Special Issue "Plant Proteomics"

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A special issue of Proteomes (ISSN 2227-7382).

Deadline for manuscript submissions: closed (30 June 2014)

Special Issue Editors

Guest Editor
Prof. Dr. Setsuko Komatsu
National Institute of Crop Science, Kannondai 2-1-18, Tsukuba 305-8518, Japan
E-Mail: skomatsu@affrc.go.jp
Phone: +81 29 838 8693
Fax: +81 29 838 8694
Interests: plant proteomics; plant biotechnology; plant physiology; abiotic stress

Guest Editor
Dr. Zahed Hossain
Department of Botany, West Bengal State University, Berunanpukuria, P.O. Malikapur Barasat, North 24 Parganas Kolkata-700 126, West Bengal, India
E-Mail: zahed_kly@yahoo.com
Phone: +91 33 2524 1975
Fax: +91 33 2524 1977
Interests: plant proteomics; plant stress biology; abiotic stress response; plant antioxidant defence

Special Issue Information

Dear Colleagues,

Proteomics, the high-throughput “omic” technique has validated its role in precise identification and characterization of individual components of plant protein networks. A comprehensive understanding of plant response mechanism is essential to elucidate the key factors affecting plant performance under adverse conditions. Various proteomic approaches that are being exploited extensively for elucidating plant response largely include gel-based and mass spectrometry-based methods that involve both label-based and label-free protein quantification. Despite of limitations in identifying low-abundance and hydrophobic proteins, exceedingly large or small proteins, as well as basic proteins, gel-based method has been accepted as a global tool to unravel the underlying molecular mechanism of stress signal perception and transduction in plant defense responses. Moreover, recent advances in the mass spectrometry-based approaches provide a better opportunity to dissect stress signaling cascades. Nevertheless, complete protein extraction from different plant organs or subcellular organelles is the most challenging facet of plant proteome analysis. Furthermore, protein-protein interactions and post-translational modifications provide deeper insight into protein molecular function. We welcome submissions of original research papers and review articles addressing recent advancements as well as strengths and shortcomings of various proteomic approaches and diverse applications of plant proteomic techniques to get new insights of plant molecular responses to various biotic and abiotic challenges.

Prof. Dr. Setsuko Komatsu
Dr. Zahed Hossain
Guest Editors

Submission

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. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as 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 refereed through a 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. For the first couple of issues the Article Processing Charge (APC) will be waived for well-prepared manuscripts. English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.

Keywords

  • plant proteomics
  • methodologies for plant proteomics
  • application of plant proteomics

Published Papers (10 papers)

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Displaying article 1-10
p. 468-484
by  and
Proteomes 2014, 2(4), 468-484; doi:10.3390/proteomes2040468
Received: 25 July 2014; in revised form: 22 September 2014 / Accepted: 23 September 2014 / Published: 29 September 2014
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(This article belongs to the Special Issue Plant Proteomics)
p. 323-340
by , , ,  and
Proteomes 2014, 2(3), 323-340; doi:10.3390/proteomes2030323
Received: 1 February 2014; in revised form: 26 May 2014 / Accepted: 10 June 2014 / Published: 1 July 2014
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(This article belongs to the Special Issue Plant Proteomics)
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p. 303-322
by ,  and
Proteomes 2014, 2(3), 303-322; doi:10.3390/proteomes2030303
Received: 2 April 2014; in revised form: 28 May 2014 / Accepted: 28 May 2014 / Published: 26 June 2014
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(This article belongs to the Special Issue Plant Proteomics)
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p. 258-271
by , , , , , , ,  and
Proteomes 2014, 2(2), 258-271; doi:10.3390/proteomes2020258
Received: 8 February 2014; in revised form: 8 April 2014 / Accepted: 21 April 2014 / Published: 5 May 2014
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(This article belongs to the Special Issue Plant Proteomics)
p. 224-242
by , ,  and
Proteomes 2014, 2(2), 224-242; doi:10.3390/proteomes2020224
Received: 3 February 2014; in revised form: 8 April 2014 / Accepted: 8 April 2014 / Published: 17 April 2014
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(This article belongs to the Special Issue Plant Proteomics)
p. 208-223
by , ,  and
Proteomes 2014, 2(2), 208-223; doi:10.3390/proteomes2020208
Received: 16 January 2014; in revised form: 15 March 2014 / Accepted: 27 March 2014 / Published: 9 April 2014
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(This article belongs to the Special Issue Plant Proteomics)
p. 169-190
by , , , , , , , , ,  and
Proteomes 2014, 2(2), 169-190; doi:10.3390/proteomes2020169
Received: 18 February 2014; in revised form: 4 March 2014 / Accepted: 6 March 2014 / Published: 28 March 2014
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(This article belongs to the Special Issue Plant Proteomics)
p. 107-127
by  and
Proteomes 2014, 2(1), 107-127; doi:10.3390/proteomes2010107
Received: 17 November 2013; in revised form: 26 February 2014 / Accepted: 27 February 2014 / Published: 7 March 2014
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(This article belongs to the Special Issue Plant Proteomics)
p. 85-106
by , , , ,  and
Proteomes 2014, 2(1), 85-106; doi:10.3390/proteomes2010085
Received: 30 October 2013; in revised form: 21 February 2014 / Accepted: 21 February 2014 / Published: 4 March 2014
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(This article belongs to the Special Issue Plant Proteomics)
p. 254-274
by , ,  and
Proteomes 2013, 1(3), 254-274; doi:10.3390/proteomes1030254
Received: 15 October 2013; in revised form: 28 November 2013 / Accepted: 28 November 2013 / Published: 5 December 2013
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Planned Papers

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.

