 | 0.14 |
7 | EGTA-326 | gi|357437609 | Beta-galactosidase [M. truncatula] | Extrac | Sol | -0.22 | 0.04 | 0.02 |
7 | EGTA-333 | gi|357437609 | Beta-galactosidase [M. truncatula] | Extrac | Sol | −0.16 | 0.02 | 0.06 |
7 | EGTA-341 | gi|357437609 | Beta-galactosidase [M. truncatula] | Extrac | Sol | −0.16 | 0.03 | 0.04 |
7 | EGTA-342 | gi|357437609 | Beta-galactosidase [M. truncatula] | Extrac | Sol | −0.19 | 0.05 | 0.01 |
7 | EGTA-379 | gi|357437609 | Beta-galactosidase [M. truncatula] | Extrac | Sol | −0.20 | −0.02 | −0.05 |
8 | CaCl2-2612 | gi|357476945 | Acid beta-fructofuranosidase | Lyso | Sol | −0.16 | 0.02 | 0.27 |
8 | CaCl2-2968 | gi|388514479 | Oxygen-evolving enhancer protein 2 | Plast | Sol | −0.16 | -0.03 | 0.28 |
8 | EGTA-1296 | gi|357438145 | Cysteine proteinase [M. truncatula] | Lyso | Sol | −0.04 | 0.03 | 0.21 |
8 | EGTA-1485 | gi|357512271 | Ribose-5-phosphate isomer. [M. truncatula] | Plast | Sol | −0.16 | 0.04 | 0.24 |
8 | EGTA-1490 | gi|357512271 | Ribose-5-phosphate isomer. [M. truncatula] | Plast | Sol | -0.18 | 0.02 | 0.19 |
8 | EGTA-1794 | gi|157973737 | PSI reaction center IV A [Cicer arietinum] | Plast | Sol | −0.01 | 0.10 | 0.30 |
8 | LiCl-1156 | gi|537317 | peroxidase [M. sativa] | Extrac | Sol | −0.07 | 0.05 | 0.24 |
8 | LiCl-1163 | gi|537317 | peroxidase [M. sativa] | Extrac | Sol | 0.03 | 0.13 | 0.22 |
8 | LiCl-300 | gi|657374433 | polygalacturonase non-catalytic | Extrac | Sol | 0.00 | 0.06 | 0.20 |
8 | LiCl-340 | gi|537317 | peroxidase [M. sativa] | Extrac | Sol | −0.06 | −0.01 | 0.20 |
9 | CaCl2-1292 | gi|388508134 | Nod factor-bind. lectin [M. truncatula] | Golgi | Memb | −0.22 | −0.15 | 0.14 |
9 | CaCl2-1940 | gi|388502358 | Xylogluc. Endotransglucosylase | Extrac | Sol | −0.31 | −0.01 | 0.11 |
9 | CaCl2-1945 | gi|357508519 | Xylogluc. Endotransglucosylase | Extrac | Sol | −0.10 | 0.01 | 0.21 |
9 | CaCl2-2042 | gi|5777611 | cysteine protease [M. sativa] | Extrac | Sol | −0.02 | −0.08 | 0.18 |
9 | CaCl2-2511 | gi|388502800 | Germin-like protein [Pisum sativum] | Extrac | Sol | −0.22 | −0.02 | 0.03 |
9 | EGTA-1376 | gi|357513539 | Stem 28 kDa glycoprotein [M. truncatula] | Extrac | Sol | −0.09 | −0.07 | 0.18 |
9 | EGTA-1391 | gi|357513539 | Stem 28 kDa glycoprotein [M. truncatula] | Extrac | Sol | −0.17 | −0.02 | 0.30 |
9 | EGTA-1661 | gi|357476945 | Acid beta-fructofuranosidase | Lyso | Sol | −0.15 | 0.01 | 0.18 |
9 | EGTA-956 | gi|537313 | plant/F18G18-200 protein [M. truncatula] | Extrac | Sol | −0.31 | −0.09 | 0.24 |
9 | EGTA-965 | gi|537313 | plant/F18G18-200 protein [M. truncatula] | Extrac | Sol | −0.23 | −0.05 | 0.24 |
10 | CaCl2-1586 | gi|537313 | plant/F18G18-200 protein [M. truncatula] | Extrac | Sol | −0.38 | −0.14 | 0.37 |
10 | CaCl2-1609 | gi|537313 | plant/F18G18-200 protein [M. truncatula] | Extrac | Sol | −0.45 | −0.20 | 0.42 |
10 | CaCl2-2570 | gi|388509752 | unknown [Lotus japonicus] (pfam03018) | Extrac | Sol | −0.16 | −0.13 | 0.26 |
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Sergeant, K.; Printz, B.; Guerriero, G.; Renaut, J.; Lutts, S.; Hausman, J.-F. The Dynamics of the Cell Wall Proteome of Developing Alfalfa Stems. Biology 2019, 8, 60. https://doi.org/10.3390/biology8030060
Sergeant K, Printz B, Guerriero G, Renaut J, Lutts S, Hausman J-F. The Dynamics of the Cell Wall Proteome of Developing Alfalfa Stems. Biology. 2019; 8(3):60. https://doi.org/10.3390/biology8030060
Chicago/Turabian StyleSergeant, Kjell, Bruno Printz, Gea Guerriero, Jenny Renaut, Stanley Lutts, and Jean-Francois Hausman. 2019. "The Dynamics of the Cell Wall Proteome of Developing Alfalfa Stems" Biology 8, no. 3: 60. https://doi.org/10.3390/biology8030060