Transcriptomic and Metabolomic Analysis of a Pseudomonas-Resistant versus a Susceptible Arabidopsis Accession
Abstract
:1. Introduction
2. Results
2.1. Appropriate Experimental Study to Dissect the Arabidopsis–Pseudomonas Pathosystem
2.2. Significant Transcriptomic Differences in the Basal Gene Expression of SA-Dependent SAR in Col-0 and C24
2.3. The Basal Expression of SA-Related Genes in C24 under Axenic Conditions
2.4. The Aliphatic Glucosinolate Biosynthesis Pathway Is Differential between Col-0 and C24
2.5. Col-0 and C24 Share JA-Dependent Responses upon Infection with Pst
2.6. JA-Related Responses after Infection with Pst Are Delayed in Col-0
2.7. Pst Induces SA-Dependent SAR-Related Gene Expression in Col-0
3. Discussion
3.1. SAR-Related Differences between Col-0 and C24 Play a Major Role in Determining Resistance to Pst
3.2. Nitrogen Metabolism and Aliphatic Glucosinolates
3.3. JA-Related Responses against Pst Are Shared between Accessions, though Are Delayed in Col-0
4. Materials and Methods
4.1. Plant Material and Growth Conditions
4.2. Bacterial Growth
4.3. Inoculation and Sampling
4.4. Transcriptomics
4.5. Metabolomics
4.6. Data Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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GO BP ID | p-Value | Count | Size | Term | |
---|---|---|---|---|---|
1 | GO:0009627 | 6.35 × 10−53 | 128 | 442 | systemic acquired resistance |
2 | GO:0009697 | 5.88 × 10−49 | 85 | 207 | salicylic acid biosynthetic process |
3 | GO:0009814 | 1.16 × 10−47 | 134 | 532 | defense response, incompatible interaction |
4 | GO:0009696 | 1.90 × 10−47 | 86 | 220 | salicylic acid metabolic process |
5 | GO:0042537 | 8.94 × 10−45 | 90 | 258 | benzene-containing compound metabolic process |
6 | GO:0006952 | 4.69 × 10−44 | 249 | 1644 | defense response |
7 | GO:0002376 | 1.78 × 10−42 | 179 | 977 | immune system process |
8 | GO:0045087 | 1.90 × 10−42 | 166 | 859 | innate immune response |
9 | GO:0006955 | 4.89 × 10−42 | 166 | 865 | immune response |
10 | GO:0071446 | 6.40 × 10−35 | 93 | 353 | cellular response to salicylic acid stimulus |
11 | GO:0009751 | 1.12 × 10−34 | 108 | 469 | response to salicylic acid stimulus |
12 | GO:0009607 | 1.15 × 10−34 | 208 | 1413 | response to biotic stimulus |
13 | GO:0009863 | 2.31 × 10−34 | 92 | 351 | salicylic acid mediated signaling pathway |
14 | GO:0051707 | 3.09 × 10−34 | 207 | 1412 | response to other organism |
15 | GO:0031348 | 6.87 × 10−33 | 79 | 273 | negative regulation of defense response |
16 | GO:0031347 | 1.27 × 10−31 | 112 | 539 | regulation of defense response |
17 | GO:0080134 | 1.07 × 10−30 | 113 | 560 | regulation of response to stress |
18 | GO:0009862 | 6.30 × 10−30 | 72 | 250 | systemic acquired resistance, salicylic acid mediated signaling pathway |
19 | GO:0051704 | 2.42 × 10−29 | 231 | 1802 | multi-organism process |
20 | GO:0050832 | 4.46 × 10−29 | 84 | 344 | defense response to fungus |
GO BP ID | p-Value | Count | Size | Term | |
---|---|---|---|---|---|
1 | GO:0006952 | 2.79 × 10−4 | 63 | 1644 | defense response |
