Skip to main content
SpringerLink
Log in

Proteomic analysis of Allium cepa var. agrogarum L. roots under copper stress

  • Regular Article
  • Published:
Plant and Soil Aims and scope Submit manuscript

Abstract

Aims

In the present study, the effects of Cu (2.0 and 8.0 μM) on root growth of Allium cepa var. agrogarum L. were addressed and protein abundance levels were analyzed using the technology of proteomics combined with transcriptomics, in order to go deeper into the understanding of the mechanism of Cu toxicity on plant root systems at the protein level and to provide valuable information for monitoring and forecasting the effects of exposure to Cu in real scenarios conditions.

Methods

Protein extraction; Two-dimensional electrophoresis (2-DE) analysis; Mass spectrometry analysis; Establishment of the in-house database; Restriction enzyme map of the in-house database and protein identification.

Results

Root growth was dramatically inhibited after 12 h Cu treatment. By establishing an in-house database and using mass spectrometry analysis, 27 differentially abundant proteins were identified. These 27 proteins were involved in multiple biological processes including defensive response, transcription regulation and protein synthesis, cell wall synthesis, cell cycle and DNA replication, and other important functions.

Conclusions

Our results provide new insights at the proteomic level into the Cu-induced responses, defensive responses and toxic effects, and provide new molecular markers of the early events of plant responses to Cu toxicity. Moreover, the establishment of an in-house database provides a big improvement for proteomics research on non-model plants.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Adams E, Frank L (1980) Metabolism of proline and the hydroxyprolines. Annu Rev Biochem 49:1005–1061

    Article  CAS  PubMed  Google Scholar 

  • Ahsan N, Renaut J, Komatsu S (2009) Recent developments in the application of proteomics to the analysis of plant responses to heavy metals. Proteomics 9:2602–2621

    Article  CAS  PubMed  Google Scholar 

  • Andrés-Colás N, Perea-García A, Puig S, Peňarrubia L (2010) Deregulated copper transport affects Arabidopsis development especially in the absence of environmental cycles. Plant Physiol 153:170–184

    Article  PubMed  PubMed Central  Google Scholar 

  • Arcuri F, Papa S, Carducci A, Romagnoli R, Liberatori S, Riparbelli MG, Sanchez JC, Tosi P, del Vecchio MT (2004) Translationally controlled tumor protein (TCTP) in the human prostate and prostate cancer cells: expression, distribution, and calcium binding activity. Prostate 60:130–140

    Article  CAS  PubMed  Google Scholar 

  • Avis JM, Clarke PR (1996) Ran, a GTPase involved in nuclear process: its regulators and effectors. J Cell Sci 109:2423–2427

    CAS  PubMed  Google Scholar 

  • Bona E, Marsano F, Cavaletto M, Berta G (2007) Proteomic characterization of copper stress response in Cannabis sativa roots. Proteomics 7:1121–1130

    Article  CAS  PubMed  Google Scholar 

  • Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248–254

    Article  CAS  PubMed  Google Scholar 

  • Burkhead JL, Reynolds KAG, Abdel-Ghany SE, Cohu CM, Pilon M (2009) Copper homeostasis. New Phytol 182:799–816

    Article  CAS  PubMed  Google Scholar 

  • Chen C, Song YF, Zhuang K, Li L, Xia Y, Shen ZG (2015) Proteomic analysis of copper-binding proteins in excess copper-stressed roots of two rice (Oryza sativa L.) varieties with different Cu tolerances. PLoS One 10:e0125367

    Article  PubMed  PubMed Central  Google Scholar 

  • Contreras L, Moenne A, Gaillard F, Potin P, Correa JA (2010) Proteomic analysis and identification of copper stress-regulated proteins in the marine alga Scytosiphon gracilis (Phaeophyceae). Aquat Toxicol 96:85–89

    Article  CAS  PubMed  Google Scholar 

  • Cvjetko P, Zovko M, Balen B (2014) Proteomics of heavy metal toxicity in plants. Arh Hig Rada Toksikol 65:1–18

    Article  CAS  PubMed  Google Scholar 

  • Díaz-Riquelme J, Martínez-Zapater JM, Carmona MJ (2014) Transcriptional analysis of tendril and inflorescence development in Grapevine (Vitis vinifera L.). PLoS One 9:e92339

