J O U R NA L OF PR O TE O MI CS 93 (2 0 1 3 ) 1 –4
Available online at www.sciencedirect.com
ScienceDirect www.elsevier.com/locate/jprot
Preface
Translational Proteomics Special Issue
As an associate editor of the JoP in charge of the plant section (JVJN), it was my compromise trying to edit a monographic issue at around every two years; so, one year ago, I began to make plans, starting by the invitation to my friend, colleague, and from now on co-editor, Dr. Luis Valledor. Then, we asked ourselves: which should be the focus? It had to depend on the papers published in the last two years and it also had to be something new or at least original. According to Web of Knowledge (Thomson Reuters), the number of plant proteomics papers published in the Journal of Proteomics (JoP) during the period April 2008–August 2013 was 144, representing a 12.8% of the articles published in the journal (1127). Considering all journals the representation of plant proteomics decreases to 7.6% (2850 out of 37,237). During this period, 2008–2013, two plant proteomics special issues have been released by JoP, the first one by April 2009 (Vol. 72, Iss. 3, Plant Proteomics), and the second one by August 2011 (Vol. 74, Iss. 8; Plant Proteomics in Europe). These special and other regular issues contained a number of reviews on plant proteomics, either generalists [1,2] or with focus on plant systems [3–6], plant organs [7], biological processes [8–12], post translational modifications [13], translational [14,15] or methodological [16–18]. Considering all of these works, if we had to summarize the state of the art in the field of plant proteomics we would say that proteomics itself is progressing at much more speed than its application to plant research, following the trend stated in previous reviews [1,6]. The full potential of proteomics as an experimental approach is quite far from being fully exploited in plant biology research. It is true that apart from the model systems (mainly Arabidopsis and rice) the number of plant species (herbaceous, woody, gymnosperms and angiosperms, monocot and dicots) and biological processes (from growth and development to responses to the environment) to which proteomics is being applied has notably increased. Methodological advances in plant proteomics, including instrumentation, workflows and protocols (with discussion on its realities, limitations, and challenges) have been collected and accurately described in a book that appears in parallel to this special issue: “Plant proteomics. Methods and protocols. 2nd edition”, edited by Jorrin-Novo, Komatsu, Weckwerth and Wienkoop. Methods in Molecular
1874-3919/$ – see front matter © 2013 Elsevier B.V. All rights reserved. http://dx.doi.org/10.1016/j.jprot.2013.10.019
Biology Series, 1072, Humana Press. In the introductory chapter, Prof. Dr. Jorrín Novo stated: “We should recognize that proteomics is starting to make contributions to a proper gene annotation, identification and characterization of gene products or protein species, and to the knowledge of living (in this case plants) organisms, having also an enormous potential of application to translational research. However, and despite its great potential, and as in any other experimental approach, it is far from being a Pandora's Box. In the case of plant research, the full potential of proteomics is quite far from being totally exploited, and second, third, and fourth generation proteomics techniques are still of very limited use. Most of the plant proteomics papers so far published belong to the descriptive, subcellular and comparative proteomics subgroup, mainly using a few experimental model systems — those whose genome has been sequenced, and being from a biological point of view quite descriptive and speculative. From now on we should put more emphasis on the study of post-translational proteomics and interactomics, and move to targeted, hypothesis driven approaches. Furthermore, and even more important, we should validate our data through other -omics or classical biochemical strategies, in an attempt to get a deeper, real and more accurate view and understanding of cell biology. In the modern Systems Biology concept, proteomics must be considered as a part of a global, multidisciplinary approach. Making biological sense of a proteomics experiment requires a proper experimental design, data validation, interpretation, and publication policy.” The last paragraph is recognized as the new direction in the JoP publication policy as written by Prof. Calvete, JoP editor in chief, in the editorial that appeared in the December 2012 issue (Vol. 76, 1–2), also been discussed in detail by Prof. Weckwerth [19]. Coming to the focus of this issue, we had three options, keeping out one more “plant proteomics” generalist issue. The first one was methodological; it did not make sense
2
J O U R NA L OF P R O TE O MI CS 9 3 (2 0 1 3 ) 1 –4
considering the publication of the above mentioned book. The second one was directed at basic research that can be called “proteomics in the frontier of plant biology research”. This was probably our preferred option but, and because of the different reasons, we should not expect many contributions to justify the issue, but for sure it will be the next. The last and more realistic one was our final choice: “practical or translational proteomics”, a topic very well covered and understood in biomedicine but not that well in agriculture. This topic was in our mind since 2010, and briefly discussed during the roundtable discussion session at the 4th EuPA meeting in Portugal and appeared in the paper by Cox et al. [20]. Later on, Agrawal et al. [21] published an excellent review on translational plant proteomics. The final aim of plant translational proteomics is the development of new practices compromised with the environment, biodiversity conservation and human health, considering the life quality of not only developed but also poor populations in a World that is expected to support nearly 10 billion figures by 2050. Considering the increase in the world population and the enormous pressure that will be put to increase agricultural production, the use of biotechnology will play a relevant role. Nowadays it is not a matter of