Special Issue "Plant Proteomics 2017"
A special issue of Proteomes (ISSN 2227-7382).
Deadline for manuscript submissions: closed (30 June 2017)
Dr. Elisabeth Jamet
Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 Chemin de Borderouge-Auzeville, BP42617, Castanet-Tolosan 31326, France
Website | E-Mail
Interests: plant; cell wall biology; development; evolution; proteomics; post-translational modification; cell wall architecture; protein/protein; protein/polysaccharide interaction
During recent years, proteomics has become the key to understand physiological processes involving the regulation of expression of many genes from transcription to production of metabolites. Each of these steps is part of the overall mechanisms tightly coordinated to allow organisms to develop or adapt to their environment. Plant proteomics has been dramatically expanding since the beginning of the 2000s thanks to major advances in the development of three technological tools. It started with the sequencing of full genomes and collection of expressed sequence tags or RNAs. The release of the Arabidopsis thaliana genome in 2000 has allowed this plant to become a pioneer model for dicots, and particularly for proteomics studies. More than 650 articles have been published in this field since 2000. A. thaliana has been quickly followed by Brachypodium distachyon as a model for monocots and by plants of agronomical interest such as rice, maize, sugarcane, alfalfa, tomato or flax. Apart from these plants, others for which sequencing data were not available could be studied as well, thanks to the possibility to work with heterologous data. In addition, over the last decade, remarkable technological advances have been achieved due to improvements in mass spectrometry which allowed refining the coverage of total proteomes and sub-proteomes from small amounts of starting material and characterizing post-translational modifications and protein-protein interactions. Furthermore, quantitative proteomics now provides detailed information on organ- and tissue-specific regulatory mechanisms responding to a variety of individual stresses or stress combinations during the plant life cycle. Finally, the development of computational tools allows managing the tremendous amount of data generated by mass spectrometers to deliver relevant biological information. Thus, powerful mass spectrometry-based technologies now provide unprecedented insights into the composition, structure, function and control of the proteome, shedding light on complex biological processes and phenotypes.
This Special issue of Proteomes welcomes submissions of original research or review articles aiming at deciphering physiological processes with the use of proteomics tools. Contributions will deal with the dynamics of proteins in their native and modified forms, with the combination of several “omics” approaches in contrasted physiological situations as well as with technical advances in the proteomic field.
Dr. Elisabeth Jamet
Dr. Véronique Santoni
Manuscript Submission Information
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- Omics data integration
- Plant development
- Plant interactions with their environment
- Plant proteomics
- Quantitative proteomics
The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.
Title: A first glance at the proteome of leaf glandular trichome from sweet basil (Ocimum basilicum L.): terpenoid-related biosynthetic pathways and possible transport proteins
Authors: Antoine Champagne and Marc Boutry
Affiliation: Institut des Sciences de la Vie, Université catholique de Louvain, Croix du Sud, 4-5, Bte 7.07.14, 1348 Louvain-la-Neuve, Belgium
Abstract: Sweet basil (Ocimum basilicum L.) is an important member of the Lamiaceae family, which contains species cultivated for their medicinal and aromatic properties. The edible leaves of basil are used daily in the kitchen and are also hydrodistilled to produce essential oil. Glandular trichomes of this species are known to produce and store specialized (secondary) metabolites, such as monoterpene, sesquiterpene, and phenolic compounds. A large 2DLC-MS/MS proteomic analysis was performed on isolated peltate glandular trichomes and 1,071 proteins were identified. Among them, up to 93 are involved in the specialized metabolism, including 37 proteins related to the biosynthesis of terpenoids and 57 to the synthesis of phenolic compounds. Five ATP-binding cassette (ABC) transporters from the subfamily G were identified and some of them might be involved in the transport of specialized metabolites, while seven uncharacterized cytochrome P450 are interesting candidates to play a role in the chemical diversity of specialized metabolites. This proteomic investigation of glandular trichomes of sweet basil leaves lays the groundwork for improving our knowledge on the function of glandular trichomes.
