Proteome analysis of rice tissues by two-dimensional electrophoresis: an approach to the investigation of gibberellin regulated proteins

Abstract

Protein databases constructed using high-resolution two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) were used to explore the proteome expressed in various rice tissues. Proteins from leaf sheath, root, and cultured suspension cells were systematically analyzed using 2D-PAGE, mass spectrometry and Edman sequencing, followed by database searching. In all, 79 of the 431 spots detected by 2D-PAGE in the leaf sheath, 73 of the 508 spots in the root and 140 of the 962 spots in the cultured suspension cells could be identified. Protein lists were constructed for each tissue and used to investigate the effects of gibberellin (GA) treatment. In the leaf sheath, root and cultured suspension cells, 8, 21, and 14 of the identified proteins, respectively, were regulated by GA. These proteins included polypeptides involved in general metabolism, energy production, transcriptional regulation and signal transduction in the leaf sheath; in metabolism and defense in the root; and in metabolism, energy production, cell growth, defense and signal transduction in the cultured suspension cells. These results indicate that the proteome databases assembled in these studies will be useful for the rapid assessment of changes in protein content in specific tissues, and that proteins regulated by GA may play a significant role in tissue growth.

Update and challenges on proteomics in rice

“…The second largest group consists of proteins involved in metabolism. This is in contrast to the total rice proteome, in which metabolic proteins form the largest percentage of proteins in leaf sheath [42], but in the phosphoproteome analysis, they formed the second largest percentage. Other identified phosphoproteins are involved in energy production and transcription, and the functions of 7 proteins are unknown.…”

“…Of these proteins, 2-D LC identified 9 that were up-regulated and 9 that were down-regulated by GA 3 treatment, while 2-D DIGE identified 4 up-regulated and 4 down-regulated proteins. In our previous studies we showed that 32 proteins from leaf sheaths grown in vitro [41] and 8 proteins from leaf sheaths in intact rice plants [42] were regulated by GA during elongation. Most of the 32 proteins detected using leaf sheath segments were stress-related proteins.…”

“…The leaf sheath proteome, which includes proteins of the basal region, has been analyzed [41,42] (Fig. 2).…”

“…Proteins from leaf sheaths, including the basal region, of seedlings have been analyzed because the tissue was found to be important in the regulation of the height of rice plants [41,42]. The detected protein spots in the basal region were more abundant than in leaf sheath, because the leaf sheath proteins form a subset of the total basal region proteome.…”

Expression and Function of Proteins during Development of the Basal Region in Rice Seedlings

“…Several studies have dealt with the construction of proteomes for complex samples from rice, such as leaf, embryo, endosperm, root, stem, shoot, anther, and callus (11)(12)(13)(14)(15)(16)(17)(18)(19), and subcellular components such as Golgi bodies, mitochondria, plasma membrane, vacuolar membrane, Golgi membrane, and chloroplasts have also been studied (20 -22). These reports have focused on mapping the proteins and constructing a data base of expressed proteins of various tissues and subcellular components but have not addressed the changes in protein expression over time that are critical to understanding development in complex organisms.…”