    Article  PubMed  PubMed Central  Google Scholar 

  • Dorion S, Clendenning A, Jeukens J, Salas JJ, Parveen N, Haner AA, Law RD (2012) A large decrease of cytosolic triosephosphate isomerase in transgenic potato roots affects the distribution of carbon in primary metabolism. Planta 236:1177–1190

    Article  CAS  PubMed  Google Scholar 

  • Doucey MA, Bender FC, Hess D, Hofsteenge J, Bron C (2006) Caveolin-1 interacts with the chaperone complex TCP-1 and modulates its protein folding activity. Cell Mol Life Sci 63:939–948

    Article  CAS  PubMed  Google Scholar 

  • Fu Y, Yang Q, Sun RX, Li DQ, Zeng R, Ling CX, Gao W (2004) Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry. Bioinformatics 20:1948–1954

    Article  CAS  PubMed  Google Scholar 

  • Fujimori T, Takigami H (2014) Pollution distribution of heavy metals in surface soil at an informal electronic-waste recycling site. Environ Geochem Health 36:159–168

    Article  CAS  PubMed  Google Scholar 

  • Gao Y, Chen XB, Zhang ZY (2007) Advances in research on lignin biosynthesis and its molecular regulation. Biotechnol Bull 2:47–51

    Google Scholar 

  • Giri PK, Jing-Song F, Shanmugam MK, Ding JL, Sethi G, Swaminathan K, Sivaraman J (2012) NMR structure of Carcinoscorpius rotundicauda thioredoxin-related protein 16 and its role in regulating transcription factor NF-κB activity. J Biol Chem 287:29417–29428

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gorecka KM, Konopka-Postupolska D, Hennig J, Buchet R, Pikula S (2005) Peroxidase activity of annexin 1 from Arabidopsis thaliana. Biochem Bioph Res Commun 336:868–875

    Article  CAS  Google Scholar 

  • Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng QD, Chen ZH, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Haensch R, Mendel RR (2009) Physiological functions of mineral micronutrients (Cu, Zn, Mn, Fe, Ni, Mo, B, Cl). Curr Opin Plant Biol 12:259–266

    Article  CAS  Google Scholar 

  • Hollingworth D, Candel AM, Nicastro G, Martin SR, Briata P, Gherzi R, Ramos A (2012) KH domains with impaired nucleic acid binding as a tool for functional analysis. Nucleic Acids Res 40:6873–6886

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hossain Z, Komatsu S (2013) Contribution of proteomic studies towards understanding plant heavy metal stress response. Front Plant Sci 3(article 310):1–12

    Google Scholar 

  • Hwang J, Oh CS, Kang BC (2013) Translation elongation factor 1B (eEF1B) is an essential host factor for Tobacco mosaic virus infection in plants. Virology 439:105–114

    Article  CAS  PubMed  Google Scholar 

  • Izuta S, Kitahara M, Hamaguchi T (2004) Regulation of eukaryotic DNA replication by proliferation associated protein, PA2G4, in vitro. Nucleic Acids Symp Ser 48:285–286

    Article  Google Scholar 

  • Khedr AHA, Abbas MA, Wahid AAA, Quick WP, Abogadallah GM (2003) Proline induces the expression of salt stress responsive proteins and may improve the adaptation of Pancratium maritimum L. to salt-stress. J Exp Bot 54:2553–2562

    Article  CAS  PubMed  Google Scholar 

  • Kim TH, Lee BR, Jung WJ, Kim KY, Avice JC, Ourry A (2004) De novo protein synthesis in relation to ammonia and proline accumulation in water stressed white clover. Funct Plant Biol 31:847–855

    Article  CAS  Google Scholar 

  • Kopczewski T, Kuźniak E (2013) Redox signals as a language of interorganellar communication in plant cells. Cent Eur J Biol 8:1153–1163

    CAS  Google Scholar 

  • Kosová K, Vítámvás P, Prášil IT, Renaut J (2011) Plant proteome changes under abiotic stress — contribution of proteomics studies to understanding plant stress response. J Proteomics 74:1301–1322

    Article  PubMed  Google Scholar 

  • Lauvergeat V, Lacomme C, Lacombe E, Lasserre E, Roby D (2001) Two cinnamoyl-CoA reductase (CCR) genes from Arabidopsis thaliana are differentially expressed during development and in response to infection with pathogenic bacteria. Phytochemistry 57:1187–1195