discussion, being more than obvious, that science and scientists should go beyond just the generation of knowledge: their research must have an additional value, even admitting this additional value is a consequence of that generation of knowledge. This is summarized in the new fashion key word “translational”, with the main goal being the use of research in generating innovative and productivity — technologies that are crucial to agricultural and economic growth, thus helping to fulfill future needs for food, fiber, and fuels. This concept is well understood in the biomedicine field, but not so well in the agricultural and environmental area, being necessary an increased interaction between bench and field. Any research, scientific area, and methodology have the potential of being translated and offering solutions, and proteomics, despite being a very young one, is not an exception. This justifies the launching of this special issue by Journal of Proteomics, actually the third monographic one plant proteomics after the special issues by “Plant Proteomics” (2009, vol. 73, Iss. 3) and “Plant Proteomics in Europe” (2011, vol. 74, Iss. 8). We should realize that it will probably be a very long journey before all the promises become reality. The full potential in plant research is far from being fully exploited since a number of technical challenges implicit to working with proteins and the lack of proteogenomic data for most of the species is limiting research. However plant translational proteomics is a field of quick evolution and a number of key discoveries and methodological advances have been recently achieved. We sent invitation letters to the authors by the end of February 2012, trying to contact with all of the research groups that have been publishing works framed under translational proteomics, covering most important research topics: food and beverage traceability, transgenic analysis, allergen identification, post-harvest technology, agronomic techniques, crop improvement, proteotyping and marker assisted breeding, biofuels, bioactive compounds and recombinant proteins, nanotechnology, and other approaches fitting in the translational
concept. It is true that only proteomics in combination with other classical and -omics approaches will get us to a deeper insights and a closer view of the cell biology and its translation in a systems biology context, and because of that the manuscripts should not only contain proteomics techniques, methods and protocols, but also include other approaches validating proteomics results. As an emerging discipline with a constant development in terms of topics and researchers, we didn't want to make this a closed issue — hence, we opened the invitation letter by making this call public in the Journal of Proteomics webpage and also by offering the possibility of being included in this special issue to the authors of fitting papers that were just accepted for publication in this journal. We contacted 75 authors, from which 22 answered positively to this invitation, constituting the most part of this special issue (19 out 26 articles). Summarizing, this issue is conformed by 26 articles, 10 reviews and 16 original research manuscripts. Plant productivity strongly depends on its genetic background, with noticeable differences in plant growth, yields, and organoleptic traits between varieties of the same species. Furthermore, environmental stresses during the growth period often reduce seedling growth and crop yield in terms of quality and quantity, and damages suffered during the harvest, conservation, and transport (post harvest) can affect the final quality of the yield. The determination of the changes in -omics profiles (including proteomics, transcriptomics and metabolomics) for linking plant phenotype and its behavior during productive processes to its molecular phenotype is one of the main challenges for improving agricultural production. The importance of these topics (plant production, stress resistance, biomarkers for breeding) is reflected in the contents of this special issue, with fifteen contributions (60% of total). Six review articles and 9 original research papers reflect the state-of-the-art in related topics to this field. Vanderschuren et al. [2] and Boggess et al. [22] described in their reviews the current status and limitations of proteomics of model and crop plant species, anticipating the future direction that could turn the contributions of plant proteomics into crop improvements. Four original research manuscripts of this issue directly target the improvement of agricultural practices by using a proteomics approach. Gomez-Garay et al. [23] contributed with a proteomic perspective of Quercus suber somatic embryogenesis bringing up some potential targets for the improvement of plant propagation, while Li et al. [24] provided molecular insights of gravitropic response in peanut gynophores thus defining the capability of forming peanuts. Post-harvesting practices towards improving the control of ripening were studied by Zheng et al. [25], who identified the proteins implied in apple-ripening modulation by exogenous ethylene, and by Liu et al. [26], who studied the effect of exogenous cytokinins towards improved practices for amelioration of postharvest yellowing in broccoli. These four approaches followed a classic 2-DE approach, despite the different protein labeling/staining systems that were used. The application of proteomics and metabolomics towards a comprehensive molecular phenotyping aimed to constitute the next generation toolbox for breeders is reviewed by Kumar et al. [27]. Kamal et al. [28] revisited the wheat chloroplast proteome introducing all of the basic and applied advances
J O U R NA L OF PR O TE O MI CS 93 (2 0 1 3 ) 1 –4
