Jorrin-Novo, J. V.

Panis, B.

Renaut, J.

Svensson, B.

Journal of Proteomics

Panis, Bartholomeus

CGSpace (CGIAR)

J O U R N A L O F P R O T E O M I C S 7 4 ( 2 0 1 1 ) 1 1 6 1 – 1 1 6 4ava i l ab l e a t www.sc i enced i r ec t . comwww.e l sev i e r . com/ loca te / j p ro tEditorialPlant proteomics in Europe — COST action FA0603The story begins in 2006, with the scientific dissatisfactionupon returning from a “Proteomics conference” and onlyhaving spotted a few lonely posters (less than 1% of total) andonly one oral presentation dedicated to plant proteomics.Although, it is clear for everyone that plants are essential forthe living, for food, feed, fibre, fuel and industrial products,1and increasing food production remains themain challenge inthis century, with more people dying from hunger-relatedcauses than from disease. After discussing with colleagues, anopportunity arose to propose an action dedicated to plantproteomics in the frame of the “European Cooperation in thefield of Scientific and Technical Research (COST, www.cost.esf.org)” in the domain “Food and Agriculture”.The main objective of this COST action was the improve-ment and exchange of scientific knowledge and technology inplant proteomics through the creation of a network betweenEuropean proteomic scientists focusing on plants. For this,COST provided us with the requested financial and adminis-trative support to organize workshops, training schools,conferences and to researchers' education.In 2007, the COST action FA0603 “Plant Proteomics inEurope or EUPP” was launched and gathered 18 countries andthe very first working group (WG)meeting was held in Munichin October 2007. After that, seven other WG workshops wereorganized in Cordoba, Luxembourg, Viterbo, Nitra, Namur,Luxembourg and Dijon. Books of abstracts of these differentmeetings can be downloaded on the Action's website (www.costfa0603.org). At the end of the Action, 26 Europeancountries (Austria, Belgium, Bulgaria, Czech Republic,Denmark, Estonia, Finland, France, Germany, Greece, Ireland,Italy, Lithuania, Luxembourg, Netherlands, Norway, Poland,Portugal, Serbia, Slovak Republic, Slovenia, Spain, Sweden,Switzerland, Turkey,UnitedKingdom)were involved aswell asNew Zealand that also joined the group.During the running of the Action, almost 250 researchersactively participated to the various activities organized inthe frame of this action and received financial support from1 Food, Feed, Fibre, Fuel and Industrial Products of the Future: Challengesand Opportunities. Understanding the Strategic Potential of Plant GeneticEngineering, Kern M., Journal of Agronomy and Crop Science (2002) 188,pp. 91–305.1874-3919/$ – see front matter © 2011 Published by Elsevier B.V.doi:10.1016/j.jprot.2011.07.005the COST office, while more than 500 people were present atthe different WG workshops, conferences and trainingschools.The Action's activities can be classified into two workinggroups: in the first one, the focus was set particularly on thetechnical aspects inherent to plant proteomics. The difficul-ties encountered have been discussed between participantsand with experts. Among the subjects that have beenaddressed, five points were extensively presented:• Experimental design, sampling, and protein extraction,these preliminary steps of the typical workflow being criticalfor the success of an experiment,• introduction of new technical approaches such as differencein gel electrophoresis and label-free quantification,• detection of post-translational modifications,• analysis of membrane proteins and• identification of proteins from ‘orphan’ plants, those whosegenome is not yet sequenced and are almost absent in DNAdatabases.Following the publication of the genomes of Arabidopsisand rice, two “model” plants, other species have beensequenced such as poplar, grape, cucumber, apple, soybean,cocoa, papaya, date palm, rice, Brachypodium, maize, sorghum,Physcomitrella patens, and other non-models plants. It appearedthat most of the laboratories from the different countriesinvolved in this Actionweremore attracted by those species oreven by ‘orphan’ species.The second working group was more devoted to thetransfer of the techniques to applied fields. Indeed, this WGgathered COST participants from laboratories studying:• plant stress (exposure to abiotic stress or biotic stress),• phytoremediation/phytoextraction,• symbiotic interactions,• allergens,• plant development, plant growth,• and crop improvement and yield.Evidently, a lot of interactions existed among the groups as,for example, the researchers involved in plant stress physiologymay encounter problems linked to the extraction of theirFig. 