Rice proteomics: A move toward expanded proteome coverage to comparative and functional proteomics uncovers the mysteries of rice and plant biology

Agrawal, Ganesh Kumar; Rakwal, Randeep

doi:10.1002/pmic.201000696

Cited by 98 publications

(62 citation statements)

References 164 publications

(240 reference statements)

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“…Moreover, rice proteomics studies can efficiently help to boost plant biology knowledge. In fact, the increasing information on the rice proteome can speed up the process of understanding not only biology of rice but also of other plants (Agrawal and Rakwal, 2011). …”

Section: Discussionmentioning

confidence: 99%

Unravelling the proteomic profile of rice meiocytes during early meiosis

2014

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Transfer of genetic traits from wild or related species into cultivated rice is nowadays an important aim in rice breeding. Breeders use genetic crosses to introduce desirable genes from exotic germplasms into cultivated rice varieties. However, in many hybrids there is only a low level of pairing (if existing) and recombination at early meiosis between cultivated rice and wild relative chromosomes. With the objective of getting deeper into the knowledge of the proteins involved in early meiosis, when chromosomes associate correctly in pairs and recombine, the proteome of isolated rice meiocytes has been characterized by nLC-MS/MS at every stage of early meiosis (prophase I). Up to 1316 different proteins have been identified in rice isolated meiocytes in early meiosis, being 422 exclusively identified in early prophase I (leptotene, zygotene, or pachytene). The classification of proteins in functional groups showed that 167 were related to chromatin structure and remodeling, nucleic acid binding, cell-cycle regulation, and cytoskeleton. Moreover, the putative roles of 16 proteins which have not been previously associated to meiosis or were not identified in rice before, are also discussed namely: seven proteins involved in chromosome structure and remodeling, five regulatory proteins [such as SKP1 (OSK), a putative CDK2 like effector], a protein with RNA recognition motifs, a neddylation-related protein, and two microtubule-related proteins. Revealing the proteins involved in early meiotic processes could provide a valuable tool kit to manipulate chromosome associations during meiosis in rice breeding programs. The data have been deposited to the ProteomeXchange with the PXD001058 identifier.

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Section: Discussionmentioning

confidence: 99%

Unravelling the proteomic profile of rice meiocytes during early meiosis

2014

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“…Therefore, the molecular characterization of M. oryzae may reveal effective strategies for preventing various plant diseases. To evaluate the interactions between rice plants and M. oryzae on the molecular, biochemical, and physiological levels, high-throughput technologies such as transcriptomics, proteomics, and metabolomics have been used (Agrawal and Rakwal, 2011;Mathioni et al, 2011;Jones et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

Proteomic analysis of mycelial proteins from Magnaporthe oryzae under nitrogen starvation

Yü²,

Cx³

et al. 2016

Genet. Mol. Res.

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ABSTRACT.Magnaporthe oryzae is an important model system in studies of plant pathogenic fungi, and nitrogen is a key nutrient source affecting microbial growth and development. In order to understand how nitrogen stress causes changes in mycelial proteins, we analyzed differentially expressed mycelial proteins from the M. oryzae virulent strain CH-63 using two-dimensional electrophoresis and mass spectrometry in complete medium or under nitrogen starvation conditions. A total of 975 ± 70 and 1169 ± 90 protein spots were detected in complete medium and under nitrogen starvation conditions, respectively. Forty-nine protein spots exhibited at least 2-fold upregulation or down-regulation at the protein level according to PDQuest7.4. Moreover, 43 protein spots were successfully identified by matrix-assisted laser desorption/ionization-time-of-flight/time-of-flight mass spectrometry. Among these spots, 6 proteins were functionally unknown and 37 proteins were categorized into 5 groups according to their functions, including development, metabolism, biosynthesis, and biological process. These 37 proteins were further analyzed for their enriched metabolic pathways by KOBAS2.0, and 14 proteins were found to be involved in glycolysis, tricarboxylic acid cycle, and nitrogen metabolism. Taken together, the regulation of M. oryzae growth under the nitrogen starvation conditions appears to be complex because of the various proteins and enzymes involved.

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“…The technique is not sufficient for higher coverage and more accurate quantification in proteomic studies [15]. Thus, mass spectrometry-based quantitative approaches have recently emerged as important tools in proteomics studies [16]. Isobaric tags for relative and absolute quantification (iTRAQ) is one of the mass-based quantitative approaches and has become increasingly popular in the field of plant proteomics.…”

Section: Introductionmentioning

confidence: 99%

Stress Responsive Proteins Are Actively Regulated during Rice (Oryza sativa) Embryogenesis as Indicated by Quantitative Proteomics Analysis

Zhang

Wang

et al. 2013

PLoS ONE

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Embryogenesis is the initial step in a plant’s life, and the molecular changes that occur during embryonic development are largely unknown. To explore the relevant molecular events, we used the isobaric tags for relative and absolute quantification (iTRAQ) coupled with the shotgun proteomics technique (iTRAQ/Shotgun) to study the proteomic changes of rice embryos during embryogenesis. For the first time, a total of 2 165 unique proteins were identified in rice embryos, and the abundances of 867 proteins were actively changed based on the statistical evaluation of the quantitative MS/MS signals. The quantitative data were then confirmed using multiple reactions monitoring (MRM) and were also supported by our previous study based on two-dimensional gel electrophoresis (2 DE). Using the proteome at 6 days after pollination (DAP) as a reference, cluster analysis of these differential proteins throughout rice embryogenesis revealed that 25% were up-regulated and 75% were down-regulated. Gene Ontology (GO) analysis implicated that most of the up-regulated proteins were functionally categorized as stress responsive, mainly including heat shock-, lipid transfer-, and reactive oxygen species-related proteins. The stress-responsive proteins were thus postulated to play an important role during seed maturation.

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Rice proteomics: A move toward expanded proteome coverage to comparative and functional proteomics uncovers the mysteries of rice and plant biology

Cited by 98 publications

References 164 publications

Unravelling the proteomic profile of rice meiocytes during early meiosis

Unravelling the proteomic profile of rice meiocytes during early meiosis

Proteomic analysis of mycelial proteins from Magnaporthe oryzae under nitrogen starvation

Stress Responsive Proteins Are Actively Regulated during Rice (Oryza sativa) Embryogenesis as Indicated by Quantitative Proteomics Analysis

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