Research Laboratory for Biotechnology and Biochemistry RLABB

Kathmandu, Nepal

Research Laboratory for Biotechnology and Biochemistry RLABB

Kathmandu, Nepal
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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.

Agrawal G.K.,Research Laboratory for Biotechnology and Biochemistry RLABB | Rakwal R.,Research Laboratory for Biotechnology and Biochemistry RLABB | Rakwal R.,Showa University | Rakwal R.,Toho University
Proteomics | Year: 2011

Growing rice is an important socio-economic activity. Rice proteomics has achieved a tremendous progress in establishing techniques to proteomes of almost all tissues, organs, and organelles during the past one decade (year 2000-2010). We have compiled these progresses time to time over this period. The present compilation discusses proteomics research in rice published between 1st April 2008 and 30th July 2010. Progress continues mainly towards protein cataloging deep into the proteome with high-confident protein assignment and some functional significance than ever before by (i) identifying previously unreported/low-abundance proteins, (ii) quantifying relative/absolute values of proteins, (iii) assigning protein responses to biotic/abiotic stresses, (iv) protein localization into organelles, (v) validating previous proteomes and eliminating false-positive proteins, and (vi) discovering potential biomarkers for tissues, organs, organelles, and for screening transgenic plants and food-safety evaluation. The notable achievements in global mapping of phosphorylation sites and identifying several novel secreted proteins into the extracellular space are worth appreciating. Our ever-increasing knowledge on the rice proteomics is beginning to impact the biology of not only rice, but also crops and plants. These major achievements will be discussed in this review keeping in mind newcomers, young, and established scientists in proteomics and plants. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

Agrawal G.K.,Research Laboratory for Biotechnology and Biochemistry RLABB | Timperio A.M.,University of Tuscia | Zolla L.,University of Tuscia | Bansal V.,RMIT University | And 4 more authors.
Journal of Proteomics | Year: 2013

Foods and beverages have been at the heart of our society for centuries, sustaining humankind - health, life, and the pleasures that go with it. The more we grow and develop as a civilization, the more we feel the need to know about the food we eat and beverages we drink. Moreover, with an ever increasing demand for food due to the growing human population food security remains a major concern. Food safety is another growing concern as the consumers prefer varied foods and beverages that are not only traded nationally but also globally. The 21st century science and technology is at a new high, especially in the field of biological sciences. The availability of genome sequences and associated high-throughput sensitive technologies means that foods are being analyzed at various levels. For example and in particular, high-throughput omics approaches are being applied to develop suitable biomarkers for foods and beverages and their applications in addressing quality, technology, authenticity, and safety issues. Proteomics are one of those technologies that are increasingly being utilized to profile expressed proteins in different foods and beverages. Acquired knowledge and protein information have now been translated to address safety of foods and beverages. Very recently, the power of proteomic technology has been integrated with another highly sensitive and miniaturized technology called nanotechnology, yielding a new term nanoproteomics. Nanoproteomics offer a real-time multiplexed analysis performed in a miniaturized assay, with low-sample consumption and high sensitivity. To name a few, nanomaterials - quantum dots, gold nanoparticles, carbon nanotubes, and nanowires - have demonstrated potential to overcome the challenges of sensitivity faced by proteomics for biomarker detection, discovery, and application. In this review, we will discuss the importance of biomarker discovery and applications for foods and beverages, the contribution of proteomic technology in this process, and a shift towards nanoproteomics to suitably address associated issues. This article is part of a Special Issue entitled: Translational plant proteomics. © 2013 Elsevier B.V.

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.

Tamogami S.,Akita Prefectural University | Agrawal G.K.,Research Laboratory for Biotechnology and Biochemistry RLABB | Rakwal R.,Research Laboratory for Biotechnology and Biochemistry RLABB | Rakwal R.,Showa University | Rakwal R.,University of Tsukuba
Advances in Botanical Research | Year: 2011

Jasmonic acid (JA) has a long history as a natural organic compound, but interest in its biology and function(s) has been surging among scientists involved in different disciplines from organic chemistry to plant functional genomics. Mounting evidence on JA functionality reveals its ever-increasing biological roles, which appears to be unique among other plant hormones. JA is a well-known regulator of secondary metabolites production as a signalling compound, growth and defensive reactions in plants. This knowledge on JA functionality did not transpire with one or few discoveries but evolved over almost 50 years since its discovery as a perfume component of the jasmine oil. In this review, we focus on JA and its metabolites from a historical point of view that encompasses chemistry in conjunction with its biological properties unravelled over the past 20 years. Our attention on this chemical/biochemical aspect is mainly due to the fact that most of the current reviews deal essentially with signalling aspects of JA or its metabolites. It has been an exciting journey from JA to jasmonates, a long-standing term reconsidered to " jasmolites" in this review, in light of previous and recent findings. Jasmolites, strength and weakness of commonly used techniques for their extraction and analyses, absolute quantification, finding new jasmolites, and their importance in signalling and metabolic pathways have been deliberated from the biochemist point of view. Moreover, synthesis or natural finding of new jasmolites will not only shed new light on their involvement in yet unknown cellular processes regulating plant growth and development under normal and adverse ever-changing environmental conditions but also could lead to practical applications as novel agrochemicals. We hope that this review will provide prominence and transparency to jasmolites and lead them to new frontiers in biological sciences. © 2011 Elsevier Ltd.

