Integrative Proteome and Phosphoproteome Profiling of Early Cold Response in Maize Seedlings
Abstract
:1. Introduction
2. Results
2.1. Proteome and Phosphoproteome Analyses of Maize Seedlings upon Short Time Cold Stress
2.2. Cold-Responsive Proteins and Phosphopeptides
2.3. Functional Analysis of the Cold-Responsive Proteome and Phosphoproteme Reveals Different Groups of Functional Terms
2.4. Site-Specific Phosphorylation Modification during Cold Treatment
2.5. Cold-Responsive Photosynthesis and Spliceosome Proteins
2.6. Cold-Responsive Kinases and Transcription Factors
3. Discussion
4. Materials and Methods
4.1. Plant Materials and Growth Conditions
4.2. Protein Extraction, Trypsin Digestion, and TMT Labeling
4.3. Peptide Fractionation and Phosphopeptide Enrichment
4.4. LC-MS/MS Analysis
4.5. LC-MS/MS Data Analysis and Bioinformatics Analysis
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Accession | Ratio (30 min) | p Value (30 min) | Ratio (2 h) | p Value (2 h) | Description |
---|---|---|---|---|---|
Kinases | |||||
A0A1D6FNF9 | 0.96 | 7.27 × 10−1 | 0.76 | 8.14 × 10−3 | ABC1-like kinase |
A0A1D6HW78 | 0.87 | 1.34 × 10−1 | 0.71 | 1.47 × 10−3 | ABC2 homolog 13 |
A0A1D6JD09 | 1.03 | 7.53 × 10−1 | 0.74 | 2.67 × 10−3 | Calcium-dependent protein kinase |
B4F9P5 | 1.09 | 1.95 × 10−1 | 0.76 | 1.09 × 10−3 | Protein-serine/threonine kinase |
B4FF99 | 0.76 | 1.32 × 10−2 | 0.70 | 8.59 × 10−4 | Calcium-dependent protein kinase 7 |
B6SVK8 | 1.02 | 8.50 × 10−1 | 0.74 | 5.73 × 10−3 | Serine/threonine-protein kinase NAK |
P28523 | 0.91 | 3.87 × 10−1 | 0.73 | 7.04 × 10−3 | Casein kinase II subunit alpha |
Transcription factors | |||||
A0A1D6JVI5 | 1.02 | 8.94 × 10−1 | 2.88 | 2.38 × 10−5 | bZIP transcription factor 16 |
B4FIJ2 | 1.15 | 8.66 × 10−2 | 1.35 | 1.42 × 10−3 | Zinc ion binding |
K7V3U5 | 0.64 | 6.49 × 10−3 | 0.99 | 9.31 × 10−1 | WRKY DNA-binding domain protein |
K7V9Y4 | 1.06 | 4.10 × 10−1 | 1.31 | 1.87 × 10−3 | HSF28 HSF type transcription factor |
Accession | Ratio (30 min) | p Value (30 min) | Ratio (2 h) | p Value (2 h) | Phos-Site | Description |
---|---|---|---|---|---|---|
Kinases | ||||||
A0A1D6F0U9 | 1.35 | 3.17 × 10−2 | 2.07 | 2.71 × 10−4 | S498/T501 | MAPK |
A0A1D6G325 | 0.64 | 6.58 × 10−4 | 0.66 | 7.95 × 10−4 | S279 | Casein kinase family protein |
A0A1D6GJU6 | 0.78 | 8.83 × 10−3 | 0.63 | 2.71 × 10−4 | S115 | MAPKKK1 |
A0A1D6GJU6 | 0.75 | 1.77 × 10−2 | 0.63 | 9.43 × 10−4 | S200 | MAPKKK1 |
A0A1D6ICZ3 | 0.64 | 9.04 × 10−4 | 0.63 | 5.87 × 10−4 | T52 | CDPK8 |
A0A1D6MYW4 | 0.68 | 2.64 × 10−3 | 0.68 | 2.22 × 10−3 | S253 | CPK21 |
A0A1D6P094 | 1.68 | 2.92 × 10−3 | 1.03 | 8.48 × 10−1 | S436 | Protein kinase |
B4FBJ3 | 0.77 | 8.28 × 10−3 | 0.64 | 3.24 × 10−4 | S464 | Casein kinase 1 |
O49975 | 0.51 | 1.42 × 10−4 | 0.57 | 3.52 × 10−4 | T30 | MEK1 |
Transcription factors | ||||||
A0A1D6EHU0 | 0.67 | 6.5 × 10−2 | 0.54 | 6.5 × 10−3 | S130 | VIP1 transcription factor |
A0A1D6EHU0 | 0.34 | 1.6 × 10−4 | 0.53 | 2.5 × 10−3 | S31 | VIP1 transcription factor |
