Advances in plant proteomics toward improvement of crop productivity and stress resistancex.

Junjie Hu,Christof Rampitsch,Natalia V Bykova

doi:10.3389/fpls.2015.00209

Junjie Hu, Christof Rampitsch + Show 1 more

Open Access

https://doi.org/10.3389/fpls.2015.00209

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Abstract

Abiotic and biotic stresses constrain plant growth and development negatively impacting crop production. Plants have developed stress-specific adaptations as well as simultaneous responses to a combination of various abiotic stresses with pathogen infection. The efficiency of stress-induced adaptive responses is dependent on activation of molecular signaling pathways and intracellular networks by modulating expression, or abundance, and/or post-translational modification (PTM) of proteins primarily associated with defense mechanisms. In this review, we summarize and evaluate the contribution of proteomic studies to our understanding of stress response mechanisms in different plant organs and tissues. Advanced quantitative proteomic techniques have improved the coverage of total proteomes and sub-proteomes from small amounts of starting material, and characterized PTMs as well as protein–protein interactions at the cellular level, providing detailed information on organ- and tissue-specific regulatory mechanisms responding to a variety of individual stresses or stress combinations during plant life cycle. In particular, we address the tissue-specific signaling networks localized to various organelles that participate in stress-related physiological plasticity and adaptive mechanisms, such as photosynthetic efficiency, symbiotic nitrogen fixation, plant growth, tolerance and common responses to environmental stresses. We also provide an update on the progress of proteomics with major crop species and discuss the current challenges and limitations inherent to proteomics techniques and data interpretation for non-model organisms. Future directions in proteomics research toward crop improvement are further discussed.

Highlights

Understanding all levels that regulate adaptive mechanisms and the resilience of crop plants in the context of climate changes is absolutely essential to reach significant achievements in genomics-driven breeding of major crops for high productivity and stress tolerance
Improved protein extraction protocols, advanced gelfree quantitative techniques and bioinformatics approaches to the identification and analysis of complex proteomes at both subcellular and whole plant proteome levels in different crops have significantly advanced our understanding of developmental process, abiotic stress sensing mechanisms, and intracellular signal transduction mechanisms
The recent proteomic studies have contributed to elucidation of complex relationship between stress tolerance and crop productivity, which would enable the development of novel breeding strategies resulting in an increase in crop productivity and environmental performance

Summary

Introduction

Understanding all levels that regulate adaptive mechanisms and the resilience of crop plants in the context of climate changes is absolutely essential to reach significant achievements in genomics-driven breeding of major crops for high productivity and stress tolerance. An increasing number of studies have been discussing the contribution of proteomics to deeper insights into the molecular mechanisms of plant responses to stresses and signaling pathways linking changes in protein expression to cellular metabolic events, such as studies using model plants Arabidopsis (Wienkoop et al, 2010), rice (see for reviews Singh and Jwa, 2013; Kim et al, 2014) and sorghum (Ngara and Ndimba, 2014). In the recent years quantitative proteomic studies using high resolution and mass accuracy instruments have been contributing with important information to our understanding of plant growth, development, and interactions with the environment This capability is especially useful for crops as it may contribute to increasing nutritional value and yield, and to understanding mechanisms of crop adaptation to responses to abiotic stresses. Proteomic analysis is achieved through (1) separation and identification of proteins based on 2-DE or coupled gel-free shotgun liquid chromatography tandem mass spectrometry (LC–MS/MS) platforms; (2) elucidation of protein functions and protein functional networks in plant metabolic and signaling pathways through the analysis of protein mapping, characterization of PTMs and protein–protein interactions; (3) bioinformatic strategies and the use of databases for both model

Methodology

Findings

Concluding Remarks and Future Challenges