derived of this knowledge. Marcon et al. [29] studied the changes associated to heterosis in seminal roots of maize by label free LC–MS/MS. This special issue also reflects the tremendous efforts focused to cope with abiotic and biotic stresses to improve agricultural productivity. Abreu et al. [30] wrote an introductory review covering the achievements and bottlenecks in the identification and validation of protein markers of relevance in abiotic stress tolerance. Specific mechanisms of stress response such as flood-response or unfolded proteins were respectively reviewed by Komatsu et al. [31] and Fanata et al. [32]. Biotic stress and its prevention, in terms of good agricultural practices or by chemical intervention, was discussed by Lim et al. (2013), showing the effects of phosphites triggering immunity in potato leaves and the related-effect over natural resistance to Phytophthora infestans. Robbins et al. (2013) presented another approach for coping with biotic stress: instead of focusing on pathogen, they studied the biosynthetic processes of phenylpropanoids a major class of compounds that function in physiological and defense mechanisms. Sharmila et al. (2013) performed a protein profiling of the infection of mint with Alternaria, advancing in the establishment of plant–pathogen interaction biomarkers. Song et al. analyzed the protein profile of Citrus sinensis roots in response to long-term boron-deficiency by using iTRAQ, covering the important field of plant nutrition. The use of traditional and new species (new varieties, GM plants, the use of exotic species) for agriculture and bioproduction in large plantations (what artificially increases the abundance of only a small number of species) may increase the risks of production in terms of human (allergies, toxicities, …) or environmental (toxicity, horizontal gene transfer, …) safety. Nakamura and Teshima (2013) reviewed proteomics-based allergen analyses including identification and quantitation of allergens, their diagnosis, and the use of allergenomics for safety assessment of GM plants. Kumar et al. (2013) studied red kidney bean-induced allergic manifestations, revealing the fact that its allergenicity potential may get augmented due to the presence of different phytohemagglutins. Uvackova et al. (2013) focused on gliadin and glutenin quantitation within the complex matrix of wheat grains, providing new insights and methods to quantitatively measure clinically relevant proteins causing celiac disease and Baker's asthma. Zezzi et al. (2013) performed comparative studies focusing on antioxidant enzymes in transgenic soybean overexpression of cp4EPSPS gene. Both last two studies conclude, respectively, that there are minor alterations of allergenicity and redox regulation. Proteomics also has a direct translational application for the characterization and improvement of industrial processes such as the production of biomolecules, biodiesel, or food and beverage preparation. For instance high-throughput -omics approaches are being applied to develop suitable biomarkers for foods and beverages — further application of these biomarkers in addressing quality, technology, authenticity, and safety issues, combined with the recent advantages in nanotechnology, will facilitate the transition from standard laboratory methods to miniaturized ones, as reviewed by Agrawal et al. (2013). Lu et al. (2013) described the differences in barley (Hordeum vulgare) malts with distinct filterability by using DIGE. The production of valuable molecules (proteins or
3
metabolites) in a profitable way is one of the cornerstones of the next green revolution, being a number of proteomic approaches addressing biopharmaceutical industrial processes (reviewed by Ribeiro et al. 2013). Among these valuable molecules are modified proteins, as mentioned in the technical review on glycoproteomics provided by Song et al. (2013). Last but not the least, it is assumed that translational proteomics will have a major impact towards the massive production of oil from microalgae and non-edible plants, which are the building blocks for the next green revolution. Ndimba et al. (2013) focused on the utility of high-throughput -omics to improve renewable energy processes, covering from crops or microalgae biomass to biofuel production. In a more specific study on Chlorella, Guarniere et al. (2013) compared different proteome profiles obtained by a shotgun approach, identifying a number of novel targets. These targets include previously unidentified transcription factors and proteins involved in signaling, and other regulators that may quickly improve the strategies for increasing algal lipid body's accumulation by providing narrow sets of targets for transgenesis. We know that there are important gaps in this SI, but it may be also considered admitted that the content of this monograph is reflecting the current status in plant translational proteomics. We must admit that plant proteomics is still mainly focused in developing classical approaches. However, it is a matter of fact that there is a huge room for further development, also in great benefit of next-generation biotechnological approaches such as proteotyping-assisted breeding, metabolic engineering or bioproduction of exotic compounds. The combination of these methodologies and new strategies (i.e. biosensors or microdevices) based in the use, i.e., of nanotechnology will boost agricultural research and plant productivity. In two years from now, plant biologists with experience in using proteomics in combination with complementary approaches will be contacted and asked for contribution to the next SI in plant proteomics, which will presumably be denominated “Proteomics in the Frontier of Plant Biology Knowledge”. By moving from first and second to next generation techniques we are sure that the descriptive era will leave way to more powerful approaches in the frontier of knowledge — for instance, this might succeed through deepening into PTMs and interactomics fields. This is a close reality for model systems, and to a lesser extent, for species with relevant economic or environmental importance. We wish to end this brief introduction appreciating the work of all of the contributors of this SI, especially authors and coauthors.
REFERENCES [1] Jorrin-Novo Jesus V, Maldonado Ana M, Echevarria-Zomeno Sira, Valledor Luis, Castillejo Mari A, Curto Miguel, et al. Plant proteomics update (2007–2008): second-generation proteomic techniques, an appropriate experimental design, and data analysis to fulfill MIAPE standards, increase plant proteome coverage and expand biological knowledge. J Proteomics 2009;72(3):285–314. [2] Vanderschuren H, Lentz E, Zainuddin I, Gruissem W. Proteomics of model and crop plant species: status, current limitations and
