Proteomics of weakly bound cell wall proteins in rice calli

Chen, Xiong-Yan; Kim, Sun Tae; Cho, Won Kyong; Rim, Yeonggil; Kim, Suwha; Kim, Seon-Won; Kang, Kyu Young; Park, Zee Yong; Kim, Jae‐Yean

doi:10.1016/j.jplph.2008.09.010

Cited by 55 publications

(74 citation statements)

References 33 publications

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“…Quantitative proteomics techniques such as stable isotope labeling by amino acids in cell culture (SILAC) have been refined to suit plant systems and exploited recently in Arabidopsis suspension cell culture systems to analyze relative protein expression levels (Gruhler et al 2005;Schütz et al 2011). High-throughput transcriptomic (Singla et al 2007;Bao et al 2009) and proteomic techniques (Yin et al 2007;Marsoni et al 2008), state-of-the-art protein analysis techniques such as liquid chromatography mass spectrometry (LC-MS) (Jung et al 2008) and multidimensional protein identification technology (MudPIT) (Chen et al 2009b;Cho et al 2009) are extremely powerful tools to simultaneously identify and monitor a large number of RNA/protein and their expression changes in vitro. Some of the techniques used for analyzing the variations generated under in vitro culture conditions are summarized in Table 1.…”

Section: Gene Expression Regulation Of Developmental Cell Fate In Vitromentioning

confidence: 99%

Recent progress in the understanding of tissue culture-induced genome level changes in plants and potential applications

2011

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In vitro cell and tissue-based systems have tremendous potential in fundamental research and for commercial applications such as clonal propagation, genetic engineering and production of valuable metabolites. Since the invention of plant cell and tissue culture techniques more than half a century ago, scientists have been trying to understand the morphological, physiological, biochemical and molecular changes associated with tissue culture responses. Establishment of de novo developmental cell fate in vitro is governed by factors such as genetic make-up, stress and plant growth regulators. In vitro culture is believed to destabilize the genetic and epigenetic program of intact plant tissue and can lead to chromosomal and DNA sequence variations, methylation changes, transposon activation, and generation of somaclonal variants. In this review, we discuss the current status of understanding the genomic and epigenomic changes that take place under in vitro conditions. It is hoped that a precise and comprehensive knowledge of the molecular basis of these variations and acquisition of developmental cell fate would help to devise strategies to improve the totipotency and embryogenic capability in recalcitrant species and genotypes, and to address bottlenecks associated with clonal propagation.

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Section: Gene Expression Regulation Of Developmental Cell Fate In Vitromentioning

confidence: 99%

Recent progress in the understanding of tissue culture-induced genome level changes in plants and potential applications

2011

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“…However, cells express a large number of proteins destined for the extracellular space. In Arabidopsis and rice, 400 and 198 proteins, respectively, have been identified as cell wall components (Chen et al 2009). This corresponds to approximately one-fourth of the expected extracellular proteins in Arabidopsis (Jamet et al 2008).…”

Section: Introductionmentioning

confidence: 99%

Morphological and proteomic analyses of sugar beet cultures and identifying putative markers for cell differentiation

Pavoković

Poljuha²,

Horvatić

et al. 2011

Plant Cell Tiss Organ Cult

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Normal (N), habituated nonorganogenic (HNO), and tumour (T) sugar beet cell lines were analysed in order to establish specific patterns of extracellular proteins and identify protein markers that might explain the distinct phenotypical characteristics. Electron microscopy showed that the ultrastructure of N cells corresponds to that of parenchyma cells, and that these cells contain plastids with large starch grains. HNO and T cells had enlarged, lobed nuclei with an increased number of nucleoli; the number of nuclei in HNO cells was greater than in T cells. The T plastids were elongated, with reduced thylakoids and abundant phytoferritin deposits, while HNO plastids were small and vacuolated, with an irregular, underdeveloped thylakoid system. The extracellular proteome of the cells was separated by sodium dodecyl sulphate polyacrylamide gel electrophoresis. Greater differences in protein expression were observed between the HNO and N lines than between the T and N lines. Sixteen of the most prominent bands differentially expressed among the cell lines were cut out from the gel and analyzed by mass spectrometry. Cell wall-modifying enzymes were identified, including a peroxidase whose expression was twofold higher in N and T tissue than in HNO tissue; pectinesterase, which was expressed at a level threefold lower in the T line than in the other cell lines; and xyloglucan endotransglucosylase, which was expressed at a level sixfold higher in HNO and T tissue. Three proteins belonged to the chitinase gene family and their expression was higher in HNO and T tissue than in N tissue. The differential expression of these proteins suggests that these play a role in cell line-specific cell wall composition and cell-to-cell adhesion.

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“…The emerging field of developmental proteomics, in which large mixtures of proteins are characterised in a single experimental sequence, may allow for the assessment of variability or similarity in an individual at the level of the proteome (Hunter et al, 2002). The developmental proteomics of rice is perhaps the least studied, but its importance was realised when the proteome of rice at 5 days and the third and fourth leaf stages were analysed (Jung et al 2008;Chen et al, 2009). When we compared the existing dataset, even though the proteomes were found to be similar, some of the CWPs which were unknown earlier were uniquely present at a particular developmental stage.…”

Section: Exploring the Variability Of The Developmental Stage Specifimentioning

confidence: 99%

Comparative Analyses of Extracellular Matrix Proteome: An Under-Explored Area in Plant Research

Narula¹,

Elagamey²,

Datta³

et al. 2012

Crop Plant

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Proteomics of weakly bound cell wall proteins in rice calli

Cited by 55 publications

References 33 publications

Recent progress in the understanding of tissue culture-induced genome level changes in plants and potential applications

Recent progress in the understanding of tissue culture-induced genome level changes in plants and potential applications

Morphological and proteomic analyses of sugar beet cultures and identifying putative markers for cell differentiation

Comparative Analyses of Extracellular Matrix Proteome: An Under-Explored Area in Plant Research

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