Time to articulate a vision for the future of plant proteomics – A global perspective: An initiative for establishing the International Plant Proteomics Organization (INPPO)

Agrawal, Ganesh Kumar; Job, Dominique; Zivy, Michel; Agrawal, Vishwanath Prasad; Bradshaw, Ralph A.; Dünn, Michael J.; Haynes, Paul A.; Wijk, Klaas J. van; Kikuchi, Shoshi; Renaut, Jenny; Weckwerth, Wolfram; Rakwal, Randeep

doi:10.1002/pmic.201000608

Cited by 32 publications

(27 citation statements)

References 86 publications

(88 reference statements)

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“…Thus, the vast majority of the proteins identified could only be extracted by homology with proteins of all the viridiplantae database. Thus, although plant proteomics is experiencing a fast growth in present days and is now well accepted by all dedicated proteomics journals [21][22][23], yet it is clear that for further progress we need the help of geneticists willing to tackle the sequencing of more and more plant genomes (most of the papers published so far deal with the proteomes of Arabidopsis thaliana and rice, Oryza sativa, and focus on profiling organs, tissues, cells or subcellular proteomes). In fact, among our identifications, the score is as follows ( A similar case has occurred in our investigation of the proteome of almond's milk [16]: of the 132 proteins identified, only 30 belonged to the Prunus (much better, anyhow, than in the case of coconut milk); the vast majority could only be identified by homology with proteins listed in the Uniprot_viridiplantae, especially those of Oryza sativa (rice), Vitis vinifera, Triticum aestivum (wheat), Arabidopsis and so on.…”

Section: Discussionmentioning

confidence: 99%

Harry Belafonte and the secret proteome of coconut milk

D’Amato

Fasoli

Righetti

2012

Journal of Proteomics

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Section: Discussionmentioning

confidence: 99%

Harry Belafonte and the secret proteome of coconut milk

D’Amato

Fasoli

Righetti

2012

Journal of Proteomics

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“…This organization initiated the process of a collective vision on how to overcome the technical and other stumbling blocks in the way of plant proteomics, especially in relation to facilitating cutting edge proteomics on the subcontinent (Agrawal et al 2011a). Achievements of INPPO in a short period of its activities were recently highlighted (Agrawal et al 2012b).…”

Section: Challenges Ahead For Plant Proteomics Researchmentioning

confidence: 99%

Plant proteomics in India and Nepal: current status and challenges ahead

Deswal¹,

Gupta²,

Dogra³

et al. 2013

Physiol Mol Biol Plants

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Plant proteomics has made tremendous contributions in understanding the complex processes of plant biology. Here, its current status in India and Nepal is discussed. Gelbased proteomics is predominantly utilized on crops and noncrops to analyze majorly abiotic (49 %) and biotic (18 %) stress, development (11 %) and post-translational modifications (7 %). Rice is the most explored system (36 %) with major focus on abiotic mainly dehydration (36 %) stress. In spite of expensive proteomics setup and scarcity of trained workforce, output in form of publications is encouraging. To boost plant proteomics in India and Nepal, researchers have discussed ground level issues among themselves and with the International Plant Proteomics Organization (INPPO) to act in priority on concerns like food security. Active collaboration may help in translating this knowledge to fruitful applications. Ground-level issues in agriculture, biodiversity and sustainabilityThe Green revolution of the sixties led agricultural practices in the Indian subcontinent to improve, and fulfil the everincreasing demand for plant-based foods. This was concomitant with the consumption of large doses of inorganic fertilizers and chemical pesticides to sustain crop productivity. Despite the transformation of India into a "bread basket", a negative aspect of the then generally beneficial model, was the erosion of crop biodiversity through increasing industrialization of agriculture. This also gave rise to other ecological problems, such as decreasing soil fertility, chemical pollution of land and water resources, pesticide poisoning, and pest infestation due to growing pest resistance to pesticides. Agricultural crops or domesticated plants went through cycles of selections depending on needs and important traits. The traits kept changing as per the demands of particular eco-geography and/or demography, while the cycle of selection continued with limited number of genotypes in particular crop species. This practice resulted in a narrow primary or secondary gene pool of crop plants and their related species causing breeding depression, low polymorphism, and allied problems. Therefore, harnessing the available diversity only within crossable genotypes and/or species now limits conventional breeding. In fact, agriculture on the Indian subcontinent is once again at the crossroads. Further development of sustainable solutions will require deeper understanding of traits at molecular level that are critical in exploring and exploiting the existing molecular diversity in native plants. Molecular understanding of fertility barriers would be equally critical to utilize the well characterized, wider germplasm collections readily available for cereal crops.Managing biotic and abiotic stresses in crop production remains a huge challenge. This is compounded with the perpetually rising numbers of pests and pathogens due to changing climate and pest/pathogen adaptation to chemicals. Harnessing the existing biodiversity in crop plants using their proximate specie...

