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Advances in Plant Proteomics: Methodology to Biology

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

Deadline for manuscript submissions: closed (31 December 2015) | Viewed by 25862

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Special Issue Editors

Dr. Ganesh Kumar Agrawal

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Guest Editor

Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO 13265, Kathmandu 44600, Nepal
Interests: plants; plant proteomics; biotic and abiotic stress biology; metabolic pathway discovery; modification (phosphorylation) biology; environmental pollution; translational research; crop design and improvement against adverse environmental factors; modeling and prediction; functional genomics; systems biology; research and discovery to education for the next generation; research and educational training

Prof. Dr. Sun Tae Kim

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Guest Editor

Department of Plant Bioscience, Pusan National University, Miryang 50463, Republic of Korea
Interests: advanced proteomics in biotic and abiotic stresses
Special Issues, Collections and Topics in MDPI journals

Dr. Randeep Rakwal

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Guest Editor

Faculty of Health and Sport Sciences & Tsukuba International Academy for Sport Studies, University of Tsukuba, Tsukuba, Ibaraki 305-8574, Japan
Interests: rice; UV irradiation; Methyltransferase; Sakuranetin; ozone; environmental gaseous pollutants; radiation; low-level gamma rays; Iitate village; IISORA; Fukushima; proteomics; DNA microarray; secondary metabolites; jasmonic acid; SDS-PAGE; 2-DGE; mass spectrometry; protocols

Special Issue Information

Dear Colleagues,

Proteomics covers not only the realm of plant biology but all living organisms, however it is plants (i.e., agriculture) that have played the most important role in nurturing human civilization. Thus, plant biology as a discipline is of paramount importance to the academic and research community. Among the tools available to science, the omics high-throughput approaches have focused on advancing not only our basic understanding but also new applications to plant biology. This Special Issue on 'Advances in Plant Proteomics: Methodology to Biology' presents original research articles, methods, bioinformatics tools, and reviews on the advancing proteomics research in plants. Plant biologists involved in this field have now started to impact plant proteomics at the global level with new advances and discoveries that make proteomics more attractive than ever to the younger generation.

Dr. Ganesh Kumar Agrawal
Dr. Sun Tae Kim
Dr. Randeep Rakwal
Guest Editors

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 submissions that pass pre-check are 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 1800 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.

Keywords

Plant proteomics
Sample preparation
Food proteomics
Quantitative proteomics
Stress and disease
New technology

Published Papers (4 papers)

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Research

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3424 KiB

Open AccessArticle

Identification of Biomarkers for Resistance to Fusarium oxysporum f. sp. cubense Infection and in Silico Studies in Musa paradisiaca Cultivar Puttabale through Proteomic Approach

by Venkatesh Ramu, Krishna Venkatarangaiah, Pradeepa Krishnappa, Santosh Kumar Shimoga Rajanna, Nagaraja Deeplanaik, Anup Chandra Pal and Kukkundoor Ramachandra Kini

Proteomes 2016, 4(1), 9; https://doi.org/10.3390/proteomes4010009 - 24 Feb 2016

Cited by 4 | Viewed by 5939

Abstract

Panama wilt caused by Fusarium oxysporum f. sp. cubense (Foc) is one of the major disease constraints of banana production. Previously, we reported the disease resistance Musa paradisiaca cv. puttabale clones developed from Ethylmethanesulfonate and Foc culture filtrate against Foc inoculation. Here, the same resistant clones and susceptible clones were used for the study of protein accumulation against Foc inoculation by two-dimensional gel electrophoresis (2-DE), their expression pattern and an in silico approach. The present investigation revealed mass-spectrometry identified 16 proteins that were over accumulated and 5 proteins that were under accumulated as compared to the control. The polyphosphoinositide binding protein ssh2p (PBPssh2p) and Indoleacetic acid-induced-like (IAA) protein showed significant up-regulation and down-regulation. The docking of the pathogenesis-related protein (PR) with the fungal protein endopolygalacturonase (PG) exemplify the three ionic interactions and seven hydrophobic residues that tends to good interaction at the active site of PG with free energy of assembly dissociation (1.5 kcal/mol). The protein-ligand docking of the Peptide methionine sulfoxide reductase chloroplastic-like protein (PMSRc) with the ligand β-1,3 glucan showed minimum binding energy (−6.48 kcal/mol) and docking energy (−8.2 kcal/mol) with an interaction of nine amino-acid residues. These explorations accelerate the research in designing the host pathogen interaction studies for the better management of diseases. Full article

