Proteomics analysis of drought stress response in two rice varieties with contrasting phenotypes

We performed an extensive quantitative proteomics study of the two rice varieties Nipponbare and IAC 1131. The IAC 1131 variety is known to be relatively tolerant to drought stress, while Nipponbare is sensitive to drought stress. We analysed protein extracts from both mature leaf tissue, and shoot growing zone tissue prepared by microscopic dissection. Both tissue samples were analysed first by label free quantitation and then by tandem mass tags (MT) quantitation using nano LC – MS/MS on a QExactive orbitrap mass spectrometer. Proteins were identified and quantified using various software packages including Xtandem, Proteome Discoverer, Scrappy and TMTPrepPro.
We found that IAC1131 and Nipponbare respond very differently to drought stress – different tissues from the same plant employ different strategies to deal with drought stress. IAC1131 appears to be better able to cope with stressful conditions by up-regulating a suite of proteins potentially involved in stress response in the mature leaf tissue, as well as maintaining the active stage of the growing zone by up-regulating a suite of proteins related to cell division. Secondary metabolism was repressed in IAC1131, apparently to save energy for stress response. Nipponbare, in contrast, lacks the range of stress responses shown by the drought tolerant variety and can not maintain cell growth under drought stress.