    Article  CAS  PubMed  Google Scholar 

  • Lee J, Lee H, Noh EK, Park M, Park H, Kim JH, Kim IC, Yim JH (2014) Expression analysis of transcripts responsive to osmotic stress in Deschampsia antarctica Desv. Genes Genom 36:283–291

    Article  CAS  Google Scholar 

  • Lee S, Lee EJ, Yang EJ, Lee JE, Park AR, Song WH, Park OK (2004) Proteomic identification of annexins, calcium-dependent membrane binding proteins that mediate osmotic stress and abscisic acid signal transduction in Arabidopsis. Plant Cell 16:1378–1391

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li DQ, Fu Y, Sun RX, Ling CX, Wei YG, Zhou H, Zeng R, Yang Q, He S, Gao W (2005) pFind: a novel database-searching software system for automated peptide and protein identification via tandem mass spectrometry. Bioinformatics 21:3049–3050

    Article  CAS  PubMed  Google Scholar 

  • Li F, Shi JY, Shen CF, Chen GC, Hu SP, Chen YX (2009) Proteomic characterization of copper stress response in Elsholtzia splendens roots and leaves. Plant Mol Biol 71:251–263

    Article  CAS  PubMed  Google Scholar 

  • Li GZ, Peng XQ, Xuan HM, Wei LT, Yang YY, Guo TC, Kang GZ (2013) Proteomic analysis of leaves and roots of common wheat (Triticum aestivum L.) under copper-stress conditions. J Proteome Res 12:4846–4861

    Article  CAS  PubMed  Google Scholar 

  • Mirlean N, Roisenberg A, Chies JO (2007) Metal contamination of vineyard soils in wet subtropics (Southern Brazil). Environ Pollut 149:10–17

    Article  CAS  PubMed  Google Scholar 

  • Mostofa MG, Fujita M (2013) Salicylic acid alleviates copper toxicity in rice (Oryza sativa L.) seedlings by up-regulating antioxidative and glyoxalase systems. Ecotoxicology 22:959–973

    Article  CAS  PubMed  Google Scholar 

  • Mota R, Pereira SB, Meazzini M, Fernandes R, Santos A, Evans CA, Philippis RD, Wright PC, Tamagnini P (2015) Effects of heavy metals on Cyanothece sp. CCY 0110 growth, extracellular polymeric substances (EPS) production, ultrastructure and protein profiles. J Proteomics 120:75–94

    Article  CAS  PubMed  Google Scholar 

  • Neave MJ, Streten-Joyce C, Nouwens AS, Glasby CJ, McGuinness KA, Parry DL, Gibb KS (2012) The transcriptome and proteome are altered in marine polychaetes (Annelida) exposed to elevated metal levels. J Proteomics 75:2721–2735

    Article  CAS  PubMed  Google Scholar 

  • Nishi R, Hashimoto H, Uchimiya H, Kato A (1993) The primary structure of two proteins from the small ribosomal subunit of rice. Biochim Biophys Acta Gene Struct Expr 1216:113–114

    Article  CAS  Google Scholar 

  • Oka T, Nemoto T, Jigami Y (2007) Functional analysis of Arabidopsis thaliana RHM2/MUM4, a multidomain protein involved in UDP-D-glucose to UDP-L-rhamnose conversion. J Biol Chem 282:5389–5403

    Article  CAS  PubMed  Google Scholar 

  • Ou CY, Stevenson RE, Brown VK, Schwartz CE, Allen WP, Khoury MJ, Rozen R, Oakley GP Jr, Adams MJ Jr (1996) 5, 10 methylenetetrahydrofolate reductase genetic polymorphism as a risk factor for neural tube defects. Am J Med Genet 63:610–614

    Article  CAS  PubMed  Google Scholar 

  • Parker CC, Parker ML, Smith AC, Waldron KW (2001) Pectin distribution at the surface of potato parenchyma cells in relation to cell-cell adhesion. J Agric Food Chem 49:4364–4371

