TMT-Based Proteomic Analysis of Continuous Cropping Response in Codonopsis tangshen Oliv.
Abstract
:1. Introduction
2. Materials and Methods
2.1. Chemicals and Instrumentation
2.2. Plant Materials and Sample Collection
2.3. Measurement of Physiological and Biochemical Properties
2.4. Protein Extraction and Digestion
2.5. Labelling and Peptide Fractionation
2.6. Liquid Chromatography–Mass Spectrometry (LC-MS/MS) Analysis and Database Search
2.7. Protein Quantification and Bioinformatics Analysis
2.8. Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) Analysis
3. Results
3.1. Physiological and Biochemical Properties
3.2. Mass Spectrometry Identification
3.3. Gene Ontology (GO) Analysis of DEPs in Response to Continuous Cropping
3.4. KEGG Pathway Analysis of Responsive DEPs
3.5. PPI Network Analysis
3.6. Validation of the DEPs by qRT-PCR
4. Discussion
4.1. Physiological and Biochemical Response in Continuously Cropped C. tangshen
4.2. Proteomic Patterns of C. tangshen in Response to Continuous Cropping
4.3. DEPs Related to Photosynthesis Pathway
4.4. DEPs Associated with Oxidative Phosphorylation
4.5. DEPs Related to Ribosome Activity
4.6. DEPs Related to Secondary Metabolites
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Accession Number | Pathway and Annotation | Mean Ratio | MW [kDa] | pI | Score Mascot |
---|---|---|---|---|---|
Photosynthesis pathway | |||||
A0A1U7AF74 | Cytochrome b6-f complex subunit 4 | 0.322 | 18.9 | 6.04 | 58 |
A0A2D1PBS6 | Photosystem II 47 kDa protein | 0.368 | 56.1 | 6.90 | 665 |
A0A291F2T6 | Photosystem II reaction center protein L | 2.211 | 4.5 | 4.50 | 112 |
A0A1L6BTC9 | ATP synthase subunit alpha | 0.574 | 54.9 | 6.34 | 671 |
A0A291F242 | ATP synthase subunit alpha | 0.571 | 54.9 | 6.04 | 600 |
B9U4M6 | ATP synthase subunit beta | 0.104 | 50.5 | 5.36 | 1120 |
B9U4I8 | ATP synthase subunit beta | 0.479 | 50.7 | 6.06 | 1198 |
H6VP95 | ATP synthase subunit beta | 0.369 | 47.1 | 5.83 | 1173 |
K9UVR2 | Chlorophyll a-b binding protein | 0.368 | 21.3 | 5.55 | 461 |
A0A288W750 | ATPase subunit 4 | 0.524 | 21.9 | 9.69 | 26 |
A0A075DZC7 | Protein PsbN | 2.621 | 4.7 | 4.28 | 31 |
Carbon fixation in photosynthetic organisms | |||||
T1WIC8 | Ribulose bisphosphate carboxylase large chain | 1.950 | 26.9 | 6.01 | 842 |
A0A023Q1G8 | Ribulose bisphosphate carboxylase large chain | 0.488 | 41.1 | 7.61 | 2141 |
A0A023Q3H2 | Ribulose bisphosphate carboxylase large chain | 0.629 | 41.7 | 7.21 | 2563 |
U6BNI3 | Ribulose bisphosphate carboxylase large chain | 0.203 | 37.9 | 8.03 | 2216 |
C7AQR5 | Ribulose bisphosphate carboxylase large chain | 0.615 | 23.2 | 7.80 | 553 |
A0A023Q2I2 | Ribulose bisphosphate carboxylase large chain | 0.420 | 28.6 | 9.13 | 1361 |
A0A023Q1M8 | Ribulose bisphosphate carboxylase large chain | 0.175 | 36.2 | 8.53 | 2133 |
C7AQT3 | Ribulose bisphosphate carboxylase large chain | 2.386 | 50.1 | 7.02 | 1668 |
H6VPA6 | Ribulose bisphosphate carboxylase large chain | 0.580 | 48.6 | 6.80 | 1569 |
Q37184 | Ribulose bisphosphate carboxylase large chain | 0.639 | 52.5 | 6.70 | 2548 |
C3S8M7 | Ribulose bisphosphate carboxylase large chain | 0.538 | 50.7 | 6.68 | 1821 |
G8D4X5 | Ribulose bisphosphate carboxylase large chain | 1.511 | 22.4 | 6.05 | 607 |
