Flooding is a serious problem for soybean cultivation because it markedly reduces growth and grain yields. Here, 2 proteomics techniques were used to evaluate whether endoplasmic reticulum (ER)-enriched fraction is altered in soybean under flooding stress. Two-day-old soybeans were treated with flooding for 2 days, and rough ER-enriched fraction was then purified from root tips. Flooding-responsive protein of ER-enriched fraction was identified using gel-free and 1D-gel based proteomics techniques, and 117 proteins were increased and 212 proteins were decreased in soybean root tips in response to flooding stress. Among the identified proteins, 111 were functionally categorized as being involved in protein synthesis, post-translational modification, protein folding, protein degradation, and protein activation. Among differentially regulated proteins, the mRNA expression levels of 14 proteins that were predicted to be localized in the ER were analyzed. Notably, 3-ketoacyl-CoA reductase 1 was up-regulated and eight genes related to stress, hormone metabolism, cell wall and DNA repair were down-regulated within 1 day under flooding conditions. In addition, the expression of luminal-binding protein 5 was specifically induced in flood-stressed roots, whereas arabinogalactan protein 2 and methyltransferase PMT2 were down-regulated. Taken together, these results suggest that flooding mainly affects the function of protein synthesis and glycosylation in the ER in root tips of soybean.
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