Title: Proteome analysis of the specific proteins produced in each organ of the Japanese white birch plantlet No.8 treated with azelaic acid
Author: Shinso Yokota
Affiliation: Faculty of Agriculture, Utsunomiya University
Abstract: In order to clarify resistance mechanisms induced by azelaic acid (AZA) signaling and AZA signal transduction pathways in the Japanese white birch plantlet No. 8, the present study identified the specific proteins produced in each organ, the 3rd internode, stalk and petiole, leaf, and root, of the plantlet treated with AZA by proteomic approach. The numbers of specifically expressed protein spots in the two-dimensional electrophoresis gels from the 3rd internode, stalk and petiole, leaf, and root of the AZA-treated plantlet were 5, 3, 3, and 2, respectively. These specific proteins were identified by sequence tag method using LC/MS/MS. It was suggested that AZA signaling in the birch plantlet functions in the upstream of systemic acquired resistance (SAR) to induce the proteins involved in the SAR induction, and that AZA serves as a long distance signal.
Title: Revealing the rice cytosolic proteome
Author: Joshua Heazlewood
Affiliation: Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
Abstract: The cytosol plays a central role in plant metabolism being location of numerous biochemical processes such as glycolysis and gluconeogenesis. While numerous subcellular proteomic studies have been conducted in plants, few attempts have been made to characterize this important compartment. Much attention in this area has focused on the reference plant Arabidopsis with numerous organelle surveys. In important crop species such as rice (Oryza sativa), few such surveys have been conducted and in particular no analysis has been undertaken to define the rice cytosol. To that effect, this study focused on the enrichment of the cytosolic fraction of rice suspension cell cultures and its characterization by shotgun proteomics to better define proteins found in this compartment. A gentle disruption approach was developed for the rice suspension cell cultures to eliminate contamination. In total, around 1000 proteins were reproducibly identified from the rice cytosol after manual curation of known contaminants. The location of a subset of these proteins were selected and their localization verified by fluorescent-tags. These data provide additional insight into the role of the cytosol within plants with a specific focus on grasses. The data have been deposited in the ProteomeXchange with the identifier PXD001116.
Title: A PROTEOMIC APPROACH TO INVESTIGATE THE RESPONSE OF TEF (ERAGROSTIS TEF) TO DROUGHT
Authors: M.S Rafudeen
Affiliation: Department of Molecular & Cell Biology, University of Cape Town, Rondebosch 7700, Cape Town, South Africa
Abstract: Eragrostis tef, commonly known as tef, is an important staple food and forage crop indigenous to Ethiopia. Tef plants are highly adaptable to abiotic stress conditions and are able to grow and produce grain yields under a wide range of environmental conditions, particularly under drought stress. In this study, tef plants were subjected to controlled dehydration stress treatment and physiologically characterised using relative water content (RWC), electrolyte leakage and chlorophyll fluorescence measurements, to establish critical water content stages for investigation of changes to the tef proteome in response to dehydration stress. Physiological testing showed tef viability to be retained to 30% RWC, however, further water loss to below 30% RWC, resulted in total loss of viability. Physiological characterisation with dehydration treatment showed a maximum leakage rate of 780 μS.min-1.gdw-1 and complete photosynthetic disruption with Fv/Fm and ɸPSII values decreasing to 0.2, below 30% RWC. Additionally, ultra-structural analysis using transmission electron microscopy showed extensive damage to the subcellular organisation of tef plant cells at water contents below 30% RWC. Based on these physiological data, it was decided to investigate the proteome of tef leaf dehydrated tissues at 50% RWC, as a non-lethal dehydration stress, as compared to hydrated tissues at 80% RWC. Proteomic analyses using iTRAQ mass spectrometry coupled to peptide OFFGEL fractionation and appropriate database searching with the Tef Extended and Liliopsida databases enabled the generation of three dataset