Rice proteomics: A cornerstone for cereal food crop proteomes

Abstract

Proteomics-a systematic study of proteins present in a cell, tissue, organ, or organism at a particular moment during the life cycle-that began with classical two-dimensional electrophoresis and its advancement during the 1990s, has been revolutionized by a series of tremendous technological developments in mass spectrometry (MS), a core technology. Proteomics is exerting its influence on biological function of genes and genomes in the era (21st century) of functional genomics, and for this reason yeast, bacterial, and mammalian systems are the best examples. Although plant proteomics is still in its infancy, evolving proteomic technologies and the availability of the genome sequences of Arabidopsis thaliana (L.) Heyhn, and rice (Oryza sativa L.), model dicotyledoneous and monocotyledoneous (monocot) species, respectively, are propelling it towards new heights, as evidenced by the rapid spurt in worldwide plant proteome research. Rice, with an immense socio-economic impact on human civilization, is a representative model of cereal food crops, and we consider it as a cornerstone for functional genomics of cereal plants. In this review, we look at the history and the current state of monocot proteomes, including barley, maize, and wheat, with a central focus on rice, which has the most extensive proteomic coverage to date. On one side, we highlight advances in technologies that have generated enormous amount of interest in plant proteomics, and the other side summarizes the achievements made towards establishing proteomes during plant growth & development and challenge to environmental factors, including disease, and for studying genetic relationships. In light of what we have learned from the proteomic journey in rice and other monocots, we finally reveal and assess their impact in our continuous strive towards completion of their full proteomes.

A proteomic approach in analyzing heat‐responsive proteins in rice leaves

“…DHAR and NDPK1 exhibited parallel expression patterns between their mRNA and protein levels; however, the mRNA levels of GST and Trx-h showed different expression patterns than those of the corresponding proteins. The result of the present investigation is supported by the previously established concept that transcription patterns are not directly concomitant with protein expression levels [10]. In addition, these results pro- Figure 6.…”

“…Proteomics, or the systemic analysis of proteins expressed by genome, is not only a powerful molecular tool used in describing complete proteomes at the organelle, cell, organ, or tissue levels [9], but it can also compare proteomes affected by different physiological conditions, such as those resulting from the exposure to high temperature or other stressful conditions. The current status of rice proteomic analysis has been reviewed recently [10], but there still are no reports regarding the effects of heat stress on rice leaves. Thus far, there have been only a few proteomic studies regarding heat stress in plants [3,5,[11][12][13].…”

Gel-based proteomics approach for detecting low nitrogen-responsive proteins in cultivated rice species

“…Extraction of total protein was performed using trichloroacetic acid/acetone extraction protocol followed by solubilization in a modified lysis buffer (Agrawal and Rakwal, 2006). Leaf samples pooled from individual seedlings in two replications were placed in liquid nitrogen and ground thoroughly to a fine powder with a mortar and pestle (pre-cooled).…”

“…We believe that using high-throughput complementary genetic and proteomics approaches, the identification of such molecular components will serve in assigning potential markers in rice breeding/genetic selection programs. Today, proteomics is one of the leading "omic" technologies being used to study globally expressed proteins in a given tissue (Park, 2004;Agrawal et al, 2005a,b,c;Agrawal and Rakwal, 2006).…”

2D-DIGE-based proteome expression changes in leaves of rice seedlings exposed to low-level gamma radiation at Iitate village, Fukushima

“…3,4 were focused on the morphological and molecular-genetic effects in the cereal crop/grass genome model, riceOryza sativa L. [5][6][7][8][9] Rice has also been a focus of our studies due to its tremendous importance as a food crop and nutrient source, especially in Asia. Those initial studies examined the effects of short-time (72 h) external radiation exposure to cut leaf segments from 2-week-old rice plants, using a rice seedling model system that was established to demonstrate the stress responses at molecular level.…”