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
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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
Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.
Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Proteomes is an international peer-reviewed open access quarterly journal published by MDPI.
Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 350 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.
- 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: 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: 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.