results. These datasets, each contained a substantial amount of database matched proteins, where 5727 proteins for the Tef Extended (TE), 2656 proteins for the Tef Extended unique (TEU) and 4328 proteins for the Monocot unique (MU) datasets, were identified. Statistical analyses on peptide relative quantification values showed differential regulation of 211 proteins for the TE dataset, 111 proteins for the TEU dataset and 174 proteins for the MU dataset, in response to dehydration stress. A reciprocal BLAST search through the use of OrthoMCL with all three differentially regulated datasets (foregrounds) showed the TE foreground to provide the most comprehensive total protein coverage for further bioinformatics inference. Bioinformatics analysis using the programs Mercator, MapMan and Blast2GO showed a diverse range of biological processes, where functional enrichment of GO-terms involved in biotic and abiotic stress response, signalling, transport, cellular homeostasis and pentose metabolic processes were enriched in tef high-abundance proteins. GO-terms linked to ROS producing processes such as photosynthetic reactions, cell wall catabolism, manganese transport and homeostasis, the synthesis of sugars and cell wall modification were enriched in tef low-abundance proteins. Additionally, KEGG analysis was used to observe tef proteins mapped to various biological pathways, of which the stress-responsive pathways, glutathione metabolism and ascorbate and aldarate metabolism were analysed in depth. Furthermore, biological validation of a few high-abundance proteins generated from iTRAQ analysis in the form of western blotting and relevant enzyme assays were conducted. The results showed the proteins fructose-bisphosphate aldolase (FBA), glutamine synthetase (GLN), functioning in plant maintenance processes as well as the stress-protective antioxidant proteins, monodehydroascorbate reductase (MDHAR), peroxidase (POX) and superoxide dismutase (SOD) to be accumulated and further support iTRAQ findings.
Title: Proteomics highlights specific feature of the isolated embryo and endosperm of the seeds of Amborella trichopoda, the most basal angiosperm
Authors: Matthieu Villegente1, Philippe Marmey2, Claudette Job3, Gwendal Cueff4,5, Béatrice Godin4,5, Loïc Rajjou4,5, Thierry Balliau6, Michel Zivy6, Bruno Fogliani1,7, Valérie Sarramegna-Burtet1, and Dominique Job3,5
1 Laboratoire Insulaire du Vivant et de l’Environnement, University of New-Caledonia, BP R4, 98851 Nouméa, New-Caledonia
2 IRD, UMR DIADE (Plant Diversity Adaptation and Environment), IRD/University of Montpellier 2/CIRAD/CNRS, Montpellier 34398, France
3 CNRS-University Claude Bernard Lyon-Institut National des Sciences Appliquées-Bayer CropScience Joint Laboratory (UMR5240), Bayer CropScience, F–69263 Lyon cedex 9, France
4 INRA, Institut Jean-Pierre Bourgin (IJPB), UMR 1318 INRA/AgroParisTech, ERL CNRS 3559, Laboratory of Excellence "Saclay Plant Sciences" (LabEx SPS), RD10, F-78026 Versailles, France
5 AgroParisTech, Chaire de Physiologie végétale, F-75231 Paris, France
6 INRA, Plateforme d'Analyse Protéomique de Paris Sud-Ouest (PAPPSO), INRA/University Paris-Sud/CNRS/AgroParisTech, UMR 0320/UMR 8120 Génétique Quantitative et Evolution – Le Moulon, F-91190 Gif-sur-Yvette, France
7 Institut Agronomique néo-Calédonien (IAC), Diversités Biologique et Fonctionnelle des Ecosystèmes Terrestres, 98890 Païta, New-Caledonia
Abstract: Toward the goal of identifying proteome signatures that could be associated with the origin and early diversification of angiosperms, we have conducted a shotgun proteomic analysis of isolated embryo and endosperm from mature seeds of Amborella trichopoda, an understory shrub endemic to New Caledonia that is considered to be the basal extant angiosperm. This work also provides novel findings in seed physiology as, in contrast to many angiosperm species, mature Amborella seeds have very small immature embryos embedded in copious endosperm. The present analysis led to the characterization of 415 and 69 proteins from the isolated embryo and endosperm tissues, respectively. The role of these proteins is discussed in terms of protein evolution and of physiological properties of the immature embryos, notably concerning the acquisition of desiccation tolerance, which is considered to correspond to the final developmental stage of mature seeds with large embryos.
