A proteomic screen and identification of waterlogging-regulated proteins in tomato roots

To gain a better understanding of the tomato root response to waterlogging stress at protein level, a proteomic approach has been conducted in combination with physiological analyses. Five-week old plants were subjected to waterlogging stress, and roots were collected 24 and 72 h after treatment. Waterlogging stress resulted in a gradual increase of lipid peroxidation and in vivo H2O2 concentration in roots. To elucidate temporal changes in protein expression in tomato roots, proteins were extracted from the root samples, separated by 2-DE, and visualized by staining with Coomassie Brilliant Blue. A total of 35 proteins were differentially expressed in tomato roots in response to waterlogging stress, and 29 were identified using MALDI-TOF analysis. Of the proteins identified, 16 proteins were up-regulated and 13 proteins were down-regulated in waterlogged tomato roots. In addition to previously identified waterlogging-regulated proteins, we identified several novel proteins, including 3-beta-hydroxylase, phenylalanine ammonia-lyase, glutamyl-tRNA reductase, flavanone 3-hydroxylase, mitochondrial ATPase alpha subunit, cysteine protease, DWARF1, and NIM1-like protein 2. These newly identified proteins are involved in several cellular processes, including hormone and secondary metabolite synthesis, programmed cell death, and stress and defense mechanisms. Five differentially accumulated proteins were further analyzed at the mRNA level, which confirmed the differential gene expression, and revealed that the transcript levels were not always consistent with the translation level. The identification of these novel proteins in the waterlogging stress response provides new insight that can lead to a better understanding of the molecular basis of waterlogging-sensitivity in plants.