Dynamic proteome response of different rice varieties to drought stress

Rice is one of the most important food crops in the world. The productivity of rice crop is threatened by a number of different environmental conditions, including drought. We set out to analyse the proteome response of rice varieties with different genetic backgrounds, when exposed to drought stress at the late vegetative stage. We performed quantitative shotgun proteomic analysis of eight different rice varieties with varying levels of drought stress tolerance. Rice plants were exposed to drought stress until the phenotypic signs of severe drought stress appeared. Leaves from stressed and control treatments were harvested for protein extraction, followed by quantitative shotgun proteomics analysis, and targeted mass spectrometric analysis for proteotypic peptides identified in earlier studies in our laboratory.
Plants from 8 different rice varieties were grown in a temperature controlled greenhouse; Nipponbare, Doongara, IAC1131, Mahsuri, Reiziq, MC05, MC06 and MC07. Plants were grown to late vegetative stage and then exposed to drought stress, with leaf samples collected at the point of severe stress, and also following recovery. Proteins were extracted from leaf tissue using trichloroacetic acid – acetone extraction and precipitation. In-gel and in-solution digested peptides were separated and identified using nanoflow reversed-phase liquid chromatography – tandem orbitrap mass spectrometry on a Thermo Q-exactive. Peptides and proteins were identified using Proteome Discoverer and Global Proteome Machine software.
Our data indicates a dynamic proteome response of each variety to drought stress, revealing how different genotypes are able to cope with drought stress by adaptive molecular changes in the major biological pathways. In this study, approximately 20 to 40% of significantly proteins reduced in abundance in stress conditions were involved in photosynthesis, indicating inhibition of photosynthesis machinery in drought stress. In contrast, significantly increased abundance of stress response related proteins and those involved in proteolytic processing pathways were observed in drought conditions. We also identified many interesting proteins uniquely differentially expressed in specific genotypes. In contrast, 8 proteins were up-regulated in all genotypes; these included actin-depolymerizing factor 3 (ADF-3) and GSH-dependent dehydroascorbate reductase 1, which is in agreement with previous studies. We have also performed Multiple Reaction Monitoring quantitative assays for closer examination of changes in particular proteins in the same set of plants exposed to drought stress.
Using the information obtained from differentially regulated proteins in drought stress sensitive and tolerant varieties will pave the way for development of rice varieties with higher drought stress tolerance, which is important for our future food security.