4
[3] [4]
[5] [6]
[7] [8]
[9]
[10]
[11] [12]
[13]
[14]
[15]
[16]
[17]
[18]
[19]
[20]
[21]
J O U R NA L OF P R O TE O MI CS 9 3 (2 0 1 3 ) 1 –4
strategic advances for crop improvement. J Proteome 2013;93:5–19. Komatsu Setsuko, Ahsan Nagib. Soybean proteomics and its application to functional analysis. J Proteomics 2009;72(3):325–36. Wienkoop Stefanie, Baginsky Sacha, Weckwerth Wolfram. Arabidopsis thaliana as a model organism for plant proteome research. J Proteomics 2010;73(11 Special Issue):2239–48. Colditz Frank, Braun Hans-Peter. Medicago truncatula proteomics. J Proteomics 2010;73(10 Special Issue):1974–85. Abril Nieves, Gion Jean-Marc, Kerner Rene, Mueller-Starck Gerhard, Cerrillo Navarro, Rafael M, et al. Proteomics research on forest trees, the most recalcitrant and orphan plant species. Phytochemistry 2011;72(10 Special Issue):1219–42. Miernyk Jan A, Hajduch Martin. Seed proteomics. J Proteomics 2011;74(4):389–400. Kosova Klara, Vitamvas Pavel, Prasil Ilja Tom, Renaut Jenny. Plant proteome changes under abiotic stress — contribution of proteomics studies to understanding plant stress response. J Proteomics 2011;74(8 Special Issue):1301–22. Sobhanian Hamid, Aghaei Keyvan, Komatsu Setsuko. Changes in the plant proteome resulting from salt stress: toward the creation of salt-tolerant crops? J Proteomics 2011;74(8 Special Issue):1323–37. Takac Tomas, Pechan Tibor, Samaj Jozef. Differential proteomics of plant development. J Proteomics 2011;74(5):577–88. Visioli Giovanna, Marmiroli Nelson. The proteomics of heavy metal hyperaccumulation by plants. J Proteomics 2013;79:133–45. Zhao Qi, Zhang Heng, Wang Tai, Chen Sixue, Dai Shaojun. Proteomics-based investigation of salt-responsive mechanisms in plant roots. J Proteomics 2013;82:230–53. Ytterberg A Jimmy, Jensen Ole N. Modification-specific proteomics in plant biology. J Proteomics 2010;73(11 Special Issue):2249–66. Nasi Antonella, Picariello Gianluca, Ferranti Pasquale. Proteomic approaches to study structure, functions and toxicity of legume seeds lectins. Perspectives for the assessment of food quality and safety. J Proteomics 2009;72(3):527–38. Palma Jose M, Corpas Francisco J, del Rio Luis A. Proteomics as an approach to the understanding of the molecular physiology of fruit development and ripening. J Proteomics 2011;74(8 Special Issue):1230–43. Oeljeklaus Silke, Meyer Helmut E, Warscheid Bettina. Advancements in plant proteomics using quantitative mass spectrometry. J Proteomics 2009;72(3):545–54. Navrot Nicolas, Finnie Christine, Svensson Birte, Hagglund Per. Plant redox proteomics. J Proteomics 2011;74(8 Special Issue):1450–62. Vertommen A, Panis B, Swennen R, Carpentier SC. Challenges and solutions for the identification of membrane proteins in non-model plants. J Proteomics 2011;74(8 Special Issue):1165–81. Weckwerth Wolfram. Green systems biology — from single genomes, proteomes and metabolomes to ecosystems research and biotechnology. J Proteomics 2011;75(1 Special Issue):284–305. Coxa Jürgen, M.A.Heerenb Ron, Jamesc Peter, Jorrin-Novod Jesús V, Eugene Kolkere F, Levanderg Fredrik, et al. Facing challenges in proteomics today and in the coming decade: report of roundtable discussions at the 4th EuPA scientific meeting, Portugal, Estoril. J Proteome 2011;75:4–17. Agrawal Ganesh Kumar, Pedreschi Romina, Barkla Bronwyn J, Bindschedler Laurence Veronique, Cramer Rainer, Sarkar Abhijit, et al. Translational plant proteomics: a perspective. J Proteomics 2012;75(15):4588–601.
[22] Boggess Mark V, Lippolis John D, Hurkman William J, Fagerquist Clifton K, Briggs Steve P, Gomes Aldrin V, et al. The need for agriculture phenotyping: “Moving from genotype to phenotype. J Proteomics 2013;93:20–39. [23] Gomez-Garay Aranzazu, Lopez Juan Antonio, Camafeita Emilio, Bueno Maria Angeles, Pintos Beatriz. A proteomic perspective of quercus suber somatic embryogenesis. J Proteomics 2013;93:314–25. [24] Li Hai-Fen, Zhu Fang-He, Li He-Ying, Zhu Wei, Chen Xiao-Ping, Hong Yan-Bin, et al. Proteomic identification of gravitropic response genes in peanut gynophores. J Proteomics 2013;93:303–13. [25] Zheng Qifa, Song Jun, Campbell-Palmera Leslie, Thompson Kristen, Li Li, Walker Brad, et al. A proteomic investigation of apple fruit during ripening and in response to ethylene treatment. J Proteomics 2013;93:276–94. [26] Liu Mao-Sen, Li Hui-Chun, Lai Ying-Mi, Lo Hsiao-Feng, Chen Long-Fang. Proteomics and transcriptomics of broccoli subjected to exogenously supplied and transgenic senescence-induced cytokinin for amelioration of postharvest yellowing. J Proteomics 2013;93:133–44. [27] Kumar Sandeep, Verma Alok Kumar, Sharma Akanksha, Kumar Dinesh, Tripathi Anurag, Chaudharic BP, et al. Phytohemagglutinins augment red kidney bean (Phaseolus vulgaris L.) induced allergic manifestations. J Proteomics 2013;93:50–64. [28] Kamal Abu Hena Mostafa, Cho Kun, Choi Jong-Soon, Bae Kwang-Hee, Komatsu Setsuko, Uozumi Nobuyuki, et al. The wheat chloroplastic proteome. J Proteomics 2013;93:326–42. [29] Marcon Caroline, Lamkemeyer Tobias, Malik Waqas Ahmed, Ungrue Denise, Piepho Hans-Peter, Hochholdinger Frank. Heterosis-associated proteome analyses of maize (Zea mays L.) seminal roots by quantitative label-free LC-MS. J Proteomics 2013;93:295–302. [30] Abreu Isabel A, Farinha Ana Paula, Negrão Sónia, Gonçalves Nuno, Fonseca Cátia, Rodrigues Mafalda, et al. Coping with abiotic stress: proteome changes for crop improvement. J Proteomics 2013;93:145–68. [31] Komatsu Setsuko, Shirasaka Naoki, Sakata Katsumi. Omics techniques for identifying flooding-response mechanisms in soybean. J Proteomics 2013;93:169–78. [32] Fanata Wahyu Indra Duwi, Lee Sang Yeol, Lee Kyun Oh. The unfolded protein response in plants: a fundamental adaptive cellular response to internal and external stresses. J Proteomics 2013;93:356–68.
Jesús Jorrín-Novo⁎ Agricultural and Plant Proteomics, Biochemistry and Molecular Biology, University of Córdoba, Cordoba, Spain ⁎Corresponding author. E-mail address: [email protected]. Luis Valledor⁎⁎ Adaption Biotechnologies, GCRC, Academy of Sciences of the Czech Republic, Brno, Czech Republic ⁎⁎Corresponding author. E-mail address: [email protected].
