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Rice proteomics: Ending phase I and the beginning of phase II
Agrawal, Ganesh Kumar,Jwa, Nam-Soo,Rakwal, Randeep WILEY-VCH Verlag 2009 Proteomics Vol.9 No.4
<P>Rice is a critically important food crop plant on our planet. It is also an excellent model plant for cereal crops, and now in position to serve as a reference plant for biofuel production. Proteomics study of rice therefore is crucial to better understand “rice” as a whole. Rice proteomics has moved well beyond the initial proteome analysis in the early to late 1990s. Since the year 2000, numerous proteomic studies have been performed in rice during growth and development and against a wide variety of environmental factors. These proteomic investigations have established the high-resolution 2-D reference gels of rice tissues, organs, and organelle under normal and adverse (stressed) conditions by optimizing suitable, reproducible systems for gel, and MS-based proteomic techniques, which “rejuvenated” the rice proteome field. This constituted the “phase I” in rice proteomics, and resulted in rice being labeled as the “cornerstone” of cereal food crop proteomes. Now, we are in position to state that rice proteomics today marks the “beginning of phase II”. This is due to the fact that rice researchers are capable of digging deeper into the rice proteome, mapping PTMs (in particular reversible protein phosphorylation), performing inter- and intra-species comparisons, integrating proteomics data with other “omic” technologies-generated data, and probing the functional aspect of individual proteins. These advancements and their impact on the future of rice proteomics are the focus of this review.</P>
Rejuvenating rice proteomics: Facts, challenges, and visions
Agrawal, Ganesh Kumar,Jwa, Nam-Soo,Iwahashi, Yumiko,Yonekura, Masami,Iwahashi, Hitoshi,Rakwal, Randeep WILEY-VCH Verlag 2006 Proteomics Vol.6 No.20
<P>Proteomics is progressing at an unprecedented pace, as can be exemplified by the progress in model organisms such as yeast, bacteria, and mammals. Proteomics research in plants, however, has not progressed at the same pace. Unscrambling of the genome sequences of the dicotyledoneous Arabidopsis thaliana (L.) and monocotyledoneous rice (Oryza sativa L.) plant species, respectively, has made them accessible reference organisms to study plant proteomics. Study of these two reference plants is expected to unravel the mystery of plant biology. Rice, a critically important food crop on the earth, has been termed a “cornerstone” and the “Rosetta stone” for functional genomics of cereal crops. Here, we look at the progress in unraveling rice proteomes and present the facts, challenges, and vision. The text is divided into two major parts: the first part presents the facts and the second part discusses the challenges and vision. The facts include the technology and its use in developing proteomes, which have been critically and constructively reviewed. The challenges and vision deal with the establishment of technologies to exhaustively investigate the protein components of a proteome, to generate high-resolution gel-based reference maps, and to give rice proteomics a functional dimension by studying PTMs and isolation of multiprotein complexes. Finally, we direct a vision on rice proteomics. This is our third review in series on rice proteomics, which aims to stimulate an objective discussion among rice researchers and to understand the necessity and impact of unraveling rice proteomes to their full potential.</P>
Biotic Stress-Responsive Rice Proteome: An Overview
Yiming Wang,김상곤,김선태,Ganesh Kumar Agrawal,Randeep Rakwal,강규영 한국식물학회 2011 Journal of Plant Biology Vol.54 No.4
Biotic stresses affect the plant growth, seed quality, and crop yield. The monocot model rice crop plant is no exception and is affected by a variety of biotic stress factors. High-throughput proteomics approaches are being applied in rice for the past several years to exploit better understanding the biotic stresses-responsive regulatory mechanisms. A large number of proteins responsive to biotic stresses, including pathogens and herbivores, have been cataloged. Cataloged proteins mainly belong to functional categories into metabolism, energy, defense mechanisms, and signaling. To date, majority of these proteins have not been functionally characterized yet,except the pathogen-related 10 protein, PBZ1. This review will briefly summarize and discuss: (1) the proteomicsbased investigation of biotic stress-responsive proteins in rice and (2) increasing importance of proteomics approach in defense biology and engineering the next-generation rice/crop plants.