Sarkar A.,Banaras Hindu University | Rakwal R.,Research Laboratory for Biotechnology and Biochemistry RLABB | Rakwal R.,Japan National Institute of Advanced Industrial Science and Technology | Agrawal S.B.,Banaras Hindu University | And 5 more authors.
Journal of Proteome Research | Year: 2010

Ozone (O3), a potent air pollutant and a significant greenhouse gas, has been recognized as a major component of global climate change. However, current increasing trends in its background level are projecting a more severe threat to natural and cultivated plants in the near future. The present study has been designed to evaluate the impact of elevated concentrations of O 3 on phenotypical, physiological, and biochemical traits in two high-yielding cultivars of wheat, followed by analysis of the leaf proteome using one/two-dimensional gel electrophoresis (1-/2-DGE) coupled to immunoblotting and mass spectrometry analyses under near-natural conditions using open top chambers. Prominently, O3 exposure caused specific foliar injury in both the wheat cultivars. Results also showed that O 3 stress significantly decreased photosynthetic rate, stomatal conductance, and chlorophyll fluorescence kinetics (Fv/Fm) in test cultivars. Biochemical evaluations further revealed a higher loss in photosynthetic pigments, whereas a significantly induced antioxidant system under elevated O3 concentrations pointed toward an ability of O 3 to generate oxidative stress. 1-DGE analysis showed drastic reductions in the abundantly present ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) large and small subunits. Western blot analysis confirmed induced accumulation of antioxidative enzymes like superoxide dismutase and ascorbate peroxidase protein(s) and common defense/stress-related thaumatin-like protein(s). 2-DGE analysis revealed a total of 38 differentially expressed protein spots, common in both the wheat cultivars. Among those, some major leaf photosynthetic proteins (including RuBisCO and RuBisCO activase) and important energy metabolism proteins (including ATP synthase, aldolase, and phosphoglycerate kinase) were drastically reduced, whereas some stress/defense-related proteins (such as harpin-binding protein and germin-like protein) were induced. In all, the present study reveals an intimate molecular network provoked by O3 affecting photosynthesis and triggering antioxidative defense and stress-related proteins culminating in accelerated foliar injury in wheat plants. © 2010 American Chemical Society.

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.

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.

Agrawal G.K.,Research Laboratory for Biotechnology and Biochemistry RLABB | Jwa N.-S.,Sejong University | Lebrun M.-H.,Bayer AG | Job D.,Bayer AG | And 2 more authors.
Proteomics | Year: 2010

Plant secretomics is a newly emerging area of the plant proteomics field. It basically describes the global study of secreted proteins into the extracellular space of plant cell or tissue at any given time and under certain conditions through various secretory mechanisms. A combination of biochemical, proteomics and bioinformatics approaches has been developed to isolate, identify and profile secreted proteins using complementary in vitro suspension-cultured cells and in planta systems. Developed inventories of secreted proteins under normal, biotic and abiotic conditions revealed several different types of novel secreted proteins, including the leaderless secretory proteins (LSPs). On average, LSPs can account for more than 50% of the total identified secretome, supporting, as in other eukaryotes, the existence of novel secretory mechanisms independent of the classical endoplasmic reticulum-Golgi secretory pathway, and suggesting that this non-classical mechanism of protein expression is, for as yet unknown reasons, more massively used than in other eukaryotic systems. Plants LSPs, which seem to be potentially involved in the defense/stress responses, might have dual (extracellular and/or intracellular) roles as most of them have established intracellular functions, yet presently unknown extracellular functions. Evidence is emerging on the role of glycosylation in the apical sorting and trafficking of secretory proteins. These initial secretome studies in plants have considerably advanced our understanding on secretion of different types of proteins and their underlying mechanisms, and opened a door for comparative analyses of plant secretomes with those of other organisms. In this first review on plant secretomics, we summarize and discuss the secretome definition, the applied approaches for unlocking secrets of the secreted proteins in the extracellular fluid, the possible functional significance and secretory mechanisms of LSPs, as well as glycosylation of secreted proteins and challenges involved ahead. Further improvements in existing and developing strategies and techniques will continue to drive forward plant secretomics research to building comprehensive and confident data sets of secreted proteins. This will lead to an increased understanding on how cells couple the concerted action of secreted protein networks to their internal and external environments. © 2010 WILEY-VCH Verlag GmbH & Co. KGaA.

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