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Agrawal G.K.,Research Laboratory for Biotechnology and Biochemistry RLABB | Bourguignon J.,French National Institute for Agricultural Research | Rolland N.,French National Institute for Agricultural Research | Ephritikhine G.,French National Center for Scientific Research | And 10 more authors.
Mass Spectrometry Reviews | Year: 2011

Organelle proteomics describes the study of proteins present in organelle at a particular instance during the whole period of their life cycle in a cell. Organelles are specialized membrane bound structures within a cell that function by interacting with cytosolic and luminal soluble proteins making the protein composition of each organelle dynamic. Depending on organism, the total number of organelles within a cell varies, indicating their evolution with respect to protein number and function. For example, one of the striking differences between plant and animal cells is the plastids in plants. Organelles have their own proteins, and few organelles like mitochondria and chloroplast have their own genome to synthesize proteins for specific function and also require nuclear-encoded proteins. Enormous work has been performed on animal organelle proteomics. However, plant organelle proteomics has seen limited work mainly due to: (i) inter-plant and inter-tissue complexity, (ii) difficulties in isolation of subcellular compartments, and (iii) their enrichment and purity. Despite these concerns, the field of organelle proteomics is growing in plants, such as Arabidopsis, rice and maize. The available data are beginning to help better understand organelles and their distinct and/or overlapping functions in different plant tissues, organs or cell types, and more importantly, how protein components of organelles behave during development and with surrounding environments. Studies on organelles have provided a few good reviews, but none of them are comprehensive. Here, we present a comprehensive review on plant organelle proteomics starting from the significance of organelle in cells, to organelle isolation, to protein identification and to biology and beyond. To put together such a systematic, in-depth review and to translate acquired knowledge in a proper and adequate form, we join minds to provide discussion and viewpoints on the collaborative nature of organelles in cell, their proper function and evolution. © 2010 Wiley Periodicals, Inc. Source

Tamogami S.,Akita Prefectural University | Kumar Agrawal G.,Research Laboratory for Biotechnology and Biochemistry RLABB | Rakwal R.,Research Laboratory for Biotechnology and Biochemistry RLABB | Rakwal R.,Japan National Institute of Advanced Industrial Science and Technology
Journal of Plant Physiology | Year: 2010

A novel technique for determining the cis-/trans-stereochemistry of jasmonoyl-isoleucine by coupling its alcoholic derivatives by sodium borohydride with high performance liquid chromatography-tandem mass spectrometry is described. Resolving cis- and trans-stereochemistry of the jasmonates in Achyranthes plants exposed to airborne (exogenous) trans-d2MeJA was demonstrated as an example. This novel application firmly establishes for the first time that trans-d2MeJA is converted exclusively into trans-JA-Ile in Achyranthes leaves, whereas the subsequent de novo biosynthesized JA-Ile possesses cis-stereochemistry. The method is simple, reproducible and could be employed for in vivo cis-/trans-stereochemistry analysis of jasmonates in plants. © 2010 Elsevier GmbH. All rights reserved. Source

Swatek K.N.,University of Missouri | Graham K.,University of Missouri | Agrawal G.K.,Research Laboratory for Biotechnology and Biochemistry RLABB | Thelen J.J.,University of Missouri
Journal of Proteome Research | Year: 2011

The 14-3-3-protein family is prominently expressed during seed filling and modulates protein interactions and enzymatic activities, in a phosphorylation-dependent manner. To investigate the role(s) of 14-3-3 proteins in oilseed development, we have begun to characterize the Arabidopsis thaliana 14-3-3 "interactome" for two phylogenetically distinct isoforms. Proteins from developing Arabidopsis seed were incubated with a Sepharose affinity matrix containing covalently bound recombinant Arabidopsis 14-3-3 isoforms chi (π) or epsilon (ε). Eluted proteins were quantitatively identified using GeLC-MS/MS coupled to spectral counting. Analysis of nine biological replicates revealed a total of 104 putative 14-3-3 binding proteins eluted from this affinity matrix compared to controls. Interestingly, these results imply that π and ε could have distinct preferences for client proteins. Both isoforms interact with client proteins involved in various metabolic pathways, including glycolysis and de novo fatty acid synthesis. These results suggest 14-3-3 proteins interact with multiple biochemical processes of Arabidopsis seed development. Furthermore, these data suggest isoform specificity of client proteins and possibly even functional specialization between the 14-3-3 isoforms χ and ε in Arabidopsis seed development. © 2011 American Chemical Society. Source

Rakwal R.,Research Laboratory for Biotechnology and Biochemistry RLABB | Rakwal R.,Showa University
Reviews of Environmental Contamination and Toxicology | Year: 2011

Ozone is now considered to be the second most important gaseous pollutant in our environment. The phytotoxic potential of O3 was first observed on grape foliage by B. L. Richards and coworkers in 1958 (Richards et al. 1958). To date, unsustainable resource utilization has turned this secondary pollutant into a major component of global climate change and a prime threat to agricultural production. The projected levels to which O3 will increase are critically alarming and have become a major issue of concern for agriculturalists, biologists, environmentalists, and others. Plants are "soft targets" for O3. Ozone enters plants through stomata, where it dissolves in the apoplastic fluid. O3 has several potential effects on plants: direct reaction with cell membranes; conversion into ROS and H2O2 (which alters cellular function by causing cell death); induction of premature senescence; and induction of and up-or down-regulation of responsive components such as genes, proteins, and metabolites. In this review, we attempt to present an overview picture of plant- O3 interactions. We summarize the vast number of available reports on plant responses to O3 at the morphological, physiological, cellular, biochemical levels, and address effects on crop yield, and on genes, proteins, and metabolites. © 2011 Springer Science+Business Media, LLC. Source

Kim S.T.,Pusan National University | Kim S.G.,Gyeongsang National University | Agrawal G.K.,Research Laboratory for Biotechnology and Biochemistry RLABB | Agrawal G.K.,GRADE Academy Private Ltd | And 5 more authors.
Proteomics | Year: 2014

Rice proteomics has progressed at a tremendous pace since the year 2000, and that has resulted in establishing and understanding the proteomes of tissues, organs, and organelles under both normal and abnormal (adverse) environmental conditions. Established proteomes have also helped in re-annotating the rice genome and revealing the new role of previously known proteins. The progress of rice proteomics had recognized it as the corner/stepping stone for at least cereal crops. Rice proteomics remains a model system for crops as per its exemplary proteomics research. Proteomics-based discoveries in rice are likely to be translated in improving crop plants and vice versa against ever-changing environmental factors. This review comprehensively covers rice proteomics studies from August 2010 to July 2013, with major focus on rice responses to diverse abiotic (drought, salt, oxidative, temperature, nutrient, hormone, metal ions, UV radiation, and ozone) as well as various biotic stresses, especially rice-pathogen interactions. The differentially regulated proteins in response to various abiotic stresses in different tissues have also been summarized, indicating key metabolic and regulatory pathways. We envision a significant role of rice proteomics in addressing the global ground level problem of food security, to meet the demands of the human population which is expected to reach six to nine billion by 2040. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Source

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