Available online at www.sciencedirect.com
ScienceDirect www.elsevier.com/locate/jprot
Preface
Translational Proteomics Special Issue
As an associate editor of the JoP in charge of the plant section (JVJN), it was my compromise trying to edit a monographic issue at around every two years; so, one year ago, I began to make plans, starting by the invitation to my friend, colleague, and from now on co-editor, Dr. Luis Valledor. Then, we asked ourselves: which should be the focus? It had to depend on the papers published in the last two years and it also had to be something new or at least original. According to Web of Knowledge (Thomson Reuters), the number of plant proteomics papers published in the Journal of Proteomics (JoP) during the period April 2008–August 2013 was 144, representing a 12.8% of the articles published in the journal (1127). Considering all journals the representation of plant proteomics decreases to 7.6% (2850 out of 37,237). During this period, 2008–2013, two plant proteomics special issues have been released by JoP, the first one by April 2009 (Vol. 72, Iss. 3, Plant Proteomics), and the second one by August 2011 (Vol. 74, Iss. 8; Plant Proteomics in Europe). These special and other regular issues contained a number of reviews on plant proteomics, either generalists [1,2] or with focus on plant systems [3–6], plant organs [7], biological processes [8–12], post translational modifications [13], translational [14,15] or methodological [16–18]. Considering all of these works, if we had to summarize the state of the art in the field of plant proteomics we would say that proteomics itself is progressing at much more speed than its application to plant research, following the trend stated in previous reviews [1,6]. The full potential of proteomics as an experimental approach is quite far from being fully exploited in plant biology research. It is true that apart from the model systems (mainly Arabidopsis and rice) the number of plant species (herbaceous, woody, gymnosperms and angiosperms, monocot and dicots) and biological processes (from growth and development to responses to the environment) to which proteomics is being applied has notably increased. Methodological advances in plant proteomics, including instrumentation, workflows and protocols (with discussion on its realities, limitations, and challenges) have been collected and accurately described in a book that appears in parallel to this special issue: “Plant proteomics. Methods and protocols. 2nd edition”, edited by Jorrin-Novo, Komatsu, Weckwerth and Wienkoop. Methods in Molecular
1874-3919/$ – see front matter © 2013 Elsevier B.V. All rights reserved. http://dx.doi.org/10.1016/j.jprot.2013.10.019
Biology Series, 1072, Humana Press. In the introductory chapter, Prof. Dr. Jorrín Novo stated: “We should recognize that proteomics is starting to make contributions to a proper gene annotation, identification and characterization of gene products or protein species, and to the knowledge of living (in this case plants) organisms, having also an enormous potential of application to translational research. However, and despite its great potential, and as in any other experimental approach, it is far from being a Pandora's Box. In the case of plant research, the full potential of proteomics is quite far from being totally exploited, and second, third, and fourth generation proteomics techniques are still of very limited use. Most of the plant proteomics papers so far published belong to the descriptive, subcellular and comparative proteomics subgroup, mainly using a few experimental model systems — those whose genome has been sequenced, and being from a biological point of view quite descriptive and speculative. From now on we should put more emphasis on the study of post-translational proteomics and interactomics, and move to targeted, hypothesis driven approaches. Furthermore, and even more important, we should validate our data through other -omics or classical biochemical strategies, in an attempt to get a deeper, real and more accurate view and understanding of cell biology. In the modern Systems Biology concept, proteomics must be considered as a part of a global, multidisciplinary approach. Making biological sense of a proteomics experiment requires a proper experimental design, data validation, interpretation, and publication policy.” The last paragraph is recognized as the new direction in the JoP publication policy as written by Prof. Calvete, JoP editor in chief, in the editorial that appeared in the December 2012 issue (Vol. 76, 1–2), also been discussed in detail by Prof. Weckwerth [19]. Coming to the focus of this issue, we had three options, keeping out one more “plant proteomics” generalist issue. The first one was methodological; it did not make sense
2
J O U R NA L OF P R O TE O MI CS 9 3 (2 0 1 3 ) 1 –4
considering the publication of the above mentioned book. The second one was directed at basic research that can be called “proteomics in the frontier of plant biology research”. This was probably our preferred option but, and because of the different reasons, we should not expect many contributions to justify the issue, but for sure it will be the next. The last and more realistic one was our final choice: “practical or translational proteomics”, a topic very well covered and understood in biomedicine but not that well in agriculture. This topic was in our mind since 2010, and briefly discussed during the roundtable discussion session at the 4th EuPA meeting in Portugal and appeared in the paper by Cox et al. [20]. Later on, Agrawal et al. [21] published an excellent review on translational plant proteomics. The final aim of plant translational proteomics is the development of new practices compromised with the environment, biodiversity conservation and human health, considering the life quality of not only developed but also poor populations in a World that is expected to support nearly 10 billion figures by 2050. Considering the increase in the world population and the enormous pressure that will be put to increase agricultural production, the use of biotechnology will play a relevant role. Nowadays it is not a matter of discussion, being more than obvious, that