Title: Proteomics from the eye of an orphan and recalcitrant experimental plant system: the forest tree Quercus ilex
Author: Jesús V. Jorrín Novo, et al
Affiliation: Agroforestry and Plant Biochemistry and Proteomics, Dpt. of Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain
Abstract: Based on the work carried out since 2003 by our research group (Agroforestry and Plant Biochemistry and Proteomics, http://www.uco.es/investiga/grupos/probiveag/) on proteomics of forest tree species, the power and limitations of the approach will be discussed. By using a proteomics approach we have investigated in this species developmental processes (seed maturation and germination), responses to biotic (fungal pathogens) and abiotic stresses (drought), and have attempted to characterize and catalogue populations based on protein profiles. We have moved from the classical 2-DE based strategy to the most recent gel-free/shotgun one. From now we pretend to take the systems biology direction through the validation of proteomics data and its integration with other –omics and classical approaches. From this work with a very orphan and recalcitrant system and from our own errors and wrong interpretations of the data we have learnt a number of lessons on how to design an experiment, to make a protein extract, to perform a MS analysis, to confidently identify and quantify protein species, and to interpret them from a biological point of view. The protein world is much more complex than we have ever imagined and the full potential of proteomics is far from being fully exploited in plant biology research, and even so it has several limitations; however, and with no doubt about, it has contributed to a deeper knowledge of the plant biology, also being employed for translational purposes.
Title: Aluminum-induced proteome expression in switchgrass roots
Authors: Mahesh Rangu, Zhujia Ye, Sarabjit Bhatti, Suping Zhou*, Yang Yong, Tara Fish, Theodore Thannhauser*
Abstract: Aluminum (Al) stress causes significant reduction in plant growth when grown in acidic soil. The most noticeable symptom of Al toxicity is the development of stunted root systems on sensitive plants. Switchgrass plants were grown hydroponically in Al-treated and control cultures. After a month of aluminum treatment plants started showing physiological stresses such as declining photosynthetic activities, from this roots were harvested. Root-tip and root-elongation zone tissues were separately analyzed using TMT-MS quantitative proteomics analysis. A total of 256 proteins (approximately 3% of total proteins) showed significant differences between control and treated samples with significant fold change, (p<0.05, FDR<0.05 [201 proteins up-regulated, 55 proteins down regulated]). MapMan software was used for the functional classification of significantly different proteins. The expressed proteins were involved in different biological pathways including; cell cycle and cell division, transcription, protein synthesis, protein degradation, stress related pathways. The highest numbers of proteins expressed were from enzyme families (22), protein synthesis (23), protein degradation (16) and stress related enzymes (26). Proteins like the germin-like proteins and peroxidase superfamily protein were down-regulated while glutathione S-transferase, phosphate transporter and histone superfamily protein were up-regulated. Various transcription factors were identified and found to be both repressed or induced depending upon their functional context.
Keywords: TMT-MS analysis, Proteomic analysis, MapMan software, significant proteins
Title: Phytase immobilized enzymatic nano-reactor liberating phytate-protein complexes for complementary proteomic profiling of maize embryo
Authors: Wenzhong Zhang1, Jun Yao2*, Fang Xu1,2*, Pengyuan Yang2
1 School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China. Email: email@example.com; firstname.lastname@example.org
2 Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China. Email: email@example.com
3 Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, NC 27599-7431,USA
A simple, robust and reliable sample pre-treatment method is indispensable for complementary proteomic profiling of plant samples. Traditional water soluble protein extraction has been an option but which might lose certain protein information because of abundant phytate co-existing in plant samples. For example, maize embryo contains up to 1 wt% of phytate, and the polyanionic phytate molecule with its six phosphate groups can bind to specific proteins thus forming insoluble complexes. Also multivalent metal ions interact with phytate and protein to form ternary complexes. The binding nature is related to type, solubility and conformational characteristics of the proteins. The formation of phytate-protein complexes occurs as water-insoluble and subsequently leading to failure of the complementary proteomic identification of plant samples.