C3S8S0 | Ribulose bisphosphate carboxylase large chain | 0.374 | 50.2 | 6.71 | 1209 |
A2VAL3 | Ribulose bisphosphate carboxylase large chain | 0.426 | 51.7 | 6.95 | 736 |
A0A1L6BRS7 | Ribulose bisphosphate carboxylase large chain | 0.628 | 52.6 | 6.70 | 1522 |
A6XBE1 | Ribulose-1,5-bisphosphate carboxylase/oxygenase | 0.319 | 20.3 | 7.27 | 1105 |
A0A1D6XPB7 | Ribulose-1,5-bisphosphate carboxylase/oxygenase | 0.632 | 12.0 | 7.34 | 230 |
Ribosome | |||||
A0A240FG30 | 30S ribosomal protein S14 | 0.344 | 11.8 | 11.53 | 28 |
A0A220D819 | 50S ribosomal protein L20 | 0.610 | 15.0 | 11.27 | 26 |
A0A2D1PBT7 | Chloroplast 30S ribosomal protein S4 | 0.594 | 23.3 | 10.51 | 131 |
A0A1Z2QRI8 | Ribosomal protein L14 | 0.556 | 13.5 | 9.19 | 176 |
A0A291F5L8 | Ribosomal protein L22 | 1.687 | 32.5 | 9.54 | 75 |
K9UUF3 | Ribosomal protein RPL32e | 2.096 | 10.6 | 10.29 | 26 |
A0A1L6BUB7 | Ribosomal protein S12 | 0.469 | 14.1 | 11.46 | 45 |
A0A2D1PBQ4 | Ribosomal protein S16 | 0.475 | 10.5 | 10.11 | 24 |
A0A2D1PBU9 | Ribosomal protein S2 | 0.287 | 26.9 | 9.69 | 45 |
A0A291F0G4 | Ribosomal protein S8 | 0.451 | 15.9 | 10.87 | 94 |
Oxidative phosphorylation | |||||
A0A2D1PBY9 | NAD(P)H-quinone oxidoreductase chain 5 | 0.504 | 84.9 | 9.10 | 21 |
A0A2D1PBT2 | NAD(P)H-quinone oxidoreductase chain J | 2.160 | 18.8 | 6.79 | 37 |
A0A240FG85 | NAD(P)H-quinone oxidoreductase subunit 4L | 0.593 | 11.2 | 9.72 | 33 |
A0A088PYE4 | NAD(P)H-quinone oxidoreductase subunit H | 0.583 | 45.5 | 5.87 | 48 |
A0A288W7F2 | NADH dehydrogenase subunit 7 | 0.354 | 44.2 | 7.05 | 69 |
A0A0K1ZFQ7 | NADH dehydrogenase subunit 9 | 0.531 | 22.5 | 7.46 | 0 |
A0A240FG45 | Cytochrome f | 1.622 | 35.1 | 8.97 | 822 |
A0A1L6BSB5 | ATP synthase CF0 subunit I | 2.819 | 21.0 | 6.02 | 0 |
H6VP90 | ATP synthase subunit beta (Fragment) | 2.091 | 47.8 | 5.19 | 1609 |
A0A1Z2QTG2 | ATP synthase subunit beta | 2.267 | 53.7 | 5.58 | 1479 |
B3SU35 | ATP synthase subunit beta, chloroplastic | 1.870 | 53.7 | 5.72 | 1461 |
A0A220D850 | ATP synthase subunit c, chloroplastic | 1.969 | 11.0 | 4.64 | 31 |
B9U4M3 | ATP synthase subunit beta (Fragment) | 1.907 | 49.5 | 5.08 | 1707 |
A0A0K1Z6V1 | ATP synthase subunit alpha | 4.268 | 54.9 | 5.91 | 560 |
Secondary metabolites | |||||
V9PEM0 | Diphosphomevalonate decarboxylase | 0.578 | 46.0 | 6.38 | 19 |
J7EQD9 | Phenylalanine ammonia-lyase | 1.557 | 77.1 | 6.10 | 264 |
Q2WFK7 | Cytosolic ascorbate peroxidase | 1.620 | 27.9 | 6.00 | 242 |
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Jiang, X.; Zhou, W.; Wang, H.; You, J.; Liu, W.; Zhang, M. TMT-Based Proteomic Analysis of Continuous Cropping Response in Codonopsis tangshen Oliv. Life 2023, 13, 765. https://doi.org/10.3390/life13030765
Jiang X, Zhou W, Wang H, You J, Liu W, Zhang M. TMT-Based Proteomic Analysis of Continuous Cropping Response in Codonopsis tangshen Oliv. Life. 2023; 13(3):765. https://doi.org/10.3390/life13030765
Chicago/Turabian StyleJiang, Xiaogang, Wuxian Zhou, Hua Wang, Jinwen You, Wenlu Liu, and Meide Zhang. 2023. "TMT-Based Proteomic Analysis of Continuous Cropping Response in Codonopsis tangshen Oliv." Life 13, no. 3: 765. https://doi.org/10.3390/life13030765