Type of Paper: Article
Title: Proteomic Analysis of Mechanisms for Disease Resistance Induction in Japanese Birch Plantlet Treated with Salicylic Acid
Authors: Hiromu Suzuki, Yuya Takashima, Futoshi Ishiguri, Kazuya Iizuka, Nobuo Yoshizawa and Shinso Yokota *
Affiliation: Department of Forest Science, Faculty of Agriculture, Utsunomiya University, Japan
Abstract: The present study was carried out to clarify the mechanisms for systemic acquired resistance (SAR) and resistance signaling pathways against the infection with Inonotus obliquus strain IO-U1 in Japanese birch plantlet No.8. Protein changes induced by salicylic acid (SA)-administration were analyzed, and SA-responsive proteins were identified. Total 10 specifically expressed, 5 significantly increased, and 3 significantly decreased protein spots were analyzed by LC/MS/MS and sequence tag method. As the results, 5 specifically expressed, 3 significantly increased, and 3 significantly decreased proteins were identified as follows: malate dehydrogenase, succinate dehydrogenase, phosphoglycerate kinase, diaminopimelate decarboxylase, arginase, chorismate mutase, cyclophilin, aminopeptidase, and unknown function proteins. It is considered that these proteins are involved in SAR establishment mechanisms in Japanese birch plantlet No.8.

Type of the Paper: Review
Title:
Plant cell wall proteins: a large corpus of data, but what about runaways?
Authors:
Cécile Albenne, Hervé Canut, Laurent Hoffmann and Elisabeth Jamet
Affiliation:
Laboratoire de recherche en Sciences Végétales (LRSV), UMR 5546 UPS/CNRS, 24 chemin de Borderouge – Auzeville, BP 42617, 31326 CASTANET TOLOSAN, France
Abstract:
Plant cell wall proteomics has been a very dynamic field of research for about fifteen years. The first studies have only led to the identification of a few proteins. However, a range of strategies has been proposed to increase the number of identified proteins and to characterize their post-translational modifications. The protocols are still improving to enlarge the coverage of cell wall proteomes, which presently accounts for about one fourth of the expected cell wall proteome in the most studied plant, Arabidopsis thaliana. The availability of genomic sequences of additional plant species has also greatly contributed to the development of this research field by allowing the precise identification of proteins from mass spectrometry data. Today, more than 1500 cell wall proteins (CWPs) have been identified in a variety of plant species and organs. In this review, we will highlight two points. First point is related to methodology and concerns the present limitations of the coverage of cell wall proteomes. Indeed, a step of cell wall purification is often performed before CWP extraction. Because of the variety of cell wall structures and of the diversity of protein/polysaccharide and protein/protein interactions in cell walls, some CWPs can be missing either because they are washed out during the purification of cell walls or because they are covalently linked to cell wall components. Second point is related to data analysis with an overview of the cell wall proteomes of dicots vs those of monocots. A large corpus of data is available particularly in A. thaliana, Brachypodium distachyon and Oryza sativa. CWP contents have some specificities in relation to the major differences in cell wall composition and structure between these plants. A special emphasis will be put on proteins acting on polysaccharides, lectins and oxidoreductases.

Type of Paper: Article
Title:
A Directed-Proteomics-Based Platform for Systems Analysis of Soybean Seed Development
Authors:
*Ján A. Miernyk1,2,3, Mark L. Johnston1, Wesner Antoine2,3, Brian P. Mooney2,4, Eliot M. Herman5
Affiliations:
1USDA, Agricultural Research Service, Plant Genetics Research Unit, University of Missouri, Columbia, MO 65211 USA
2 Department of Biochemistry, University of Missouri, Columbia, MO
3Interdisciplinary Plant Group, University of Missouri, Columbia,    
4
Charles W. Gehrke Proteomics Center, Christopher S. Bond Life Sciences Center, University of Missouri,
5
School of Plant Sciences, University of Arizona, Tucson, AZ 85721
Abstract
: A simple but robust system based upon fresh weight and color was used to delineate nine stages of soybean (Glycine max (L.) Merrill, cv. Jack) seed development.  Storage proteins and oil were extracted and quantified from each stage, and the morphological plus biochemical characteristics were combined to establish a preliminary model.  Results from transcript profiling were used to define molecular markers for embryogenesis/cell division, cellular specialization/reserve polymer accumulation, and dehydration/preparation for quiescence.  Total soluble protein fractions were isolated from each developmental stage, and separated on 2-dimensional gels.  Difference in-gel electrophoresis was used to quantify target spots displaying changes in abundance between the various stages of seed development.  The patterns of change in abundance of target proteins were analyzed by a unique application of model-building, hierarchical clustering, and multidimensional scaling.  All of the protein dynamics data was accommodated by five expression patterns.  Mass spectrometry was used to identify the most abundant proteins in the targeted spots, and the identified proteins were grouped according to function.  Systems cartography was used to display potential relationships between and among proteins of differing functional and developmental groups.  In toto, our results establish a proteomics-based platform suitable for use in systems-analysis of soybean seed development.


Last update: 24 April 2014

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