1 – Maps representing the countries hosting STSMs (a) and those sending successful STSM applicants (b).1162 J O U R N A L O F P R O T E O M I C S 7 4 ( 2 0 1 1 ) 1 1 6 1 – 1 1 6 41163J O U R N A L O F P R O T E O M I C S 7 4 ( 2 0 1 1 ) 1 1 6 1 – 1 1 6 4proteins, and the researchers having developed expertise inprotein preparation want to see their work applied to concretebiological issue. It is also worthwhile to notice that beside theparticipants that were reimbursed by the COST office for theiractive participation, an important number of non-reimbursedscientists were also attending these workshops dedicated toplant proteomics, showing the need for such events in the plantcommunity. A continuation of such gatherings is foreseen byorganizing, every two years, a conference dedicated to plantsand microorganisms in Luxembourg (ProteomLux).The possibilities offered by COST allowed the network toprovide training schools, typically for young researchers, andexchange of young scientists among different countries withthe accomplishment of 32 short-term scientific missions(STSMs) (Fig. 1). These STSMs aimed mainly at establishingformal collaborations between laboratories and also to allowthe applicants to learn new techniques or to use techniquesthey do not have access to in their home laboratories duringtheir project. Major outcomes of these STSMs are co-authoredresearch articles and establishment of long lasting collabora-tions between the 2 laboratories involved. In this current issueof JOP, two papers are the result of such STSMs; “The alterationof plasma membrane-bound redox systems of iron deficientpea roots by chitosan” and “The assessment of response toionizing radiation in Arabidopsis thaliana” by C. Meisrimler andM. Gicquel, respectively.Four training schools were offered to improve skills indifferent domains: Membrane proteomics by 2D-BN-PAGE,Forest and water stress in a changing environment: from cellto ecosystems, Comparative label-free LCMS for QuantitativeProteomics and From 2D gel to bioinformatics.Fig. 2 – Group picture ofIn this special issue, dedicated to COST action FA0603,review papers have been written by major players in plantproteomics field. These reviews focus on N-glycoproteomics,membrane proteomics, redox proteomics, pretreatment ofcomplex mixtures with hexapeptides, fruit development andplant response to stress. Also an important number of originalresearch articles are published in this issue, some of themresulting from STSMs as described above.During the action, informal and formal collaborations aroseand different projects established among participants havebeen funded by national and international agencies such as FP7projects or projects approved in the frame of the EUROCORES.Gel-based plant proteomics is now well established andduring the course of this Action significant progress has beenmade regarding gel-free proteomics, improvement of pro-tocols for membrane proteomics or for non-model plants,together with mass spectrometry.To cover the different approaches tackled in this action, thecurrent issue is divided into 3 different parts: a first one onmethods, a second one on plant's development and geneticvariability and a third one on abiotic stress. For the sake ofclarity, wewill present the articles ranked by the name of theirfirst author.A certain number of reviews and research papers of thecurrent issue are targeting the recent methodological de-velopments in plant proteomics, as illustrated by the reviewsof Annelies Vertommen on the identification of membraneproteins in non-model plants and Andreas Fröhlich on thepretreatment of complex mixtures with combinatorial hex-apeptides ligand libraries. Additionally, this chapter containsresearch articles by Irene Granlund on bioinformaticsthe meeting in Dijon.1164 