Label-Free Quantitative Proteomics Reveal the Involvement of PRT6 in Arabidopsis thaliana Seed Responsiveness to Ethylene
Abstract
:1. Introduction
2. Results
2.1. Effects of Ethylene Treatment on the Germination of Dormant Seeds
2.2. Ethylene-Induced Proteome Changes Observed at 30 h but Not 16 h after Treatments
2.3. Effects of Ethylene on the Expression of DEPs
2.4. Effect of prt6 on the Expression of DEPs in the Absence of Ethylene after 30 h of Imbibition
2.5. Functional Class Scoring Analysis without Filtering DEPs in 30 h-Proteome
2.6. Effect of prt6 on the Fate of Storage Proteins during Germination
2.7. Hormone-Related Proteins in Seed
3. Discussion
4. Materials and Methods
4.1. Seed Materials
4.2. Germination Assay
4.3. Seed Treatment
4.4. Protein Extraction and LC-MS Analysis
4.5. Protein Identification and Quantification
4.6. Bioinformatic Analysis
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Duration of Seed Incubation in the Presence of Ethylene (h) | Germination (%) after 7 Days at 25 °C in Air after Ethylene Treatment | |
---|---|---|
2016 Harvest | 2018 Harvest | |
0 | 11.9 ± 4.0 | 0 |
10 | 39.9 ± 3.0 | - |
16 | 48.3 ± 4.0 | 7.7 ± 7.5 |
24 | 54.5 ± 6.2 | 21.0 ± 1.0 |
30 | - | 54.6 ± 4.6 |
48 | 61.9 ± 3.7 | 81.3 ± 4.0 |
ID. | Description | prt6−/Col− |
---|---|---|
Hypoxia-responsive | ||
AT1G19530 | DNA polymerase epsilon catalytic subunit A | 1.64 |
AT2G16060 | Hemoglobin 1 | 18.74 |
AT1G43800 | Plant stearoyl-acyl-carrier-protein desaturase family protein | 21.64 |
Carbohydrate metabolism | ||
AT4G33820 | Glycosyl hydrolase superfamily protein | 0.39 |
AT5G63800 | Glycosyl hydrolase family 35 protein | 0.48 |
AT3G09260 | Glycosyl hydrolase superfamily protein | 5.78 |
AT1G53580 | Glyoxalase II 3 | 1.52 |
AT4G34260 | 1,2-alpha-L-fucosidase | 0.70 |
AT5G26120 | Alpha-L-arabinofuranosidase 2 | 0.65 |
AT4G15210 | Beta-amylase 5 | 1.98 |
AT4G36360 | Beta-galactosidase 3 | 0.60 |
AT5G49360 | Beta-xylosidase 1 | 1.51 |
AT1G02640 | Beta-xylosidase 2 | 1.47 |
AT5G57550 | Xyloglucan endotransglucosylase/hydrolase 25 | 0.47 |
AT2G47510 | Fumarase 1 | 1.30 |
AT1G12780 | UDP-D-glucose/UDP-D-galactose 4-epimerase 1 | 1.57 |
AT2G39730 | Rubisco activase | 1.80 |
Cell wall | ||
AT1G19900 | Glyoxal oxidase-related protein (involved in cell wall modification) | 0.51 |
AT5G15490 | UDP-glucose 6-dehydrogenase protein (required for the formation of cell wall ingrowths) | 1.47 |
AT5G05290 | Expansin A2 | 4.24 |
AT3G14310 | Pectin methylesterase 3 | 1.32 |
Oxidation and reduction | ||
AT3G61070 | Peroxin 11E (integral to peroxisome membrane, controls peroxisome proliferation) | 1.34 |
AT2G46750 | D-arabinono-1,4-lactone oxidase activity | 0.51 |
AT3G14415 | Aldolase-type TIM barrel family protein (modulates ROS-mediated signal transduction) | 1.95 |
AT4G35000 | Ascorbate peroxidase 3 | 1.67 |
AT4G20860 | FAD-binding Berberine family protein (involved in the generation of H2O2) | 0.53 |
