Integrated Transcriptome and Proteome Analysis Reveals the Regulatory Mechanism of Root Growth by Protein Disulfide Isomerase in Arabidopsis
Abstract
:1. Introduction
2. Results
2.1. 16F16 Inhibits the Activity of AtPDI In Vitro
2.2. Effect of 16F16 Stress on Root Elongation in Arabidopsis
2.3. Transcriptome and Proteome Data Quality Assessment
2.4. Analysis of DEGs and DEPs and Subcellular Localization of DEPs
2.5. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes Pathway Analysis of Differentially Expressed Genes and Differentially Expressed Proteins
2.6. Analysis of the Association between the Proteomic and Transcriptomic Data
2.7. Transcription Factor Analysis of 16F16-Treated Arabidopsis Seedlings
3. Discussion
4. Materials and Methods
4.1. Plant Materials and Growth Conditions
4.2. Protein Disulfide Isomerase Activity Assay
4.3. RNA Extraction, RNA Sequencing, and Data Analysis
4.4. Transcription Data Filtering, Differential Gene Screening and Enrichment Analysis
4.5. TMT-Based Quantitative Proteomics and Data Analysis
4.5.1. Sample Preparation
4.5.2. Protein Digestion
4.5.3. TMT Labeling of Peptides
4.5.4. LC–MS/MS Analysis
4.5.5. Database Searches and Analysis
4.5.6. Bioinformatics Analysis
4.6. Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Sample | Reads No. | Clean Reads | Bases (bp) | Q30 (bp) | N (%) | Q20 (%) | Q30 (%) |
---|---|---|---|---|---|---|---|
CT1 | 43,871,862 | 40,883,152 | 6,624,651,162 | 6,239,513,563 | 0.000748 | 98.06 | 94.18 |
CT2 | 41,291,352 | 38,451,224 | 6,234,994,152 | 5,834,960,997 | 0.000696 | 97.81 | 93.58 |
CT3 | 42,679,328 | 39,797,694 | 6,444,578,528 | 6,069,764,697 | 0.000696 | 98.05 | 94.18 |
CT4 | 42,475,758 | 39,601,164 | 6,413,839,458 | 6,012,276,058 | 0.000709 | 97.87 | 93.73 |
FT1 | 40,937,568 | 38,143,410 | 6,181,572,768 | 5,792,475,690 | 0.000699 | 97.87 | 93.7 |
FT2 | 39,994,820 | 37,256,048 | 6,039,217,820 | 5,663,898,333 | 0.000709 | 97.89 | 93.78 |
FT3 | 43,689,960 | 40,734,992 | 6,597,183,960 | 6,179,973,447 | 0.0007 | 97.85 | 93.67 |
FT4 | 40,593,030 | 37,838,228 | 6,129,547,530 | 5,752,737,744 | 0.000697 | 97.92 | 93.85 |
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Liu, Y.; Song, P.; Yan, M.; Luo, J.; Wang, Y.; Fan, F. Integrated Transcriptome and Proteome Analysis Reveals the Regulatory Mechanism of Root Growth by Protein Disulfide Isomerase in Arabidopsis. Int. J. Mol. Sci. 2024, 25, 3596. https://doi.org/10.3390/ijms25073596
Liu Y, Song P, Yan M, Luo J, Wang Y, Fan F. Integrated Transcriptome and Proteome Analysis Reveals the Regulatory Mechanism of Root Growth by Protein Disulfide Isomerase in Arabidopsis. International Journal of Molecular Sciences. 2024; 25(7):3596. https://doi.org/10.3390/ijms25073596
Chicago/Turabian StyleLiu, Yanan, Peng Song, Meilin Yan, Jinmei Luo, Yingjuan Wang, and Fenggui Fan. 2024. "Integrated Transcriptome and Proteome Analysis Reveals the Regulatory Mechanism of Root Growth by Protein Disulfide Isomerase in Arabidopsis" International Journal of Molecular Sciences 25, no. 7: 3596. https://doi.org/10.3390/ijms25073596