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“…For the past 13 years, a rapid progress in the study of plant genomics is also evident. The completion of the genome sequencing projects of the model system such as Arabidopsis thaliana in 2000 (The Arabidopsis Genome Initiative 2000 ), followed by rice in 2002 (Goff et al 2002 ;Yu et al 2000 ;IRGSP 2005 ), poplar (Tuskan et al 2006 ), castor (Lu et al 2007 ), sorghum (Bedell et al 2005 ), rape seed (Jaillon et al 2007 ), soybean (Schmutz et al 2010 ), tomato ( http:// solgenomics.net/organism/Solanum_lycopersi-cum/genome ), maize (Wilson et al 2009 ;Gore et al 2009 ;Dolgin 2009 ), banana ( http://bananagenome.cirad.fr/ ) and Medicago truncatula ( http://www.medicago.org/ ) have paved the way for further intricate research using the advanced high-throughput omic technologies (Agrawal et al 2011 ).…”

Section: Introductionmentioning

confidence: 99%

Translating the Genome for Translational Research: Proteomics in Agriculture

Caguioa

Raorane

Kohli

2015

Plant Biology and Biotechnology

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The increasing number of novel tools, methods and capacities to elucidate and understand the genome of various organisms is steadily leading the path for similar groundbreaking studies in downstream comprehension of the genomes. Platforms for analytical and functional transcriptomics have seen a similar surge in operational outputs. The cryptic complexity of the DNA in the genomes is manifested in various forms and functions of the RNA it codes for. Such complexity reaches much more elaborate intricacies in the translational protein products of the RNA. Although transcripts regulate a number of biological processes, proteins form the basic functional unit of most procedures that are evinced as a phenotype. Progressively increasing realization that there is limited correspondence between the level of a specifi c transcript and protein is only the beginning of appreciating that predictive biology would be less dependent on transcripts than on proteins. Principles of protein function that were explored much before the DNA and RNA paradigms are coming back to inform the omics world in the functional and regulatory capacity of proteins. Combined with the evolution of the high-throughput analytical capacity for proteins, these are clubbed into what is called proteomics, which is also riding the wave of computational and electronic revolutions in biology. Using such omic technologies for agriculture however lags behind compared to their use in medicine. Nevertheless, the recent appreciation of the need for food and feed security under the predicted climatodemographic scenarios is pushing the frontiers of agricultural research. The use of proteomics in particular is gaining ground rather quickly, and an increased understanding of crop phenotype as related to proteomics is

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Time to articulate a vision for the future of plant proteomics – A global perspective: An initiative for establishing the International Plant Proteomics Organization (INPPO)

Cited by 32 publications

References 86 publications

Harry Belafonte and the secret proteome of coconut milk

Harry Belafonte and the secret proteome of coconut milk

Plant proteomics in India and Nepal: current status and challenges ahead

Translating the Genome for Translational Research: Proteomics in Agriculture

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