Qingfeng Meng,GUPTARAVI,권순재,Yiming Wang,Ganesh Kumar Agrawal,Randeep Rakwal,박상렬,김선태 한국식물병리학회 2018 Plant Pathology Journal Vol.34 No.4
Rice blast disease, caused by Magnaporthe oryzae, results in an extensive loss of rice productivity. Previously, we identified a novel M. oryzae secreted protein, termed MSP1 which causes cell death and pathogen-associated molecular pattern (PAMP)-triggered immune (PTI) responses in rice. Here, we report the transcriptome profile of MSP1-induced response in rice, which led to the identification of 21,619 genes, among which 4,386 showed significant changes (P < 0.05 and fold change > 2 or < 1/2) in response to exogenous MSP1 treatment. Functional annotation of differentially regulated genes showed that the suppressed genes were deeply associated with photosynthesis, secondary metabolism, lipid synthesis, and protein synthesis, while the induced genes were involved in lipid degradation, protein degradation, and signaling. Moreover, expression of genes encoding receptor-like kinases, MAPKs, WRKYs, hormone signaling proteins and pathogenesis-related (PR) proteins were also induced by MSP1. Mapping these differentially expressed genes onto various pathways revealed critical information about the MSP1-triggered responses, providing new insights into the molecular mechanism and components of MSP1-triggered PTI responses in rice.
Gupta, Ravi,Min, Cheol Woo,Meng, Qingfeng,Agrawal, Ganesh Kumar,Rakwal, Randeep,Kim, Sun Tae Elsevier 2018 Vol. No.
<P><B>Abstract</B></P> <P>Abscisic acid (ABA) and ethylene play key roles in growth and development of plants. Several attempts have been made to investigate the ABA and ethylene-induced signaling in plants, however, the involvement of phosphorylation and dephosphorylation in fine-tuning of the induced response has not been investigated much. Here, a phosphoproteomic analysis was carried out to identify the phosphoproteins in response to ABA, ethylene (ET) and combined ABA + ET treatments in soybean leaves. Phosphoproteome analysis led to the identification of 802 phosphopeptides, representing 422 unique protein groups. A comparative analysis led to the identification of 40 phosphosites that significantly changed in response to given hormone treatments. Functional annotation of the identified phosphoproteins showed that these were majorly involved in nucleic acid binding, signaling, transport and stress response. Localization prediction showed that 67% of the identified phosphoproteins were nuclear, indicating their potential involvement in gene regulation. Taken together, these results provide an overview of the ABA, ET and combined ABA + ET signaling in soybean leaves at phosphoproteome level.</P> <P><B>Highlights</B></P> <P> <UL> <LI> A total of 802 phosphopeptides representing 422 unique protein groups were identified. </LI> <LI> Of these, 40 phosphosites showed significant change upon hormone treatments. </LI> <LI> Significant (67%) proportion of the identified phosphoproteins were nuclear. </LI> <LI> ABA alters phosphorylation of plasma membrane localized transporters. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>
Ginseng (Panax sp.) proteomics: an update
김수원,이서현,민철우,조익현,방경환,현동윤,Ganesh Kumar Agrawal,Randeep Rakwal,Sajad Majeed Zargar,GUPTARAVI,김선태 한국응용생명화학회 2017 Applied Biological Chemistry (Appl Biol Chem) Vol.60 No.3
Panax ginseng, commonly known as ginseng, is a well-known medicinal plant that has been used as traditional medicine in China and Korea. Research in the past few decades supports the pharmacological effects of ginseng. For example, ginseng roots (extracts) exhibit multiple medicinal effects, such as anticancer, antiaging, and protection against circulatory shock, in humans. In this review, we summarize the progress made so far in the ginseng proteomics, starting from sample preparation to establishments of proteomes and databases. Both gel-based (1-DE and 2-DE in combination with LC–MS/MS) and gel-free proteomics technologies have been applied on wide range of samples, collected during different growth and developmental stages and under normal or adverse stress conditions. In particular, comparative proteome analysis has been carried out to investigate the protein profiles of Oriental, American and Indian ginsengs using majorly root and leaf tissues. Moreover, identification of stress-responsive proteins was a key focus that led to the detection of some of the common proteins such as heat shock protein (HSP), ATPase, enolase, glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and ribonuclease/ ginseng major protein (GMP). Acquired proteomicsbased knowledge has been very fruitful in providing better insight into the ginseng biology, opening a door for comparative and translation research of other important medicinal plants. However, due to the fact that proteins undergo various post-transcriptional and post-translational modifications, obtained proteomics data do not always complement the transcriptomics data perfectly; therefore, future efforts would require the utilization of an integrated/holistic molecular-genetic (or omics) approach to explore the biology of this golden plant.