J O U R N A L O F P R O T E O M I C S 7 4 ( 2 0 1 1 ) 1 1 6 1 – 1 1 6 4development for the clustering of MS spectra from MALDI-MS/MS, Noor Remmerie on the use of BN PAGE/LC–MS/MS andclustering methods, and A. Vertommen on peptide-basedproteomics for membrane proteome analysis of banana.The second chapter is dedicated to plant's developmentand its genetic variability, introduced by a review of José Palmaon fruit development and ripening, followed by articles of JoséValero Galvan on the variability between protein profiles ofacorns, Matthias Plöscher on the membrane of etioplasts andchloroplasts, Candido Ricardo on the formation of cork in oak,and two articles on plant allergens by Colette Larré (allergensin different wheat cultivars) and Martijn Schenk (studying theallergen Bet v 1 in 15 birch species).The third part of this issue is dedicated to plant stressphysiology, opening with 2 reviews, the first by Klara Kosovaon abiotic stress in general and a second one from HamidSobhanian on salt stress and crops. The content of thischapter represents without any doubt the interest of manyresearch groups involved in the action on the response ofplant to abiotic stress: heavymetals (e.g. arsenic by Elisa Bona,boron by Marta Alves), radiations (e.g. in Arabidopsis byMorgane Gicquel, and in flax seeds from Chernobyl area byKatarina Klubicova), drought (in Oak by Kjell Sergeant andpoplar by Thomas Durand), wounding (in potato by NelsonSoares) and response to elicitors (in grapevine by MariaMartínez-Esteso and in the membranes of iron deficient pearoots by Claudia Meisrimler).This special issue will be concluded by 3 reviews on a topicthat is receiving a fast increasing interest by plant proteo-mists: the study of PTMs and their implication in plant's lifecycle. This starts with Nicolas Navrot on plant redoxproteomics, then Sander van der Krol on N-glycoproteomicsand Philippe Grappin on protein isomerization, showing hownew interests and technical improvements will help toelucidate the functioning of plants.Other initiatives on plant proteomics have run in parallelwith the COST Action, including The Multinational Arabidop-sis Steering Subcommittee for Proteomics (http://www.arabidopsis.org/portals/masc/Subcommittees.jsp#prot). Re-cently, HUPO has settled the initiative on Model OrganismProteomes (http://www.hupo.org/research/imop/); however,this project does not include the whole plant proteomicscommunity. It is worthwhile also to mention the internationalplant proteomics organization or INPPO2 (www.inppo.com), inwhich the COST participants also play key roles.This special issue reflects the current situation of plantproteomics, at least in Europe. We should recognize that thefull potential of proteomics is far from being fully exploited inplant biology research, and we should go one step ahead, asthere are a lot of exciting challenges waiting for us. We are inthe way, and the COST Action played a protagonist role withinthe plant proteomics history in the last five years.Wewould like to conclude this foreword by thanking all theparticipants of COST Action FA0603 for their active contribu-tion to all events that were organized (Fig. 2). These four yearsshowed that high quality science can take place in a veryfriendly and open atmosphere. Moreover all the contributorsof this issue are thanked for their excellent papers. Finally wewould like to acknowledge the COST office for the opportunitythat they have given us to put European plant proteomics onthe world map.Jenny Renaut*Birte SvenssonJesus V. Jorrín-NovoBart Panis⁎Corresponding author. Tel.: +352 470261860; fax: +352 470264.E-mail address: renaut@lippmann.lu ( J. Renaut).2 Time to articulate a vision for the future of plant proteomics—A global perspective: An initiative for establishing the Interna-tional Plant Proteomics Organization (INPPO), Agrawal GK, Job D,Zivy M, Agrawal VP, Bradshaw RA, Dunn MJ, Haynes PA, van WijkKJ, Kikuchi S, Renaut J, WeckwerthW, Rakwal R. Proteomics (2011)11, pp. 1559–1568.

Editorial: Plant proteomics in Europe - COST action FAO603

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Editorial: Plant proteomics in Europe - COST action FAO603

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