science and scientists should go beyond just the generation of knowledge: their research must have an additional value, even admitting this additional value is a consequence of that generation of knowledge. This is summarized in the new fashion key word “translational”, with the main goal being the use of research in generating innovative and productivity — technologies that are crucial to agricultural and economic growth, thus helping to fulfill future needs for food, fiber, and fuels. This concept is well understood in the biomedicine field, but not so well in the agricultural and environmental area, being necessary an increased interaction between bench and field. Any research, scientific area, and methodology have the potential of being translated and offering solutions, and proteomics, despite being a very young one, is not an exception. This justifies the launching of this special issue by Journal of Proteomics, actually the third monographic one plant proteomics after the special issues by “Plant Proteomics” (2009, vol. 73, Iss. 3) and “Plant Proteomics in Europe” (2011, vol. 74, Iss. 8). We should realize that it will probably be a very long journey before all the promises become reality. The full potential in plant research is far from being fully exploited since a number of technical challenges implicit to working with proteins and the lack of proteogenomic data for most of the species is limiting research. However plant translational proteomics is a field of quick evolution and a number of key discoveries and methodological advances have been recently achieved. We sent invitation letters to the authors by the end of February 2012, trying to contact with all of the research groups that have been publishing works framed under translational proteomics, covering most important research topics: food and beverage traceability, transgenic analysis, allergen identification, post-harvest technology, agronomic techniques, crop improvement, proteotyping and marker assisted breeding, biofuels, bioactive compounds and recombinant proteins, nanotechnology, and other approaches fitting in the translational
concept. It is true that only proteomics in combination with other classical and -omics approaches will get us to a deeper insights and a closer view of the cell biology and its translation in a systems biology context, and because of that the manuscripts should not only contain proteomics techniques, methods and protocols, but also include other approaches validating proteomics results. As an emerging discipline with a constant development in terms of topics and researchers, we didn't want to make this a closed issue — hence, we opened the invitation letter by making this call public in the Journal of Proteomics webpage and also by offering the possibility of being included in this special issue to the authors of fitting papers that were just accepted for publication in this journal. We contacted 75 authors, from which 22 answered positively to this invitation, constituting the most part of this special issue (19 out 26 articles). Summarizing, this issue is conformed by 26 articles, 10 reviews and 16 original research manuscripts. Plant productivity strongly depends on its genetic background, with noticeable differences in plant growth, yields, and organoleptic traits between varieties of the same species. Furthermore, environmental stresses during the growth period often reduce seedling growth and crop yield in terms of quality and quantity, and damages suffered during the harvest, conservation, and transport (post harvest) can affect the final quality of the yield. The determination of the changes in -omics profiles (including proteomics, transcriptomics and metabolomics) for linking plant phenotype and its behavior during productive processes to its molecular phenotype is one of the main challenges for improving agricultural production. The importance of these topics (plant production, stress resistance, biomarkers for breeding) is reflected in the contents of this special issue, with fifteen contributions (60% of total). Six review articles and 9 original research papers reflect the state-of-the-art in related topics to this field. Vanderschuren et al. [2] and Boggess et al. [22] described in their reviews the current status and limitations of proteomics of model and crop plant species, anticipating the future direction that could turn the contributions of plant proteomics into crop improvements. Four original research manuscripts of this issue directly target the improvement of agricultural practices by using a proteomics approach. Gomez-Garay et al. [23] contributed with a proteomic perspective of Quercus suber somatic embryogenesis bringing up some potential targets for the improvement of plant propagation, while Li et al. [24] provided molecular insights of gravitropic response in peanut gynophores thus defining the capability of forming peanuts. Post-harvesting practices towards improving the control of ripening were studied by Zheng et al. [25], who identified the proteins implied in apple-ripening modulation by exogenous ethylene, and by Liu et al. [26], who studied the effect of exogenous cytokinins towards improved practices for amelioration of postharvest yellowing in broccoli. These four approaches followed a classic 2-DE approach, despite the different protein labeling/staining systems that were used. The application of proteomics and metabolomics towards a comprehensive molecular phenotyping aimed to constitute the next generation toolbox for breeders is reviewed by Kumar et al. [27]. Kamal et al. [28] revisited the wheat chloroplast proteome introducing all of the basic and applied advances
J O U R NA L OF PR O TE O MI CS 93 (2 0 1 3 ) 1 –4
