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Physiological studies and proteomic analysis for differentially expressed proteins and their possible role in the root of N-efficient rice (Oryza sativa L.)

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Abstract

The root proteome of nitrogen-efficient and nitrogen-inefficient rice cultivars was compared in this study in order to investigate the differential expression of proteins under deficient (1 mM), low (10 mM) and high (25 mM) levels of nitrogen (N). Nitrogen use efficiency (NUE) was assessed by biochemical assays such as N-uptake kinetics and activities of N-assimilation enzymes. Two-dimensional gel electrophoresis and MALDI–TOF–MS analysis resulted in the identification of 504 protein spots (210 and 294 spots in cvs. Rai Sudha and Munga Phool, respectively). A positive correlation was observed between physiological parameters and the concentration of a number of root proteins. Sixty-three spots showed a significant cultivar × N-treatment effect on the level of expression. Functional aspects of eleven spots with major alterations in expression over control were critically analyzed. The data suggest that glutamine synthetase, cysteine proteinase inhibitor-I, porphobilinogen deaminase (fragment) and ferritin were involved in conferring N efficiency to the N-efficient rice cultivars/genotypes. Interestingly, these proteins are involved directly or indirectly in N assimilation. Such studies should help us in identifying and understanding the structural or functional protein(s) involved in the response to the level of nitrogen fertilization.

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Abbreviations

CHCA:

Cyanohydroxycinnamic acid

DDW:

Double-distilled water

DW:

Dry weight

ETC:

Electron-transport chain

GAPDH:

Glyceraldehyde-3-phosphate dehydrogenase

γ-GHA:

γ-Glutamyl hydroxamate

Gln:

Glutamine

Glu:

Glutamate

GOGAT:

Glutamate synthase

GS:

Glutamine synthetase

HNE:

High nitrogen efficient

LNE:

Low nitrogen efficient

MNE:

Moderate nitrogen efficient

NE:

Nitrogen efficiency

NiR:

Nitrite reductase

NR:

Nitrate reductase

NUE:

Nitrogen use efficiency

PBG:

Porphobilinogen

PMF:

Peptide mass fingerprinting

ROS:

Reactive oxygen species

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Acknowledgments

K.R.H. is grateful to the University Grants Commission, Government of India, for granting him a Junior Research Fellowship. M.I.Q. is grateful to DST and UGC, Govt. of India. Part of the study was done when M.I. was Visiting Professor at the Plant Production Department of King Saud University, Riyadh, Saudi Arabia.

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Authors and Affiliations

  1. Molecular Ecology Laboratory, Department of Botany, Faculty of Science, Jamia Hamdard, New Delhi, 110062, India

    Khalid Rehman Hakeem, Altaf Ahmad & Muhammad Iqbal

  2. Faculty of Forestry, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia

    Khalid Rehman Hakeem

  3. Department of Genetics, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, 0002, South Africa

    Bilal Ahmad Mir

  4. Proteomics and Bioinformatics Lab, Department of Biotechnology, Jamia Millia Islamia, New Delhi, 110025, India

    Mohd. Irfan Qureshi

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  1. Khalid Rehman Hakeem
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  2. Bilal Ahmad Mir
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Correspondence to Khalid Rehman Hakeem.

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Hakeem, K.R., Mir, B.A., Qureshi, M.I. et al. Physiological studies and proteomic analysis for differentially expressed proteins and their possible role in the root of N-efficient rice (Oryza sativa L.). Mol Breeding 32, 785–798 (2013). https://doi.org/10.1007/s11032-013-9906-0

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