    Article  CAS  PubMed  Google Scholar 

  • Qin R, Jiao YQ, Zhang SS, Jiang WS, Liu DH (2010) Effects of aluminum on nucleoli in root tip cells and selected physiological and biochemical characters in Allium cepa var. agrogarum L. BMC Plant Biol 10:225

    PubMed  PubMed Central  Google Scholar 

  • Qin R, Wang CY, Chen D, Björn LO, Li SS (2015) Copper induced root growth inhibition of Allium cepa var. agrogarum L. involves disturbances in cell division and DNA damage. Environ Toxicol Chem 34:1045–1055

    Article  CAS  PubMed  Google Scholar 

  • Qin XR, Zhang MJ, Wu L (2012) Purification and characterization of Cu, Zn superoxide dismutase from pumpkin (Cucurbita moschata) pulp. Eur Food Res Technol 235:1049–1054

    Article  CAS  Google Scholar 

  • Quintero-Reyes IE, Garcia-Orozco KD, Sugich-Miranda R, Arvizu-Flores AA, Velazquez-Contreras EF (2012) Shrimp oncoprotein nm23 is a functional nucleoside diphosphate kinase. J Bioenerg Biomembr 44:325–331

    Article  CAS  PubMed  Google Scholar 

  • Ravanel S, Block MA, Rippert P, Jabrin S, Curien G, Rebeille F, Douce R (2004) Methionine metabolism in plants: chloroplasts are autonomous for de novo methionine synthesis and can import S-adenosylmethionine from the cytosol. J Biol Chem 279:22548–22557

    Article  CAS  PubMed  Google Scholar 

  • Saunders KM, Harrison JJ, Butler ECV, Hodgson DA, McMinn A (2013) Recent environmental change and trace metal pollution in World Heritage Bathurst Harbour, southwest Tasmania, Australia. J Paleolimnol 50:471–485

    Article  Google Scholar 

  • Shah K, Kumar RG, Verma A, Dubey RS (2001) Effect of cadmium on lipid peroxidation, superoxide anion generation and activities of antioxidant enzymes in growing rice seedlings. Plant Sci 161:1135–1144

    Article  CAS  Google Scholar 

  • Singla-Pareek SL, Yadav SK, Pareek A, Reddy MK, Sopory SK (2006) Transgenic tobacco overexpressing glyoxalase pathway enzymes grow and set viable seeds in zinc spiked soils. Plant Physiol 140:613–623

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Song YF, Cui J, Zhang HX, Wang GP, Zhao FJ, Shen ZG (2013) Proteomic analysis of copper stress responses in the roots of two rice (Oryza sativa L.) varieties differing in Cu tolerance. Plant Soil 366:647–658

    Article  CAS  Google Scholar 

  • Song YF, Zhang HX, Chen C, Wang GP, Zhuang K, Cui J, Shen ZG (2014) Proteomic analysis of copper-binding proteins in excess copper-stressed rice roots by immobilized metal affinity chromatography and two-dimensional electrophoresis. Biometals 27:265–276

    Article  CAS  PubMed  Google Scholar 

  • Su YP, Lu XD, Shen SD, Zhang CY (2011) GATL 12 is essential for chloroplast biogenesis in Arabidopsis. Chin Bull Bot 46:379–385

    Article  CAS  Google Scholar 

  • Sugimoto M, Sakamoto W (1997) Putative phospholipid hydroperoxide glutathione peroxidase gene from Arabidopsis thaliana induced by oxidative stress. Genes Genet Syst 72:311–316

    Article  CAS  PubMed  Google Scholar 

  • Sun DF, Weng YR, Chen YX, Lu R, Wang X, Fang JY (2008) Knock-down of methylenetetrahydrofolate reductase reduces gastric cancer cell survival: an in vitro study. Cell Biol Int 32:879–887

    Article  CAS  PubMed  Google Scholar 

  • Tan YF, O’Toole N, Taylor NL, Millar AH (2010) Divalent metal ions in plant mitochondria and their role in interactions with proteins and oxidative stress-induced damage to respiratory function. Plant Physiol 152:747–761

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wagner U, Edwards R, Dixon DP, Mauch F (2002) Probing the diversity of the Arabidopsis glutathione S-transferase gene family. Plant Mol Biol 49:515–532