A0A1D6EK20 | 0.71 | 3.6 × 10−3 | 0.74 | 4.7 × 10−3 | S930 | RNA binding family protein |
A0A1D6EK20 | 0.58 | 2.5 × 10−4 | 0.72 | 2.7 × 10−3 | S949 | RNA binding family protein |
A0A1D6ELA3 | 1.15 | 1.8 × 10−1 | 1.40 | 5.8 × 10−3 | S180 | G-box-binding factor 1 |
A0A1D6H3I5 | 1.27 | 5.4 × 10−2 | 1.43 | 6.3 × 10−3 | S83 | HY5 transcription factor homolog |
A0A1D6IJ69 | 1.56 | 6.9 × 10−4 | 1.46 | 1.3 × 10−3 | S205 | NF-Y subunit B-3 |
A0A1D6IK52 | 0.81 | 5.2 × 10−2 | 0.70 | 3.3 × 10−3 | S172 | CAMTA 2 |
A0A1D6JVI5 | 0.93 | 7.0 × 10−1 | 0.46 | 8.8 × 10−4 | S203 | bZIP transcription factor 16 |
A0A1D6JVI5 | 0.95 | 6.4 × 10−1 | 0.41 | 6.9 × 10−5 | S148; S151 | bZIP transcription factor 16 |
A0A1D6JVI5 | 1.06 | 5.4 × 10−1 | 0.38 | 3.3 × 10−3 | S290 | bZIP transcription factor 16 |
A0A1D6K5M3 | 1.57 | 4.9 × 10−3 | 1.52 | 4.9 × 10−3 | S121 | NF-Y subunit B-2 |
A0A1D6K5M3 | 1.47 | 3.5 × 10−3 | 1.36 | 6.9 × 10−3 | S212 | NF-Y subunit B-2 |
A0A1D6K5M3 | 1.53 | 2.1 × 10−2 | 1.61 | 7.9 × 10−3 | S210; S213 | NF-Y subunit B-2 |
A0A1D6MZQ6 | 1.39 | 1.1 × 10−2 | 1.45 | 4.5 × 10−3 | S124 | VIP1 transcription factor |
A0A1D6PUS5 | 1.65 | 3.2 × 10−3 | 1.24 | 7.6 × 10−2 | S89 | Homeobox-leucine zipper protein MERISTEM L1 |
B4F937 | 1.51 | 3.5 × 10−3 | 1.33 | 1.4 × 10−2 | S147 | G-box binding factor |
B4FWJ9 | 0.53 | 2.7 × 10−4 | 0.47 | 1.1 × 10−4 | S139 | bZIP transcription factor |
B4FWJ9 | 0.60 | 8.5 × 10−5 | 0.66 | 2.7 × 10−4 | S31 | bZIP transcription factor |
C4J4L1 | 0.69 | 7.5 × 10−3 | 0.69 | 5.2 × 10−3 | T134 | ABI5-like protein 2 |
K7TX82 | 0.78 | 1.7 × 10−2 | 0.66 | 8.9 × 10−4 | S192 | VIP1 transcription factor |
K7VAC7 | 1.07 | 6.9 × 10−1 | 1.93 | 1.6 × 10−3 | S132 | HY5 transcription factor homolog |
K7VQH0 | 1.12 | 3.4 × 10−1 | 1.50 | 4.7 × 10−3 | S30 | HY5 transcription factor homolog |
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Xing, J.; Tan, J.; Feng, H.; Zhou, Z.; Deng, M.; Luo, H.; Deng, Z. Integrative Proteome and Phosphoproteome Profiling of Early Cold Response in Maize Seedlings. Int. J. Mol. Sci. 2022, 23, 6493. https://doi.org/10.3390/ijms23126493
Xing J, Tan J, Feng H, Zhou Z, Deng M, Luo H, Deng Z. Integrative Proteome and Phosphoproteome Profiling of Early Cold Response in Maize Seedlings. International Journal of Molecular Sciences. 2022; 23(12):6493. https://doi.org/10.3390/ijms23126493
Chicago/Turabian StyleXing, Jiayun, Jinjuan Tan, Hanqian Feng, Zhongjing Zhou, Min Deng, Hongbing Luo, and Zhiping Deng. 2022. "Integrative Proteome and Phosphoproteome Profiling of Early Cold Response in Maize Seedlings" International Journal of Molecular Sciences 23, no. 12: 6493. https://doi.org/10.3390/ijms23126493
APA StyleXing, J., Tan, J., Feng, H., Zhou, Z., Deng, M., Luo, H., & Deng, Z. (2022). Integrative Proteome and Phosphoproteome Profiling of Early Cold Response in Maize Seedlings. International Journal of Molecular Sciences, 23(12), 6493. https://doi.org/10.3390/ijms23126493