AT2G02930 | Glutathione S-transferase F3 | 0.52 |
AT2G30870 | Glutathione S-transferase PHI 10 | 1.95 |
AT2G47730 | Glutathione S-transferase phi 8 | 2.14 |
AT5G66920 | SKU5 similar 17 (oxidation-reduction process) | 1.63 |
AT3G27820 | Monodehydroascorbate reductase 4 | 1.83 |
AT1G60680 | NAD(P)-linked oxidoreductase superfamily protein | 0.66 |
AT3G44880 | Pheophorbide a oxygenase family protein with Rieske 2Fe-2S domain-containing protein | 1.38 |
AT5G63030 | Thioredoxin superfamily protein | 0.67 |
Transcription | ||
AT5G02490 | Heat shock protein 70 (HSP 70) (mediator of RNA polymerase II transcription subunit 37c) | 1.38 |
AT4G25630 | Ibrillarin 2 (Mediator of RNA polymerase II transcription subunit 36a) | 1.45 |
AT3G08030 | DNA-directed RNA polymerase subunit beta | 1.77 |
AT3G03270 | Adenine nucleotide alpha hydrolases-like superfamily protein | 7.91 |
AT1G74260 | Purine biosynthesis 4 | 1.61 |
AT3G57610 | Adenylosuccinate synthase (purine synthesis) | 1.50 |
AT2G45300 | RNA 3’-terminal phosphate cyclase/enolpyruvate transferase%2C alpha/beta | 1.80 |
AT3G52150 | RNA-binding (RRM/RBD/RNP motifs) family protein | 1.37 |
AT3G19130 | RNA-binding protein 47B | 1.86 |
AT5G63420 | RNA-metabolising metallo-beta-lactamase family protein | 1.34 |
AT3G58510 | DEA(D/H)-box RNA helicase family protein | 1.31 |
Translation | ||
AT4G01310 | Ribosomal L5P family protein | 1.35 |
AT5G23900 | Ribosomal protein L13e family protein | 1.38 |
AT3G63490 | Ribosomal protein L1p/L10e family | 1.44 |
AT1G50920 | Nucleolar GTP-binding protein ( Involved in the biogenesis of the 60S ribosomal subunit) | 1.57 |
ATCG00830 | Ribosomal protein L2 | 1.67 |
AT2G33800 | Ribosomal protein S5 family protein | 1.67 |
AT1G32990 | Plastid ribosomal protein l11 | 1.91 |
AT2G40290 | Eukaryotic translation initiation factor 2 subunit 1 | 1.39 |
AT3G56150 | Eukaryotic translation initiation factor 3C | 1.74 |
AT4G20360 | RAB GTPase homolog E1B (Elongation factor Tu) | 1.55 |
Protein folding | ||
AT3G13470 | TCP-1/cpn60 chaperonin family protein (protein folding) | 1.49 |
AT1G56340 | Calreticulin 1a (Molecular calcium-binding chaperone promoting folding) | 2.38 |
AT1G09210 | Calreticulin 1b (Molecular calcium-binding chaperone promoting folding) | 2.07 |
AT3G09440 | Heat shock protein 70 (HSP70) (mediate the folding of newly translated peptides) | 1.48 |
AT1G55490 | Chaperonin 60 beta (suppressing protein aggregation in vitro) | 1.34 |
AT3G16420 | PYK10-binding protein 1 (chaperone that facilitates the correct polymerization of PYK10) | 4.71 |
Protein transport | ||
AT4G10480 | Nascent polypeptide-associated complex (NAC) 2C alpha | 1.50 |
AT3G49470 | Nascent polypeptide-associated complex subunit alpha-like protein 2 | 1.40 |
AT3G15980 | Coatomer subunit beta -3 | 1.44 |
AT3G46830 | RAB GTPase homolog A2C | 1.44 |
Protein modification | ||
AT4G17040 | CLP protease R subunit 4 | 1.38 |
