Proteomic Characterization of the Greening Process in Rice Seedlings Using the MS Spectral Intensity-based Label Free Method

Abstract

Illumination-induced greening in dark-grown plants is one of the most dramatic developmental processes known in plants. In our current study, we characterized the greening process of rice seedlings using comparative proteome analysis. We identified 886 different proteins in both whole cell lysates of illuminated and nonilluminated rice shoots and performed comparative proteome analysis based on the MS spectral intensities obtained for unique peptides from respective proteins. Furthermore, the changes in the levels of individual proteins were then compared with those of the corresponding mRNAs. The results revealed well-coordinated increases in the enzymes involved in the Calvin cycle at both the protein and mRNA levels during greening, and that the changes at the mRNA level precede those at the protein level. Although a much lower effect of illumination was found on the enzymes associated with glycolysis and the TCA cycle, coordinated increases during greening were evident for the enzymes involved in photorespiration and nitrogen assimilation as well as the components of the chloroplastic translational machinery. These results thus define the differential regulation of distinct biological systems during greening in rice and demonstrate the usefulness of comprehensive and comparative proteome analysis for the characterization of biological processes in plant cells.

Overexpression of BAX INHIBITOR-1 Links Plasma Membrane Microdomain Proteins to Stress

“…We performed one-dimensional-PAGE/LC-MS/ MS-based shotgun analysis to evaluate BI-1-mediated changes in a comprehensive DRM proteome, which identified 398 DRM proteins with at least one unique (gene-specific) peptide (for comprehensive proteome data and general analyses, see Supplemental Data Set S1, Supplemental Information S1, and Supplemental Table S6). Based on a label-free comparative analysis (Hamamoto et al, 2012), eight up-regulated and nine down-regulated proteins in OX cells were identified (Table II; all spectra with MS intensities are shown in Supplemental Table S4). The four proteins identified by the gel-based comparison described above (FLOT, HIR3, r40c1, and r40g2) were again included in this list with significant changes in mean ratio.…”

“…The spectra obtained were searched against the Rice Annotation Project Database using Spectrum Mill software (Agilent Technologies). MS intensity-based semiquantitative analysis was performed as described in detail previously (Hamamoto et al, 2012). Proteins with a mean ratio greater than 3-fold were considered different in abundance.…”

Mass Spectrometric Analyses Reveal a Central Role for Ubiquitylation in Remodeling the Arabidopsis Proteome during Photomorphogenesis

“…More recent MS studies with Arabidopsis , rice, and maize have in turn provided a preliminary glimpse into how the corresponding proteomes are affected (Wang et al, 2006; Shen et al, 2009; Hamamoto et al, 2012). As expected, the dominant feature is the rapid accumulation of proteins involved in photosynthetic light capture and carbon assimilation as etioplasts convert to chloroplasts during the acquisition of photoautotrophic metabolism.…”

Proteomic Analysis Reveals Nitric Oxide Functions in Promoting Etiolated Barley Seedlings Greening

“…54, march-april 2014 L ight is an essential environmental signal that plays an important role in crop growth and development (Neff et al, 2000;Wang and Deng, 2003). Dark-grown seedlings exhibit a series of etiolated characters such as elongated hypocotyls and undifferentiated chloroplast precursors Hamamoto et al, 2012). Dark-grown seedlings exhibit a series of etiolated characters such as elongated hypocotyls and undifferentiated chloroplast precursors Hamamoto et al, 2012).…”

“…This is one of the most dramatic developmental processes in plants, which includes a massive reorganization of the transcriptional program, inhibition of hypocotyl growth, promotion of cotyledon expansion, chlorophyll (Chl) synthesis and photosystems assembly in thylakoids (Ma et al, 2001;Hu et al, 2002). Besides phytochromes, greening is also tightly related to glycolysis, the tricarboxylic acid (TCA) cycle, adenosine triphosphate (ATP) synthesis, photorespiration and nitrogen assimilation (Symons and Reid, 2003;Alabadi et al, 2007;Hamamoto et al, 2012). Phytochromes are the red/far-red-absorbing photoreceptors which play an important role in regulating greening (Chen et al, 2004).…”