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Comparative proteomics illustrates the complexity of Fe, Mn and Zn deficiency-responsive mechanisms of potato (Solanum tuberosum L.) plants in vitro

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Abstract

Main conclusion

The present study is the first to integrate physiological and proteomic data providing information on Fe, Mn and Zn deficiency-responsive mechanisms of potato plants in vitro.

Abstract

Micronutrient deficiency is an important limiting factor for potato production that causes substantial tuber yield and quality losses. To under the underlying molecular mechanisms of potato in response to Fe, Mn and Zn deficiency, a comparative proteomic approach was applied. Leaf proteome change of in vitro-propagated potato plantlets subjected to a range of Fe-deficiency treatments (20, 10 and 0 μM Na-Fe-EDTA), Mn-deficiency treatments (1 and 0 μM MnCl2·4H2O) and Zn-deficiency treatment (0 μM ZnCl2) using two-dimensional gel electrophoresis was analyzed. Quantitative image analysis showed a total of 146, 55 and 42 protein spots under Fe, Mn and Zn deficiency with their abundance significantly altered (P < 0.05) more than twofold, respectively. By MALDI-TOF/TOF MS analyses, the differentially abundant proteins were found mainly involved in bioenergy and metabolism, photosynthesis, defence, redox homeostasis and protein biosynthesis/degradation under the metal deficiencies. Signaling, transport, cellular structure and transcription-related proteins were also identified. The hierarchical clustering results revealed that these proteins were involved in a dynamic network in response to Fe, Mn and Zn deficiency. All these metal deficiencies caused cellular metabolic remodeling to improve metal acquisition and distribution in potato plants. The reduced photosynthetic efficiency occurred under each metal deficiency, yet Fe-deficient plants showed a more severe damage of photosynthesis. More defence mechanisms were induced by Fe deficiency than Mn and Zn deficiency, and the antioxidant systems showed different responses to each metal deficiency. Reprogramming of protein biosynthesis/degradation and assembly was more strongly required for acclimation to Fe deficiency. The signaling cascades involving auxin and NDPKs might also play roles in micronutrient stress signaling and pinpoint interesting candidates for future studies. Our results first provide an insight into the complex functional and regulatory networks in potato plants under Fe, Mn and Zn deficiency.

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Abbreviations

CAT:

Catalase

2-DE:

Two-dimensional gel electrophoresis

DHAR:

Dehydroascorbate reductase

Fd:

Ferredoxin

FDH:

Formate dehydrogenase

FeSOD:

Superoxide dismutase [Fe]

FNR:

Ferredoxin NADP+ reductase

NDPKs:

Nucleoside diphosphate kinases

nsLTP:

Non-specific lipid-transfer protein

OEE:

Oxygen-evolving enhancer protein

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Acknowledgements

This work was supported by programs for National Key R&D Program of China (2017YFD0101905), National Natural Science Foundation of China (31471433, 31171477), Gansu High Educational Scientific Special Project (2018C-17), Gansu Provincial Key Laboratory of Aridland Crop Science (GSCS-2016-02).

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  1. College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, 730070, China

    Lixiang Cheng, Shaomei Zhang, Lili Yang, Bin Yu & Feng Zhang

  2. College of Horticulture, Gansu Agricultural University, Lanzhou, China

    Yuping Wang

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  1. Lixiang Cheng
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425_2019_3163_MOESM1_ESM.tif

Supplemental Fig. S1 The primary 2-DE gel maps at least three biological replicates for the potato leaf proteome of control (124 μM Na-Fe-EDTA) and Fe-deficiency treatments (20, 10 and 0 μM Na-Fe-EDTA) in vitro under Fe deficiency (TIFF 47071 kb)

425_2019_3163_MOESM2_ESM.tif

Supplemental Fig. S2 The primary 2-DE gel maps at least three biological replicates for the potato leaf proteome of control (100 μM MnCl2·4H2O) and Mn-deficiency treatments (1 and 0 μM MnCl2·4H2O) in vitro under Mn deficiency (TIFF 34022 kb)

425_2019_3163_MOESM3_ESM.tif

Supplemental Fig. S3 The primary 2-DE gel maps at least three biological replicates for the potato leaf proteome of control (30 μM ZnCl2) and Zn-deficiency treatment (0 μM ZnCl2) in vitro under Zn deficiency (TIFF 21350 kb)

425_2019_3163_MOESM4_ESM.tif

Supplemental Fig. S4 The detailed information on differentially abundant proteins within each cluster in the clustering analysis under Fe deficiency. The four columns of hierarchical cluster tree represent control (124 μM Na-Fe-EDTA) and Fe-deficiency treatments (20, 10 and 0 μM Na-Fe-EDTA), respectively. Each rows represent individual proteins. The up- and down-regulation of proteins are indicated in red and green, respectively. The intensity of colors is increased when the expression differences increased, as shown in the bar at the top. The differentially abundant proteins were grouped into eight clusters under Fe deficiency. The detailed information on these proteins within each cluster is presented, including the protein identification number and protein name (TIFF 889 kb)