AT2G47390 | Prolyl oligopeptidase family protein | 1.46 |
AT2G38280 | AMP deaminase%2C putative / myoadenylate deaminase | 1.34 |
AT3G45010 | Serine carboxypeptidase-like 48 | 3.57 |
AT5G10240 | Asparagine synthetase 3 | 1.45 |
AT5G11880 | Pyridoxal-dependent decarboxylase family protein | 1.33 |
AT1G61790 | Oligosaccharyltransferase complex/protein N-linked glycosylation | 1.41 |
AT1G48630 | Receptor for activated C kinase 1B (shuttle activated protein kinase C ) | 2.04 |
AT3G18130 | Receptor for activated C kinase 1C (shuttle activated protein kinase C ) | 1.66 |
AT1G25490 | ARM repeat superfamily protein (encoding phosphoprotein phosphatase) | 1.69 |
LEAs | ||
AT3G22500 | Seed maturation protein (LEA protein) | 0.63 |
AT3G51810 | Stress induced protein (LEA protein) | 0.69 |
AT5G66780 | Late embryogenesis abundant protein | 0.55 |
Hormone | ||
AT1G04580 | Aldehyde oxidase 4 (ABA synthesis) | 0.61 |
AT3G17390 | S-adenosylmethionine synthetase family protein (ethylene synthesis) | 2.45 |
AT2G36880 | Methionine adenosyltransferase 3 (ethylene synthesis) | 1.50 |
Locus | Description | 0 | 16 | 30 |
---|---|---|---|---|
AT5G44120.3 | Cruciferin A | 1.44 | 2.73 | 0.56 |
AT5G44120.1 | Cruciferin A | 1.13 | 1.74 | 0.88 |
AT1G03880 | Cruciferin B | 1.12 | 1.43 | 0.81 |
AT4G28520 | Cruciferin C | 1.00 | 1.04 | 0.73 |
AT4G30880 | 2S albumin | 1.59 | 1.42 | 0.90 |
AT3G22640 | Cupin | 0.97 | 1.14 | 0.73 |
AT1G07750 | RmlC-like cupins | 0.73 | 1.65 | 1.05 |
AT4G36700 | RmlC-like cupins | 0.77 | 1.19 | 0.81 |
AT1G03890 | RmlC-like cupins | 0.85 | 1.01 | 0.75 |
AT2G28490 | RmlC-like cupins | 0.94 | 1.09 | 0.83 |
AT2G18540 | RmlC-like cupins | 1.07 | 1.17 | 0.85 |
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Wang, X.; Davanture, M.; Zivy, M.; Bailly, C.; Nambara, E.; Corbineau, F. Label-Free Quantitative Proteomics Reveal the Involvement of PRT6 in Arabidopsis thaliana Seed Responsiveness to Ethylene. Int. J. Mol. Sci. 2022, 23, 9352. https://doi.org/10.3390/ijms23169352
Wang X, Davanture M, Zivy M, Bailly C, Nambara E, Corbineau F. Label-Free Quantitative Proteomics Reveal the Involvement of PRT6 in Arabidopsis thaliana Seed Responsiveness to Ethylene. International Journal of Molecular Sciences. 2022; 23(16):9352. https://doi.org/10.3390/ijms23169352
Chicago/Turabian StyleWang, Xu, Marlène Davanture, Michel Zivy, Christophe Bailly, Eiji Nambara, and Françoise Corbineau. 2022. "Label-Free Quantitative Proteomics Reveal the Involvement of PRT6 in Arabidopsis thaliana Seed Responsiveness to Ethylene" International Journal of Molecular Sciences 23, no. 16: 9352. https://doi.org/10.3390/ijms23169352
APA StyleWang, X., Davanture, M., Zivy, M., Bailly, C., Nambara, E., & Corbineau, F. (2022). Label-Free Quantitative Proteomics Reveal the Involvement of PRT6 in Arabidopsis thaliana Seed Responsiveness to Ethylene. International Journal of Molecular Sciences, 23(16), 9352. https://doi.org/10.3390/ijms23169352