derived of this knowledge. Marcon et al. [29] studied the changes associated to heterosis in seminal roots of maize by label free LC–MS/MS. This special issue also reflects the tremendous efforts focused to cope with abiotic and biotic stresses to improve agricultural productivity. Abreu et al. [30] wrote an introductory review covering the achievements and bottlenecks in the identification and validation of protein markers of relevance in abiotic stress tolerance. Specific mechanisms of stress response such as flood-response or unfolded proteins were respectively reviewed by Komatsu et al. [31] and Fanata et al. [32]. Biotic stress and its prevention, in terms of good agricultural practices or by chemical intervention, was discussed by Lim et al. (2013), showing the effects of phosphites triggering immunity in potato leaves and the related-effect over natural resistance to Phytophthora infestans. Robbins et al. (2013) presented another approach for coping with biotic stress: instead of focusing on pathogen, they studied the biosynthetic processes of phenylpropanoids a major class of compounds that function in physiological and defense mechanisms. Sharmila et al. (2013) performed a protein profiling of the infection of mint with Alternaria, advancing in the establishment of plant–pathogen interaction biomarkers. Song et al. analyzed the protein profile of Citrus sinensis roots in response to long-term boron-deficiency by using iTRAQ, covering the important field of plant nutrition. The use of traditional and new species (new varieties, GM plants, the use of exotic species) for agriculture and bioproduction in large plantations (what artificially increases the abundance of only a small number of species) may increase the risks of production in terms of human (allergies, toxicities, …) or environmental (toxicity, horizontal gene transfer, …) safety. Nakamura and Teshima (2013) reviewed proteomics-based allergen analyses including identification and quantitation of allergens, their diagnosis, and the use of allergenomics for safety assessment of GM plants. Kumar et al. (2013) studied red kidney bean-induced allergic manifestations, revealing the fact that its allergenicity potential may get augmented due to the presence of different phytohemagglutins. Uvackova et al. (2013) focused on gliadin and glutenin quantitation within the complex matrix of wheat grains, providing new insights and methods to quantitatively measure clinically relevant proteins causing celiac disease and Baker's asthma. Zezzi et al. (2013) performed comparative studies focusing on antioxidant enzymes in transgenic soybean overexpression of cp4EPSPS gene. Both last two studies conclude, respectively, that there are minor alterations of allergenicity and redox regulation. Proteomics also has a direct translational application for the characterization and improvement of industrial processes such as the production of biomolecules, biodiesel, or food and beverage preparation. For instance high-throughput -omics approaches are being applied to develop suitable biomarkers for foods and beverages — further application of these biomarkers in addressing quality, technology, authenticity, and safety issues, combined with the recent advantages in nanotechnology, will facilitate the transition from standard laboratory methods to miniaturized ones, as reviewed by Agrawal et al. (2013). Lu et al. (2013) described the differences in barley (Hordeum vulgare) malts with distinct filterability by using DIGE. The production of valuable molecules (proteins or
3
metabolites) in a profitable way is one of the cornerstones of the next green revolution, being a number of proteomic approaches addressing biopharmaceutical industrial processes (reviewed by Ribeiro et al. 2013). Among these valuable molecules are modified proteins, as mentioned in the technical review on glycoproteomics provided by Song et al. (2013). Last but not the least, it is assumed that translational proteomics will have a major impact towards the massive production of oil from microalgae and non-edible plants, which are the building blocks for the next green revolution. Ndimba et al. (2013) focused on the utility of high-throughput -omics to improve renewable energy processes, covering from crops or microalgae biomass to biofuel production. In a more specific study on Chlorella, Guarniere et al. (2013) compared different proteome profiles obtained by a shotgun approach, identifying a number of novel targets. These targets include previously unidentified transcription factors and proteins involved in signaling, and other regulators that may quickly improve the strategies for increasing algal lipid body's accumulation by providing narrow sets of targets for transgenesis. We know that there are important gaps in this SI, but it may be also considered admitted that the content of this monograph is reflecting the current status in plant translational proteomics. We must admit that plant proteomics is still mainly focused in developing classical approaches. However, it is a matter of fact that there is a huge room for further development, also in great benefit of next-generation biotechnological approaches such as proteotyping-assisted breeding, metabolic engineering or bioproduction of exotic compounds. The combination of these methodologies and new strategies (i.e. biosensors or microdevices) based in the use, i.e., of nanotechnology will boost agricultural research and plant productivity. In two years from now, plant biologists with experience in using proteomics in combination with complementary approaches will be contacted and asked for contribution to the next SI in plant proteomics, which will presumably be denominated “Proteomics in the Frontier of Plant Biology Knowledge”. By moving from first and second to next generation techniques we are sure that the descriptive era will leave way to more powerful approaches in the frontier of knowledge — for instance, this might succeed through deepening into PTMs and interactomics fields. This is a close reality for model systems, and to a lesser extent, for species with relevant economic or environmental importance. We wish to end this brief introduction appreciating the work of all of the contributors of this SI, especially authors and coauthors.
REFERENCES [1] Jorrin-Novo Jesus V, Maldonado Ana M, Echevarria-Zomeno Sira, Valledor Luis, Castillejo Mari A, Curto Miguel, et al. Plant proteomics update (2007–2008): second-generation proteomic techniques, an appropriate experimental design, and data analysis to fulfill MIAPE standards, increase plant proteome coverage and expand biological knowledge. J Proteomics 2009;72(3):285–314. [2] Vanderschuren H, Lentz E, Zainuddin I, Gruissem W. Proteomics of model and crop plant species: status, current limitations and
