Proteomic analysis of RNA-binding proteins in dry seeds of rice after fractionation by ssDNA affinity column chromatography

Masaki, Shunpei; Yamada, Tetsuya; Hirasawa, Tadashi; Todaka, Daisuke; Kanekatsu, Motoki

doi:10.1007/s10529-007-9619-8

Cited by 22 publications

(31 citation statements)

References 19 publications

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“…Highly complex protein samples can be separated according to their pI and their molecular weight using 2-DE [11][12][13][14][15]. The separated proteins can subsequently be visualized using standard protein stains (e.g., Coomasssie blue and silver staining).…”

Section: Detection Of Phosphoproteinsmentioning

confidence: 99%

“…Since ETD and ECD are optimal methods for fragmentation of multiply charged peptide ions (e.g., charges of 13,14), an alternative protease might be a better choice as trypsin mainly produces doubly charged ions, which are suitable for CID. Lys-C is a logical choice as it generates trypsin-like peptide ions, but only cleaves C-terminal to lysine, thus creating longer peptides.…”

Section: Electron Transfer Dissociationmentioning

confidence: 99%

“…However, one must bear in mind that such data need to be normalized to corresponding protein abundance in order to verify regulations as phosphorylation-directed, and not related to protein synthesis or degradation. Many quantitation techniques introduce a stable isotope label or tag on proteins or peptides containing e.g., 2 H, 13 C, 18 O, or 15 N. The abundance of the labeled species originating from e.g., diseased tissue can then be compared to the abundance of the nonlabeled or differently labeled species originating from e.g., healthy tissue. Quantitation methods differ at the level in which the label is introduced into the sample.…”

Section: Quantitation Strategies For Phosphoproteomic Studiesmentioning

confidence: 99%

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Analytical strategies for phosphoproteomics

2009

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Protein phosphorylation is a key regulator of cellular signaling pathways. It is involved in most cellular events in which the complex interplay between protein kinases and protein phosphatases strictly controls biological processes such as proliferation, differentiation, and apoptosis. Defective or altered signaling pathways often result in abnormalities leading to various diseases, emphasizing the importance of understanding protein phosphorylation. Phosphorylation is a transient modification, and phosphoproteins are often very low abundant. Consequently, phosphoproteome analysis requires highly sensitive and specific strategies. Today, most phosphoproteomic studies are conducted by mass spectrometric strategies in combination with phosphospecific enrichment methods. This review presents an overview of different analytical strategies for the characterization of phosphoproteins. Emphasis will be on the affinity methods utilized specifically for phosphoprotein and phosphopeptide enrichment prior to MS analysis, and on recent applications of these methods in cell biological applications.

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Section: Detection Of Phosphoproteinsmentioning

confidence: 99%

Section: Electron Transfer Dissociationmentioning

confidence: 99%

Section: Quantitation Strategies For Phosphoproteomic Studiesmentioning

confidence: 99%

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Analytical strategies for phosphoproteomics

2009

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“…A recent proteomic analysis of RNA-binding proteins revealed the existence and regulation of RNA-binding proteins in dry seeds of rice (Masaki et al , 2008). The rice genome encodes at least six GRPs, which share a high degree of sequence homology in the ribonucleoprotein1 (RNP1) and RNP2 regions, but vary in the length of the C-terminal glycine-rich domain (Table 1; see Supplementary Fig.…”

Section: Introductionmentioning

confidence: 99%

Glycine-rich RNA-binding proteins are functionally conserved in Arabidopsis thaliana and Oryza sativa during cold adaptation process

Kim

Kwak

et al. 2010

Journal of Experimental Botany

137

102

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Contrary to the increasing amount of knowledge regarding the functional roles of glycine-rich RNA-binding proteins (GRPs) in Arabidopsis thaliana in stress responses, the physiological functions of GRPs in rice (Oryza sativa) currently remain largely unknown. In this study, the functional roles of six OsGRPs from rice on the growth of E. coli and plants under cold or freezing stress conditions have been evaluated. Among the six OsGRPs investigated, OsGRP1, OsGRP4, and OsGRP6 were shown to have the ability to complement cold-sensitive BX04 E. coli mutant cells under low temperature conditions, and this complementation ability was correlated closely with their DNA- and RNA-melting abilities. Moreover, OsGRP1 and OsGRP4 rescued the growth-defect of a cold-sensitive Arabidopsis grp7 mutant plant under cold and freezing stress, and OsGRP6 conferred freezing tolerance in the grp7 mutant plant, in which the expression of AtGRP7 was suppressed and is sensitive to cold and freezing stresses. OsGRP4 and OsGRP6 complemented the defect in mRNA export from the nucleus to the cytoplasm in grp7 mutants during cold stress. Considering that AtGRP7 confers freezing tolerance in plants and harbours RNA chaperone activity during the cold adaptation process, the results of the present study provide evidence that GRPs in rice and Arabidopsis are functionally conserved, and also suggest that GRPs perform a function as RNA chaperones during the cold adaptation process in monocotyledonous plants, as well as in dicotyledonous plants.

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“…As the importance of RBPs in plant development and stress response becomes increasingly clear, it is imperative that more focus be directed at identifying and elucidating their activity (Fedoroff, 2002; Bailey-Serres et al, 2009; Lorkovic, 2009). A few groups have attempted to do so by combining nucleic acid and ion exchange affinity chromatography with 2D gel electrophoresis (2DE) to enrich for low abundance RBPs in Arabidopsis, spinach, and rice (Baginsky et al, 2007; Xu et al, 2007; Masaki et al, 2008; Ni et al, 2010). …”

Section: Introductionmentioning

confidence: 99%

RiceRBP: A Resource for Experimentally Identified RNA Binding Proteins in Oryza sativa

et al. 2012

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RNA binding proteins (RBPs) play an important role not only in nuclear gene expression, but also in cytosolic events, including RNA transport, localization, translation, and stability. Although over 200 RBPs are predicted from the Arabidopsis genome alone, relatively little is known about these proteins in plants as many exhibit no homology to known RBPs in other eukaryotes. Furthermore, RBPs likely have low expression levels making them difficult to identify and study. As part of our continuing efforts to understand plant cytosolic gene expression and the factors involved, we employed a combination of affinity chromatography and proteomic techniques to enrich for low abundance RBPs in developing rice seed. Our results have been compiled into RiceRBP (), a database that contains 257 experimentally identified proteins, many of which have not previously been predicted to be RBPs. For each of the identified proteins, RiceRBP provides information on transcript and protein sequence, predicted protein domains, details of the experimental identification, and whether antibodies have been generated for public use. In addition, tools are available to analyze expression patterns for the identified genes, view phylogentic relationships and search for orthologous proteins. RiceRBP is a valuable tool for the community in the study of plant RBPs.

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Proteomic analysis of RNA-binding proteins in dry seeds of rice after fractionation by ssDNA affinity column chromatography

Cited by 22 publications

References 19 publications

Analytical strategies for phosphoproteomics

Analytical strategies for phosphoproteomics

Glycine-rich RNA-binding proteins are functionally conserved in Arabidopsis thaliana and Oryza sativa during cold adaptation process

RiceRBP: A Resource for Experimentally Identified RNA Binding Proteins in Oryza sativa

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