2 | GO:0007165 | 4.80 × 10−4 | 71 | 1948 | signal transduction |
3 | GO:0044700 | 8.90 × 10−4 | 72 | 2027 | single organism signaling |
4 | GO:0023052 | 9.02 × 10−4 | 72 | 2028 | signaling |
5 | GO:0007154 | 4.15 × 10−3 | 78 | 2367 | cell communication |
6 | GO:0016145 | 4.35 × 10−3 | 3 | 14 | S-glycoside catabolic process |
7 | GO:0080028 | 5.70 × 10−3 | 2 | 5 | nitrile biosynthetic process |
8 | GO:0006591 | 8.41 × 10−3 | 2 | 6 | ornithine metabolic process |
9 | GO:0015824 | 9.54 × 10−3 | 6 | 74 | proline transport |
10 | GO:0015804 | 1.15 × 10−2 | 6 | 77 | neutral amino acid transport |
11 | GO:0032890 | 1.16 × 10−2 | 2 | 7 | regulation of organic acid transport |
12 | GO:0050898 | 1.16 × 10−2 | 2 | 7 | nitrile metabolic process |
13 | GO:0051952 | 1.16 × 10−2 | 2 | 7 | regulation of amine transport |
14 | GO:0070417 | 1.22 × 10−2 | 3 | 20 | cellular response to cold |
15 | GO:0000304 | 1.52 × 10−2 | 2 | 8 | response to singlet oxygen |
16 | GO:0019674 | 1.52 × 10−2 | 2 | 8 | NAD metabolic process |
Content Fold Change after 48 h | ||
---|---|---|
KNApSAcK ID: Name(s) | Col-0 | C24 |
Mock vs. Pst | Mock vs. Pst | |
C00007850: 5-Oxooctyl glucosinolate; Glucocappasalin | n.d. | 1.63 |
C00007855: 4-Phenylbutyl glucosinolate | n.d. | 1.53 |
C00007801: 5-Hexenyl glucosinolate | n.d. | 1.37 |
3-Hydroxy-5-(methylthio)pentyl glucosinolate | n.d. | 1.21 |
C00001463: Glucobrassicanapin; 4-Pentenyl glucosinolate | n.d. | 1.19 |
C00007340: 3-Hydroxypropyl glucosinolate | n.d. | 1.16 |
C00007817: 2-Hydroxypropyl glucosinolate | ||
C00007826: 1-Methyl-2-hydroxyetyl glucosinolate; Glucosisymbrin | ||
C00001488: Sinigrin; 2-Phenylethyl glucosinolate; | n.d. | 1.11 |
Allyl glucosinolate | ||
C00007845: 9-Methylthiononyl glucosinolate | n.d. | 1.01 |
C00007800: 6-Heptenyl glucosinolate | 2.92 ** | 1.28 |
C00001473: Glucoiberverin; | 2.59 *** | 1.26 |
3-(Methylthio)propyl glucosinolate | ||
C00000125: Glucobrassicin; Glucobrassicine; 3-Indolylmethylglucosinolate | 1.71 *** | 2.17 * |
C00007856: 3-Phenylpropyl glucosinolate | 1.67 ** | 1.26 |
C00000130: 5-Hydroxyglucobrassicin; 5-Hydroxy-3-indolylmethylglucosinolate | 1.63 | 2.03 * |
C00007348: 6-Methylsulfinylhexyl glucosinolate; Glucohesperin | 1.53 * | 1.24 |
C00007813: 3-Hydroxy-6-(methylthio)hexyl glucosinolate | ||
C00007352: 7-(Methylsulfinyl)heptyl glucosinolate; Glucoibarin | 1.52 * | 1.29 |
C00007624: 5-Methylthiopentyldesulfoglucosinolate | 1.47 * | 1.21 |
C00007355: 8-Methylsulfinyloctyl glucosinolate; Glucohirsutin | 1.41 * | 1.13 |
C00007593: 5-Methylthiopentylglucosinolate; Glucoberteroin | 1.32 * | 1.22 |
C00007353: 7-Methylthioheptyl glucosinolate | 1.31 * | 1.19 |
C00007356: 8-Methylthio-octyl glucosinolate | 1.28 * | 1.07 |
C00001474: Glucolepidiin; Ethyl glucosinolate | 1.16 | n.d. |
Gene Annotation | Group | 2 h Col-0 Pst—Mock | 4 h Col-0 Pst—Mock | 8 h Col-0 Pst—Mock | 16 h Col-0 Pst—Mock | 24 h Col-0 Pst—Mock | 48 h Col-0 Pst—Mock | 2 h C24 Pst—Mock | 4 h C24 Pst—Mock | 8 h C24 Pst—Mock | 16 h C24 Pst—Mock | 24 h C24 Pst—Mock | 48 h C24 Pst—Mock |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Interval 1 | Interval 2 | Interval 1 | Interval 2 | ||||||||||