In our recent study, enzyme phytase was innovatively considered to overcome the problem of phytate-protein complexes throughout water-soluble protein extraction of plant samples, because phytase could decompose its substrate phytate into inositol phosphates and inorganic phosphate
Being compatible with mass spectrometry, hybrid phytase immobilized enzymatic nano-reactor (PIENR) was designed by us to resolve the interference of phytate through soluble protein extraction of maize embryo. After proteomic analysis, 422 proteins were identified under PIENR-assisted conditions in comparison to 256 proteins using traditional sample extraction protocol. The identified proteins in both methods were correspondently discussed with regards to isoelectric point, amino acid distributions as well as potential copper ion binding nature. PIENAR-assisted strategy exhibited its advantage for complementary proteomic profiling of maize embryos and its real application could be further extended to wider scope of plant proteomics.
Title: Proteomics investigations of proteases involved in the senescence of cotyledons: a model to explore the genotypic variability of proteolysis machinery associated with the nitrogen remobilization efficiency during leaf senescence of oilseed rape
Authors: Marine Poret1, 2, 3, Balakumaran Chandrasekar4, 5, Renier A. L. van der Hoorn4, Laurent Coquet1, 6, Thierry Jouenne1, 6, Jean-Christophe Avice1, 2, 3*
1 Université de Caen Normandie, F-14032 Caen, France
2 UCN, UMR INRA–UCBN 950 Ecophysiologie Végétale, Agronomie & Nutritions N.C.S., F-14032 Caen, France, F-14032 Caen, France
3 INRA, UMR INRA–UCBN 950 Ecophysiologie Végétale, Agronomie & Nutritions N.C.S., F-14032 Caen, France
4 The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, United Kingdom
5 The Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, 50829 Cologne, Germany
6 CNRS UMR6270, “PISSARO” facilities of IRIB-HN, Mont-Saint-Aignan, France
Abstract: Oilseed rape (Brassica napus L.) is characterized by a low nitrogen remobilization efficiency (NRE) during leaf senescence. A proteomics study of genotypic variability in leaves of oilseed rape has recently reported that the induction of specific serine and cysteine proteases activities were associated with a better NRE at the vegetative stage (rosette) and during the transition between vegetative and reproductive stages. Because cotyledons are subjected to senescence, it could be hypothesized that contrasted protease activities between genotypes may be distinguishable precociously during the senescence of cotyledons. To verify this assumption, our goals were (i) to characterize protease activities between two genotypes with contrasting NRE (Ténor and Samouraï) during the senescence of cotyledons under limiting or ample nitrate supply, and (ii) to test the role of salicylic and abscisic acid on the regulation of proteolysis. In order to rich these goals, proteases activities were measured and identified by a specific proteomics approach combining activity-based protein profiling (ABPP) with LC-MS/MS analysis. As observed in leaves, chlorophyll and soluble protein contents decrease during senescence of cotyledons and is correlated with an increase of serine hydrolases and cysteine protease activities particularly under nitrate limitation. Two RD21-like proteases previously associated with an efficient proteolysis in senescing leaves of Ténor are also detected in senescing cotyledons. An exogenous application of abscisic acid provokes the decrease of chlorophyll and soluble protein contents with an increase of several cysteine protease activities while several activities of cysteine proteases and serine hydrolases increase in response to the salicylic acid infiltration. The study of protease activities during senescence of cotyledons seems to be a promising experimental model system to investigate the genotypic variability for contrasting NRE and the regulation of proteolysis associated with an efficient N remobilization.