425_2019_3163_MOESM5_ESM.tif

Supplemental Fig. S5 The detailed information on differentially abundant proteins within each cluster in the clustering analysis under Mn deficiency. The three columns of hierarchical cluster tree represent control (100 μM MnCl2·4H2O) and Mn-deficiency treatments (1 and 0 μM MnCl2·4H2O), respectively. Each rows represent individual proteins. The up- and down-regulation of proteins are indicated in red and green, respectively. The intensity of colors is increased when the expression differences increased, as shown in the bar at the top. The differentially abundant proteins were grouped into six clusters under Mn deficiency. The detailed information on these proteins within each cluster is presented, including the protein identification number and protein name (TIFF 496 kb)

425_2019_3163_MOESM6_ESM.tif

Supplemental Fig. S6 The detailed information on differentially abundant proteins within each cluster in the clustering analysis under Zn deficiency. The two columns of hierarchical cluster tree represent control (30 μM ZnCl2) and Zn-deficiency treatment (0 μM ZnCl2), respectively. Each rows represent individual proteins. The up- and down-regulation of proteins are indicated in red and green, respectively. The intensity of colors is increased when the expression differences increased, as shown in the bar at the top. The differentially abundant proteins were grouped into two clusters under Zn deficiency. The detailed information on these proteins within each cluster is presented, including the protein identification number and protein name (TIFF 308 kb)

Supplemental Table S1 The detailed MS medium formulation for Fe-, Mn- and Zn-deficiency treatment (XLSX 11 kb)

425_2019_3163_MOESM8_ESM.docx

Supplemental Table S2 Identification of differentially abundant proteins of potato leaves in vitro under Fe deficiency (DOCX 14218 kb)

425_2019_3163_MOESM9_ESM.docx

Supplemental Table S3 Identification of differentially abundant proteins of potato leaves in vitro under Mn deficiency (DOCX 198 kb)

425_2019_3163_MOESM10_ESM.docx

Supplemental Table S4 Identification of differentially abundant proteins of potato leaves in vitro under Zn deficiency (DOCX 141 kb)

425_2019_3163_MOESM11_ESM.xlsx

Supplemental Table S5 The primary identification information of differentially abundant proteins of potato leaves in vitro under Fe deficiency using MALDI-TOF/TOF MS. Protein identifications were performed by searching for the NCBInr-S. tuberosum database using peptide mass fingerprinting (PMF) and MS/MS data from a MALDI-TOF/TOF mass spectrometry analysis. a The spot number of identified proteins. b Gene identification number as in GenBank. c The number of matched peptides. d MASCOT score reported after searching against the NCBInr database. e The sequence coverage percentage (%). f Theoretical pI and mass (Da) values of identified proteins estimated with MASCOT (XLSX 194 kb)

425_2019_3163_MOESM12_ESM.xlsx

Supplemental Table S6 The primary identification information of differentially abundant proteins of potato leaves in vitro under Mn deficiency using MALDI-TOF/TOF MS. Protein identifications were performed by searching for the NCBInr-S. tuberosum database using peptide mass fingerprinting (PMF) and MS/MS data from a MALDI-TOF/TOF mass spectrometry analysis. a The spot number of identified proteins. b Gene identification number as in GenBank. c The number of matched peptides. d MASCOT score reported after searching against the NCBInr database. e The sequence coverage percentage (%). f Theoretical pI and mass (Da) values of identified proteins estimated with MASCOT (XLSX 88 kb)

425_2019_3163_MOESM13_ESM.xlsx

Supplemental Table S7 The primary identification information of differentially abundant proteins of potato leaves in vitro under Zn deficiency using MALDI-TOF/TOF MS. Protein identifications were performed by searching for the NCBInr-S. tuberosum database using peptide mass fingerprinting (PMF) and MS/MS data from a MALDI-TOF/TOF mass spectrometry analysis. a The spot number of identified proteins. b Gene identification number as in GenBank. c The number of matched peptides. d MASCOT score reported after searching against the NCBInr database. e The sequence coverage percentage (%). f Theoretical pI and mass (Da) values of identified proteins estimated with MASCOT (XLSX 70 kb)

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Cheng, L., Zhang, S., Yang, L. et al. Comparative proteomics illustrates the complexity of Fe, Mn and Zn deficiency-responsive mechanisms of potato (Solanum tuberosum L.) plants in vitro. Planta 250, 199–217 (2019). https://doi.org/10.1007/s00425-019-03163-w

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  • DOI: https://doi.org/10.1007/s00425-019-03163-w

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