Proteome Analysis of Rice Nuclear Proteins

Abstract

Plants sense and respond to environmental stimuli, including nutritional deficiency, and biotic and abiotic stresses. The modulation in gene expression patterns is one of the most important processes for adaptation to environmental changes. To develop the method to monitor changes in the composition of nuclear proteins that were induced by environmental stimuli, we attempted nuclear proteome analysis with aerial parts of 5-week-old rice seedling. Purified nuclei were obtained using percoll-density gradient centrifugation and nucleocytoplasmic fraction was extracted with salt. By analyses using a nanoLC/MS system, we identified 182 proteins, which were mostly consisted from histones, ribosomal proteins and RNA helicases. Among these identified proteins, regulatory proteins including transcription factors were estimated to be only ~10%. To improve the coverage of regulatory proteins such as transcription factors, we tried to enrich DNA-binding proteins using heparin- and DNA-affinity chromatography. Results obtained by these methods will also be discussed.