Deep Learning Neural Network Prediction Method Improves Proteome Profiling of Vascular Sap of Grapevines during Pierce’s Disease Development
Abstract
:1. Introduction
2. Material and Methods
2.1. Plant Material and X. fastidiosa Inoculation
2.2. Vascular Sap Extraction and X. fastidiosa Quantification
2.3. Protein Digestion of Vascular Leaf Sap
2.4. Liquid Chromatography Tandem Mass Spectrometry
2.5. Chromatogram Library Creation
2.6. Analytic Samples, Data Analysis and Raw Data Processing
2.7. Spectral Library Search
2.8. Quantification and Criteria for Protein Identification
2.9. Functional Enrichment Analysis
3. Results
3.1. Creating a DIA Library and Improving the Data Mining of Vascular Sap Proteome Data
3.2. Plant Secreted Proteins in Response to Pierce’s Disease
3.3. Enriched Biological Processes in Grapevine Vascular Leaf Sap
4. Discussion
4.1. A New Proteomic Approach for Vascular Sap Studies
4.2. Plant Response to X. fastidiosa Infection as Assessed Using the Vascular Sap
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Vitis sp. Variety | Biological Material | Xf Inoc. | Method | Peptide Spectra Analysis | Total Proteins | Molecular Weight (kDa) | Matched Peptides | Signal Peptide | Ref. |
---|---|---|---|---|---|---|---|---|---|
Chardonnay | Xylem sap | No | 2D-PAGE MALDI-TOF MS/MS | GPM | 10 | 25–150 | 1 | No | [21] |
PD tolerant/susceptible varieties | Xylem sap | No | 2D-PAGE LC-MS/MS | Mascot | 100 * | 20–75 | 1–4 | No | [22] |
PD tolerant/susceptible varieties | Stem | Yes | 2D-PAGE nano-LC-MS/MS | Bioworks | 200 * | 14.4–45 | 2–32 | No | [23] |
Chardonnay | Leaf and apoplastic fluid | No | 2D-PAGE MALDI-TOF MS/MS | Mascot | 227 | 15–120 | NA | No | [24] |
PD tolerant/susceptible varieties | Xylem tissue | No | 2D-PAGE MALDI-TOF MS/MS | Mascot | 200 * | 20–75 | NA | No | [25] |
Thompson Seedless | Xylem sap | Yes | LC-MS/MS | Scaffold | 91 | 10–114 | 2–23 | Yes | [26] |
Thompson Seedless | Vascular leaf sap | Yes | LC-MS/MS | ScaffoldDIA (GPF) | 145 | 12–217 | 2–22 | Yes | This study |
Thompson Seedless | Vascular leaf sap | Yes | LC-MS/MS | ScaffoldDIA+Prosit | 360 | 8–217 | 2–31 | Yes | This study |
Accession Number | Arabidopsis Best Match | Protein Name | GPF DIA | DIA + Prosit | ||||
---|---|---|---|---|---|---|---|---|
Matched Peptide | Ratio * (log2) | FDR | Matched Peptide | Ratio * (log2) | FDR | |||
Pathogenesis-related (PR1) | ||||||||
VIT_03s0088g00810 | AT2G14610.1 | pathogenesis-related gene 1 | 2 | 6.85 | 9.37 × 10−12 | 2 | 8.76 | 8.77 × 10−13 |
Beta-1,3-glucanases (PR2) | ||||||||
VIT_08s0007g06060 | AT3G57240.1 | beta-1,3-glucanase 3 | 11 | 8.92 | 9.73 × 10−17 | 10 | 9.09 | 1.43 × 10−9 |
VIT_08s0007g06040 | AT3G57240.1 | beta-1,3-glucanase 3 | 9 | 5.36 | 8.31 × 10−10 | 6 | 5.50 | 2.82 × 10−7 |
VIT_06s0061g00120 | AT3G57240.1 | beta-1,3-glucanase 3 | 13 | 4.79 | 1.08 × 10−10 | 11 | 5.37 | 1.48 × 10−9 |
Pathogenesis-related (PR3) | ||||||||
VIT_04s0008g00120 | AT3G12500.1 | basic chitinase | 6 | 5.80 | 3.09 × 10−13 | 10 | 6.57 | 2.33 × 10−12 |
Pathogenesis-related (PR4) | ||||||||
VIT_14s0081g00030 | AT3G04720.1 | pathogenesis-related 4 | 3 | 4.96 | 4.05 × 10−11 | 3 | 5.44 | 1.07 × 10−8 |
Chitinases | ||||||||
VIT_16s0050g02230 | AT5G24090.1 | chitinase A | 7 | 4.37 | 3.63 × 10−4 | 9 | 8.41 | 1.06 × 10−12 |
VIT_15s0046g01570 | AT5G24090.1 | chitinase A | 3 | 3.54 | 1.36 × 10−6 | 3 | 3.44 | 3.72 × 10−5 |
VIT_11s0149g00380 | AT4G19810.1 | Glycosyl hydrolase ** | 5 | −2.94 | 2.26 × 10−4 | 3 | −2.47 | 9.29 × 10−3 |
VIT_11s0206g00030 | AT4G19810.1 | Glycosyl hydrolase ** | 4 | −4.94 | 2.62 × 10−7 | 3 | −4.44 | 1.60 × 10−4 |
VIT_16s0050g02210 | AT5G24090.1 | chitinase A | 6 | 6.03 | 2.88 × 10−8 | |||
Peroxidases | ||||||||
VIT_06s0004g07740 | AT5G05340.1 | Peroxidase superfamily | 8 | 3.82 | 3.10 × 10−7 | 6 | 4.15 | 1.36 × 10−6 |
VIT_07s0191g00050 | AT2G22420.1 | Peroxidase superfamily | 6 | −3.53 | 1.46 × 10−5 | 7 | −2.72 | 1.20 × 10−3 |
VIT_12s0055g01000 | AT5G64120.1 | Peroxidase superfamily | ND | ND | ND | 7 | −4.13 | 2.04 × 10−3 |
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Helena Duarte Sagawa, C.; Zaini, P.A.; de A. B. Assis, R.; Saxe, H.; Salemi, M.; Jacobson, A.; Wilmarth, P.A.; Phinney, B.S.; M. Dandekar, A. Deep Learning Neural Network Prediction Method Improves Proteome Profiling of Vascular Sap of Grapevines during Pierce’s Disease Development. Biology 2020, 9, 261. https://doi.org/10.3390/biology9090261
Helena Duarte Sagawa C, Zaini PA, de A. B. Assis R, Saxe H, Salemi M, Jacobson A, Wilmarth PA, Phinney BS, M. Dandekar A. Deep Learning Neural Network Prediction Method Improves Proteome Profiling of Vascular Sap of Grapevines during Pierce’s Disease Development. Biology. 2020; 9(9):261. https://doi.org/10.3390/biology9090261
Chicago/Turabian StyleHelena Duarte Sagawa, Cíntia, Paulo A. Zaini, Renata de A. B. Assis, Houston Saxe, Michelle Salemi, Aaron Jacobson, Phillip A. Wilmarth, Brett S. Phinney, and Abhaya M. Dandekar. 2020. "Deep Learning Neural Network Prediction Method Improves Proteome Profiling of Vascular Sap of Grapevines during Pierce’s Disease Development" Biology 9, no. 9: 261. https://doi.org/10.3390/biology9090261