Rejuvenating rice proteomics: Facts, challenges, and visions

Abstract

Proteomics is progressing at an unprecedented pace, as can be exemplified by the progress in model organisms such as yeast, bacteria, and mammals. Proteomics research in plants, however, has not progressed at the same pace. Unscrambling of the genome sequences of the dicotyledoneous Arabidopsis thaliana (L.) and monocotyledoneous rice (Oryza sativa L.) plant species, respectively, has made them accessible reference organisms to study plant proteomics. Study of these two reference plants is expected to unravel the mystery of plant biology. Rice, a critically important food crop on the earth, has been termed a "cornerstone" and the "Rosetta stone" for functional genomics of cereal crops. Here, we look at the progress in unraveling rice proteomes and present the facts, challenges, and vision. The text is divided into two major parts: the first part presents the facts and the second part discusses the challenges and vision. The facts include the technology and its use in developing proteomes, which have been critically and constructively reviewed. The challenges and vision deal with the establishment of technologies to exhaustively investigate the protein components of a proteome, to generate high-resolution gel-based reference maps, and to give rice proteomics a functional dimension by studying PTMs and isolation of multiprotein complexes. Finally, we direct a vision on rice proteomics. This is our third review in series on rice proteomics, which aims to stimulate an objective discussion among rice researchers and to understand the necessity and impact of unraveling rice proteomes to their full potential.

Gel‐based proteomics reveals potential novel protein markers of ozone stress in leaves of cultivated bean and maize species of Panama

“…Guarare 8128), a necessary and proper study of the O 3 effects in these two plants was conducted. A proteomics [21][22][23][24][25][26][27][28] approach was considered for conducting an initial investigation, due to the fact that our group possesses antibodies for various ozone-responsive proteins, and second, 2-DE was previously and successfully used for investigating rice responses to O 3 [29,30]. Using both 1-DE coupled to Western analysis and 2-DE for identifying protein changes in conjunction with MS we have successfully identified protein changes in leaves of both bean and maize plants exposed to O 3 .…”

System, trends and perspectives of proteomics in dicot plantsPart III: Unraveling the proteomes influenced by the environment, and at the levels of function and genetic relationships

“…With the proteomes investigated/established for the complex developmental stages [1], the next stage involves for extended proteomic studies in the dicotyledoneous (dicot) plants, mainly due to unfavorable conditions for plant in their environment. A unique symbiotic interaction between bacteria and dicot plants in the environment gives rise to the symbiosome within infected cells of root nodules.…”

“…Proteomics has also invaded the classical field of taxonomy, with genetic relationships between species and genera that are being established based on the comparison of protein patterns. As in developmental proteomics [1], both two-dimensional gel electrophoresis (2-DGE [2][3][4]) and mass spectrometry (MS [5][6][7]) have been instrumental in the investigation of their proteomes (Fig. 1); these core technologies have been discussed in detail in part I of the review [8].…”

Translating the Genome for Translational Research: Proteomics in Agriculture

“…Others have described plant proteomics as in its infancy (Agrawal et al 2006 It possesses an established database for a single species (human) and encourages the spread of proteomics technologies. Plant proteomics will have a long mile to tread before the proteome databases of important crops are gathered from among other nations to facilitate exchange of resources and information from among plant proteomic researchers.…”