4
[3] [4]
[5] [6]
[7] [8]
[9]
[10]
[11] [12]
[13]
[14]
[15]
[16]
[17]
[18]
[19]
[20]
[21]
J O U R NA L OF P R O TE O MI CS 9 3 (2 0 1 3 ) 1 –4
strategic advances for crop improvement. J Proteome 2013;93:5–19. Komatsu Setsuko, Ahsan Nagib. Soybean proteomics and its application to functional analysis. J Proteomics 2009;72(3):325–36. Wienkoop Stefanie, Baginsky Sacha, Weckwerth Wolfram. Arabidopsis thaliana as a model organism for plant proteome research. J Proteomics 2010;73(11 Special Issue):2239–48. Colditz Frank, Braun Hans-Peter. Medicago truncatula proteomics. J Proteomics 2010;73(10 Special Issue):1974–85. Abril Nieves, Gion Jean-Marc, Kerner Rene, Mueller-Starck Gerhard, Cerrillo Navarro, Rafael M, et al. Proteomics research on forest trees, the most recalcitrant and orphan plant species. Phytochemistry 2011;72(10 Special Issue):1219–42. Miernyk Jan A, Hajduch Martin. Seed proteomics. J Proteomics 2011;74(4):389–400. Kosova Klara, Vitamvas Pavel, Prasil Ilja Tom, Renaut Jenny. Plant proteome changes under abiotic stress — contribution of proteomics studies to understanding plant stress response. J Proteomics 2011;74(8 Special Issue):1301–22. Sobhanian Hamid, Aghaei Keyvan, Komatsu Setsuko. Changes in the plant proteome resulting from salt stress: toward the creation of salt-tolerant crops? J Proteomics 2011;74(8 Special Issue):1323–37. Takac Tomas, Pechan Tibor, Samaj Jozef. Differential proteomics of plant development. J Proteomics 2011;74(5):577–88. Visioli Giovanna, Marmiroli Nelson. The proteomics of heavy metal hyperaccumulation by plants. J Proteomics 2013;79:133–45. Zhao Qi, Zhang Heng, Wang Tai, Chen Sixue, Dai Shaojun. Proteomics-based investigation of salt-responsive mechanisms in plant roots. J Proteomics 2013;82:230–53. Ytterberg A Jimmy, Jensen Ole N. Modification-specific proteomics in plant biology. J Proteomics 2010;73(11 Special Issue):2249–66. Nasi Antonella, Picariello Gianluca, Ferranti Pasquale. Proteomic approaches to study structure, functions and toxicity of legume seeds lectins. Perspectives for the assessment of food quality and safety. J Proteomics 2009;72(3):527–38. Palma Jose M, Corpas Francisco J, del Rio Luis A. Proteomics as an approach to the understanding of the molecular physiology of fruit development and ripening. J Proteomics 2011;74(8 Special Issue):1230–43. Oeljeklaus Silke, Meyer Helmut E, Warscheid Bettina. Advancements in plant proteomics using quantitative mass spectrometry. J Proteomics 2009;72(3):545–54. Navrot Nicolas, Finnie Christine, Svensson Birte, Hagglund Per. Plant redox proteomics. J Proteomics 2011;74(8 Special Issue):1450–62. Vertommen A, Panis B, Swennen R, Carpentier SC. Challenges and solutions for the identification of membrane proteins in non-model plants. J Proteomics 2011;74(8 Special Issue):1165–81. Weckwerth Wolfram. Green systems biology — from single genomes, proteomes and metabolomes to ecosystems research and biotechnology. J Proteomics 2011;75(1 Special Issue):284–305. Coxa Jürgen, M.A.Heerenb Ron, Jamesc Peter, Jorrin-Novod Jesús V, Eugene Kolkere F, Levanderg Fredrik, et al. Facing challenges in proteomics today and in the coming decade: report of roundtable discussions at the 4th EuPA scientific meeting, Portugal, Estoril. J Proteome 2011;75:4–17. Agrawal Ganesh Kumar, Pedreschi Romina, Barkla Bronwyn J, Bindschedler Laurence Veronique, Cramer Rainer, Sarkar Abhijit, et al. Translational plant proteomics: a perspective. J Proteomics 2012;75(15):4588–601.
[22] Boggess Mark V, Lippolis John D, Hurkman William J, Fagerquist Clifton K, Briggs Steve P, Gomes Aldrin V, et al. The need for agriculture phenotyping: “Moving from genotype to phenotype. J Proteomics 2013;93:20–39. [23] Gomez-Garay Aranzazu, Lopez Juan Antonio, Camafeita Emilio, Bueno Maria Angeles, Pintos Beatriz. A proteomic perspective of quercus suber somatic embryogenesis. J Proteomics 2013;93:314–25. [24] Li Hai-Fen, Zhu Fang-He, Li He-Ying, Zhu Wei, Chen Xiao-Ping, Hong Yan-Bin, et al. Proteomic identification of gravitropic response genes in peanut gynophores. J Proteomics 2013;93:303–13. [25] Zheng Qifa, Song Jun, Campbell-Palmera Leslie, Thompson Kristen, Li Li, Walker Brad, et al. A proteomic investigation of apple fruit during ripening and in response to ethylene treatment. J Proteomics 2013;93:276–94. [26] Liu Mao-Sen, Li Hui-Chun, Lai Ying-Mi, Lo Hsiao-Feng, Chen Long-Fang. Proteomics and transcriptomics of broccoli subjected to exogenously supplied and transgenic senescence-induced cytokinin for amelioration of postharvest yellowing. J Proteomics 2013;93:133–44. [27] Kumar Sandeep, Verma Alok Kumar, Sharma Akanksha, Kumar Dinesh, Tripathi Anurag, Chaudharic BP, et al. Phytohemagglutinins augment red kidney bean (Phaseolus vulgaris L.) induced allergic manifestations. J Proteomics 2013;93:50–64. [28] Kamal Abu Hena Mostafa, Cho Kun, Choi Jong-Soon, Bae Kwang-Hee, Komatsu Setsuko, Uozumi Nobuyuki, et al. The wheat chloroplastic proteome. J Proteomics 2013;93:326–42. [29] Marcon Caroline, Lamkemeyer Tobias, Malik Waqas Ahmed, Ungrue Denise, Piepho Hans-Peter, Hochholdinger Frank. Heterosis-associated proteome analyses of maize (Zea mays L.) seminal roots by quantitative label-free LC-MS. J Proteomics 2013;93:295–302. [30] Abreu Isabel A, Farinha Ana Paula, Negrão Sónia, Gonçalves Nuno, Fonseca Cátia, Rodrigues Mafalda, et al. Coping with abiotic stress: proteome changes for crop improvement. J Proteomics 2013;93:145–68. [31] Komatsu Setsuko, Shirasaka Naoki, Sakata Katsumi. Omics techniques for identifying flooding-response mechanisms in soybean. J Proteomics 2013;93:169–78. [32] Fanata Wahyu Indra Duwi, Lee Sang Yeol, Lee Kyun Oh. The unfolded protein response in plants: a fundamental adaptive cellular response to internal and external stresses. J Proteomics 2013;93:356–68.
Jesús Jorrín-Novo⁎ Agricultural and Plant Proteomics, Biochemistry and Molecular Biology, University of Córdoba, Cordoba, Spain ⁎Corresponding author. E-mail address: [email protected]. Luis Valledor⁎⁎ Adaption Biotechnologies, GCRC, Academy of Sciences of the Czech Republic, Brno, Czech Republic ⁎⁎Corresponding author. E-mail address: [email protected].
