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Correlation analysis of proteins responsive to Zn, Mn, or Fe deficiency in Arabidopsis roots based on iTRAQ analysis

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Abstract

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For discovering the functional correlation between the identified and quantified proteins by iTRAQ analysis, here we propose a correlation analysis method with cosine correlation coefficients as a powerful tool.

Abstract

iTRAQ analysis is a quantitative proteomics approach that enables identification and quantification of a large number of proteins. In order to obtain proteins responsive to Zn, Mn, or Fe mineral deficiency, we conducted iTRAQ analysis using a microsomal fraction of protein extractions from Arabidopsis root tissues. We identified and quantified 730 common proteins in three biological replicates with less than 1 % false discovery rate. To determine the role of these proteins in tolerating mineral deficiencies and their relation to each other, we calculated cosine correlation coefficients and represented the outcomes on a correlation map for visual understanding of functional relations among the identified proteins. Functionally similar proteins were gathered into the same clusters. Interestingly, a cluster of proteins (FRO2, IRT1, AHA2, PDR9/ABCG37, and GLP5) highly responsive to Fe deficiency was identified, which included both known and unknown novel proteins involved in tolerating Fe deficiency. We propose that the correlation analysis with the cosine correlation coefficients is a powerful method for finding important proteins of interest to several biological processes through comprehensive data sets.

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Acknowledgments

This work was supported by a Grant-in-Aid for Scientific Research on Innovative Areas (No. 23119512 to Y.F.) from the Ministry of Education, Culture, Sports, Science and Technology of Japan.; a Grant-in-Aid for Scientific Research from Nara Institute of Science and Technology supported by The Ministry of Education, Culture, Sports, Science and Technology, Japan. This research was supported by Japan Advanced Plant Science Network.

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No potential conflicts of interest were disclosed.

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Authors and Affiliations

  1. Plant Global Education Project Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama, 8916-5, Ikoma, 630-0192, Japan

    Sajad Majeed Zargar, Masayuki Fujiwara, Shoko Inaba, Mami Kobayashi & Yoichiro Fukao

  2. School of Biotechnology, SK University of Agricultural Sciences and Technology, Chatha, Jammu, Jammu and Kashmir, 180009, India

    Sajad Majeed Zargar

  3. Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan

    Masayuki Fujiwara, Rie Kurata & Yoichiro Fukao

  4. Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, 599-8531, Japan

    Yoshiyuki Ogata

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  1. Sajad Majeed Zargar
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  2. Masayuki Fujiwara
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  3. Shoko Inaba
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  4. Mami Kobayashi
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  5. Rie Kurata
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  6. Yoshiyuki Ogata
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  7. Yoichiro Fukao
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Correspondence to Yoichiro Fukao.

Additional information

Communicated by Manoj Prasad.

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299_2014_1696_MOESM1_ESM.xlsx

Supplemental Table S1 List of all proteins identified by iTRAQ analysis using roots grown on 0-Zn, 0-Mn, or 0-Fe media. (XLSX 124 kb)

Supplemental Table S2 Elemental analysis of Col-0 roots grown on Basal, 0-Zn, 0-Mn, or 0-Fe media. (XLSX 10 kb)

299_2014_1696_MOESM3_ESM.eps

Supplemental Fig. S1 The enlarged cluster composed of mainly ribosomal proteins in correlation analysis represented in Fig. 2a (EPS 10860 kb)

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Zargar, S.M., Fujiwara, M., Inaba, S. et al. Correlation analysis of proteins responsive to Zn, Mn, or Fe deficiency in Arabidopsis roots based on iTRAQ analysis. Plant Cell Rep 34, 157–166 (2015). https://doi.org/10.1007/s00299-014-1696-2

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  • DOI: https://doi.org/10.1007/s00299-014-1696-2

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