ABO3 | I | 0.103 | −0.012 | 0.366 | −0.181 | 1.630 | 1.265 | 0.971 | 0.393 | 0.764 | 0.071 | 0.589 | 0.536 |
ACT11 | I | −0.226 | −0.402 | −0.731 | −0.359 | −0.850 | −1.324 | −0.627 | −0.724 | −0.560 | −0.053 | −0.024 | −0.773 |
AOC3 | II | 0.328 | 0.529 | 0.892 | 0.897 | 1.573 | 2.488 | 0.967 | 0.540 | 0.347 | 1.386 | 1.594 | 1.313 |
ASB1 | I | 0.298 | −0.187 | 0.006 | 0.799 | 1.482 | 1.588 | 0.966 | 0.865 | 0.963 | −0.168 | 1.132 | −0.674 |
AT1G26390 | II | 0.685 | 0.642 | 1.478 | 0.340 | 0.852 | 3.186 | 1.371 | 0.819 | 0.858 | 0.868 | 0.676 | 2.555 |
AT1G53885 | II | 0.449 | 0.307 | 0.441 | 2.016 | 2.292 | 3.491 | 0.609 | 0.437 | 1.076 | 2.354 | 2.846 | 3.425 |
AT1G53885 | II | 0.449 | 0.307 | 0.441 | 2.016 | 2.292 | 3.491 | 0.609 | 0.437 | 1.076 | 2.354 | 2.846 | 3.425 |
AT1G60730 | II | 0.321 | 0.378 | 0.520 | 0.452 | 0.524 | 1.035 | 0.684 | 0.747 | 0.406 | 0.690 | 0.510 | 0.788 |
AT1G66310 | I | −0.296 | −0.121 | −0.794 | −0.718 | −1.015 | −0.734 | −0.016 | −0.885 | −0.933 | 0.352 | −0.472 | 0.443 |
AT2G45220 | II | 0.376 | 0.369 | 2.129 | 0.467 | 0.965 | 3.166 | 0.987 | 1.035 | 1.201 | 0.818 | 0.546 | 1.904 |
AT3G04000 | II | 0.529 | 0.432 | 0.664 | 0.359 | 0.487 | 1.505 | 0.574 | 0.721 | 0.735 | 0.686 | 1.116 | 1.529 |
AT3G11340 | II | 0.311 | 1.576 | 2.301 | 1.246 | 3.784 | 4.448 | 1.297 | 1.275 | 1.021 | 1.130 | 2.061 | 0.305 |
AT3G22600 | II | 0.324 | 0.524 | 2.631 | 1.069 | 1.626 | 1.798 | 1.040 | 0.859 | 0.477 | 0.387 | 0.883 | 1.069 |
AT3G46080 | I | 0.082 | −0.065 | 0.103 | −0.019 | 1.822 | 2.888 | 1.302 | 0.915 | 1.227 | 0.472 | 0.883 | 1.278 |
AT4G03130 | I | 0.383 | −0.324 | −0.452 | −0.726 | −0.209 | −1.041 | −0.513 | −0.414 | −1.063 | 0.567 | 0.210 | 0.324 |
AT4G11890 | I | 0.251 | 0.398 | 1.576 | 0.830 | 1.309 | 1.781 | 0.466 | 0.915 | 0.396 | 0.404 | 0.188 | 0.098 |
AT4G19970 | II | −0.096 | −0.208 | 1.366 | 0.529 | 0.393 | 1.702 | 0.977 | 0.687 | 1.105 | 0.142 | 0.742 | 1.559 |
AT5G05600 | II | 0.111 | 0.545 | 0.909 | 1.480 | 1.805 | 3.007 | 0.852 | 0.593 | 1.127 | 1.921 | 1.887 | 1.873 |
AT5G08240 | II | 0.644 | 0.272 | 0.675 | 0.497 | 0.655 | 1.840 | 0.949 | 0.698 | 0.572 | 0.485 | 0.566 | 0.800 |
AT5G39050 | I | 0.168 | 0.613 | 0.472 | 0.551 | 0.919 | 1.364 | 0.808 | 0.598 | 0.581 | 0.255 | 0.576 | 0.674 |
AT5G57510 | II | 0.984 | 0.034 | 0.666 | 0.159 | 0.914 | 3.287 | 1.357 | 0.702 | 0.672 | 0.654 | 1.405 | 2.171 |
CEN2 | II | −0.228 | 0.843 | 1.387 | 0.228 | 2.256 | 2.978 | 0.562 | 1.072 | 0.688 | 0.771 | 1.000 | 1.479 |
COBL5 | I | 0.023 | 0.641 | 0.809 | 0.533 | 0.778 | 1.461 | 0.567 | 0.681 | 0.553 | 0.448 | 0.525 | 0.302 |
DUR | II | 0.534 | 0.791 | 1.592 | 0.092 | 1.595 | 3.018 | 0.785 | 0.803 | 0.729 | 0.730 | 0.979 | 1.989 |
EDS1 | I | −0.275 | −0.142 | 0.000 | 0.429 | 0.690 | 1.035 | 1.260 | 0.528 | 0.346 | 0.326 | −0.263 | −0.433 |
FMO1 | II | 0.779 | 0.480 | 2.049 | −0.297 | 3.178 | 5.345 | 1.072 | 0.803 | 1.119 | 1.146 | 2.160 | 1.341 |