    Article  CAS  PubMed  Google Scholar 

  • Wang LH, Li DQ, Fu Y, Wang HP, Zhang JF, Yuan ZF, Sun RX, Zeng R, He SM, Gao W (2007) pFind 2.0: a software package for peptide and protein identification via tandem mass spectrometry. Rapid Commun Mass Spectrom 21:2985–2991

    Article  CAS  PubMed  Google Scholar 

  • Wang YT, Björn LO (2014) Heavy metal pollution in Guangdong Province, China, and the strategies to manage the situation. Front Environ Sci 2(article 9):1–12

    CAS  Google Scholar 

  • Yan SP, Tang ZC, Su WA, Sun WN (2005) Proteomic analysis of salt stress-responsive proteins in rice root. Proteomics 5:235–244

    Article  CAS  PubMed  Google Scholar 

  • Yang CL, Guo RP, Yue L, Zhou K, Wu ZF (2013) Environmental quality assessment and spatial pattern of potentially toxic elements in soils of Guangdong Province, China. Environ Earth Sci 70:1903–1910

    Article  CAS  Google Scholar 

  • Yruela I (2009) Copper in plants: acquisition, transport and interactions. Funct Plant Biol 36:409–430

    Article  CAS  Google Scholar 

  • Zhang SS, Zhang HM, Qin R, Jiang WS, Liu DH (2009) Cadmium induction of lipid peroxidation and effects on root tip cells and antioxidant enzyme activities in Vicia faba L. Ecotoxicology 18:814–823

    Article  CAS  PubMed  Google Scholar 

  • Zou HX, Pang QY, Zhang AQ, Lin LD, Li N, Yan XF (2015) Excess copper induced proteomic changes in the marine brown algae Sargassum fusiforme. Ecotoxicol Environ Saf 111:271–280

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This work was supported by the National Natural Science Foundation of China (31070242), the Leading Scientists Project of Guangdong Province, the Guangdong Pearl River Scholar Funded Scheme (2012), the Research Fund for the Doctoral Program of Higher Education of China (20114407110006), the Science and Technology Program of Guangzhou, China (2014J4100053) and the Scientific Research Foundation of Graduate School of South China Normal University (2012kyjj114). The authors are grateful to Dr. Rachel Naele (QIMR Berghofer Medical Research Institute, Australia), Dr. Andy McLeod (The University of Edinburgh, Edinburgh, UK) and Prof. John Richard Schrock (Emporia State University, Kansas, USA) for language revision.

Author information

Author notes

    Authors and Affiliations

    1. Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education, School of Life Science, South China Normal University, Guangzhou, 510631, China

      Rong Qin, Chanjuan Ning, Lars O. Björn & Shaoshan Li

    2. Department of Biology, Molecular Cell Biology, Lund University, Lund, 22467, Sweden

      Lars O. Björn

    Authors
    1. Rong Qin
      View author publications

      You can also search for this author in PubMed Google Scholar

    2. Chanjuan Ning
      View author publications

      You can also search for this author in PubMed Google Scholar

    3. Lars O. Björn
      View author publications

      You can also search for this author in PubMed Google Scholar

    4. Shaoshan Li
      View author publications

      You can also search for this author in PubMed Google Scholar

    Corresponding author

    Correspondence to Shaoshan Li.

    Ethics declarations

    Conflict of interest

    We declare that we have no conflict of interest.

    Additional information

    Responsible Editor: Henk Schat.

    Rong Qin and Chanjuan Ning contributed equally to this work.

    Electronic supplementary material

    Below is the link to the electronic supplementary material.

    Electronic supplementary material 1

    (PDF 48292 kb)

    Electronic supplementary material 2

    (PDF 5493 kb)

    Electronic supplementary material 3

    (PDF 273 kb)

    Electronic supplementary material 4

    (PDF 143 kb)

    Rights and permissions

    Reprints and permissions

    About this article

    Check for updates. Verify currency and authenticity via CrossMark

    Cite this article

    Qin, R., Ning, C., Björn, L.O. et al. Proteomic analysis of Allium cepa var. agrogarum L. roots under copper stress. Plant Soil 401, 197–212 (2016). https://doi.org/10.1007/s11104-015-2741-9

    Download citation

    • Received:

    • Accepted:

    • Published:

    • Issue Date:

    • DOI: https://doi.org/10.1007/s11104-015-2741-9

    Keywords

    Search

    Navigation