GRX480 | II | −0.088 | 0.007 | 1.703 | 1.759 | 2.910 | 3.277 | 0.987 | 0.613 | 0.316 | 0.846 | 1.046 | 0.796 |
GSTU11 | II | 0.029 | 0.257 | 0.254 | 0.333 | 1.101 | 3.677 | 1.264 | 0.997 | 0.128 | 2.348 | 2.694 | 2.566 |
GSTU4 | II | 0.999 | 0.931 | 1.966 | 1.391 | 1.722 | 4.467 | 1.929 | 1.435 | 1.548 | 1.520 | 1.509 | 0.904 |
GSTU8 | I | −0.586 | −0.769 | 1.098 | 0.937 | 1.166 | 1.823 | 1.408 | 1.644 | 1.064 | 1.143 | 0.616 | 0.585 |
IAR3 | II | −0.053 | 0.397 | 0.932 | 0.884 | 1.251 | 2.349 | 0.860 | 0.533 | 0.611 | 0.727 | 0.986 | 1.138 |
KCO2 | I | −0.318 | 0.669 | −1.301 | −1.217 | −0.333 | −0.673 | −0.033 | −1.172 | −0.582 | −0.079 | −0.793 | −0.726 |
LHT7 | II | −0.610 | 0.736 | 2.174 | 1.331 | 3.433 | 3.421 | 0.126 | 1.278 | 0.406 | 1.260 | 1.436 | 0.584 |
MYB13 | II | 0.059 | 0.560 | 0.600 | 0.328 | 0.797 | 1.428 | 0.569 | 0.875 | 0.743 | 0.386 | 0.958 | 0.935 |
MYC2 | II | −0.030 | 0.155 | 0.367 | 1.191 | 1.256 | 1.525 | 0.791 | 0.782 | 0.190 | 1.131 | 0.931 | 0.983 |
PDF1.2 | II | −0.351 | 0.428 | 2.226 | 2.240 | 1.757 | 2.317 | 1.654 | 1.651 | 2.028 | 1.620 | 1.277 | 0.082 |
RAP2.6 | II | −0.201 | −0.194 | 0.100 | 0.302 | 1.627 | 3.460 | 1.092 | 0.340 | 0.895 | 0.679 | 0.745 | 1.586 |
Rap2.6L | II | 0.595 | 0.889 | 0.897 | 0.431 | 1.205 | 2.564 | 0.747 | 1.115 | 0.810 | 0.579 | 0.975 | 1.987 |
RLP43 | I | 0.503 | 0.117 | 1.137 | 0.388 | 1.122 | 1.656 | 0.829 | 0.937 | 0.422 | 0.084 | 0.557 | 0.447 |
SBT3.3 | II | −0.498 | 0.952 | 1.016 | 0.524 | 0.655 | 2.469 | 1.394 | 0.949 | 1.221 | 1.041 | 1.584 | 1.582 |
TPS04 | II | 0.253 | 0.916 | 0.453 | 1.528 | 2.856 | 5.219 | 1.063 | 1.163 | 0.861 | 2.564 | 1.961 | 1.249 |
UGT73D1 | II | 0.123 | −0.107 | 0.044 | 0.770 | 0.723 | 2.176 | 0.469 | 1.061 | 0.903 | 0.544 | 1.313 | 0.924 |
WAK3 | II | 0.359 | 0.272 | 1.733 | 1.003 | 1.688 | 2.445 | 0.824 | 0.669 | 0.489 | 0.276 | 0.767 | 0.962 |
WRKY75 | II | 0.759 | 0.181 | 1.547 | 0.269 | 1.214 | 4.190 | 1.208 | 1.271 | 0.733 | 0.886 | 0.674 | 1.676 |
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Orf, I.; Tenenboim, H.; Omranian, N.; Nikoloski, Z.; Fernie, A.R.; Lisec, J.; Brotman, Y.; Bromke, M.A. Transcriptomic and Metabolomic Analysis of a Pseudomonas-Resistant versus a Susceptible Arabidopsis Accession. Int. J. Mol. Sci. 2022, 23, 12087. https://doi.org/10.3390/ijms232012087
Orf I, Tenenboim H, Omranian N, Nikoloski Z, Fernie AR, Lisec J, Brotman Y, Bromke MA. Transcriptomic and Metabolomic Analysis of a Pseudomonas-Resistant versus a Susceptible Arabidopsis Accession. International Journal of Molecular Sciences. 2022; 23(20):12087. https://doi.org/10.3390/ijms232012087
Chicago/Turabian StyleOrf, Isabel, Hezi Tenenboim, Nooshin Omranian, Zoran Nikoloski, Alisdair R. Fernie, Jan Lisec, Yariv Brotman, and Mariusz A. Bromke. 2022. "Transcriptomic and Metabolomic Analysis of a Pseudomonas-Resistant versus a Susceptible Arabidopsis Accession" International Journal of Molecular Sciences 23, no. 20: 12087. https://doi.org/10.3390/ijms232012087