(This article belongs to the Special Issue Advances in Plant Proteomics: Methodology to Biology)

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1826 KiB

Open AccessArticle

Comparative Proteomic Analysis of Cotton Fiber Development and Protein Extraction Method Comparison in Late Stage Fibers

by Hana Mujahid, Ken Pendarvis, Joseph S. Reddy, Babi Ramesh Reddy Nallamilli, K. R. Reddy, Bindu Nanduri and Zhaohua Peng

Proteomes 2016, 4(1), 7; https://doi.org/10.3390/proteomes4010007 - 03 Feb 2016

Cited by 9 | Viewed by 7121

Abstract

The distinct stages of cotton fiber development and maturation serve as a single-celled model for studying the molecular mechanisms of plant cell elongation, cell wall development and cellulose biosynthesis. However, this model system of plant cell development is compromised for proteomic studies due to a lack of an efficient protein extraction method during the later stages of fiber development, because of a recalcitrant cell wall and the presence of abundant phenolic compounds. Here, we compared the quality and quantities of proteins extracted from 25 dpa (days post anthesis) fiber with multiple protein extraction methods and present a comprehensive quantitative proteomic study of fiber development from 10 dpa to 25 dpa. Comparative analysis using a label-free quantification method revealed 287 differentially-expressed proteins in the 10 dpa to 25 dpa fiber developmental period. Proteins involved in cell wall metabolism and regulation, cytoskeleton development and carbohydrate metabolism among other functional categories in four fiber developmental stages were identified. Our studies provide protocols for protein extraction from maturing fiber tissues for mass spectrometry analysis and expand knowledge of the proteomic profile of cotton fiber development. Full article

(This article belongs to the Special Issue Advances in Plant Proteomics: Methodology to Biology)

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1360 KiB

Open AccessArticle

Quantitative Proteomic Analysis of the Response to Zinc, Magnesium, and Calcium Deficiency in Specific Cell Types of Arabidopsis Roots

by Yoichiro Fukao, Mami Kobayashi, Sajad Majeed Zargar, Rie Kurata, Risa Fukui, Izumi C. Mori and Yoshiyuki Ogata

Proteomes 2016, 4(1), 1; https://doi.org/10.3390/proteomes4010001 - 12 Jan 2016

Cited by 13 | Viewed by 5045

Abstract

The proteome profiles of specific cell types have recently been investigated using techniques such as fluorescence activated cell sorting and laser capture microdissection. However, quantitative proteomic analysis of specific cell types has not yet been performed. In this study, to investigate the response of the proteome to zinc, magnesium, and calcium deficiency in specific cell types of Arabidopsis thaliana roots, we performed isobaric tags for relative and absolute quantification (iTRAQ)-based quantitative proteomics using GFP-expressing protoplasts collected by fluorescence-activated cell sorting. Protoplasts were collected from the pGL2-GFPer and pMGP-GFPer marker lines for epidermis or inner cell lines (pericycle, endodermis, and cortex), respectively. To increase the number of proteins identified, iTRAQ-labeled peptides were separated into 24 fractions by OFFGFEL electrophoresis prior to high-performance liquid chromatography coupled with mass spectrometry analysis. Overall, 1039 and 737 proteins were identified and quantified in the epidermal and inner cell lines, respectively. Interestingly, the expression of many proteins was decreased in the epidermis by mineral deficiency, although a weaker effect was observed in inner cell lines such as the pericycle, endodermis, and cortex. Here, we report for the first time the quantitative proteomics of specific cell types in Arabidopsis roots. Full article

(This article belongs to the Special Issue Advances in Plant Proteomics: Methodology to Biology)

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Review

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2931 KiB

Open AccessReview

The Pollen Coat Proteome: At the Cutting Edge of Plant Reproduction

by Juan David Rejón, François Delalande, Christine Schaeffer-Reiss, Juan De Dios Alché, María Isabel Rodríguez-García, Alain Van Dorsselaer and Antonio Jesús Castro

Proteomes 2016, 4(1), 5; https://doi.org/10.3390/proteomes4010005 - 29 Jan 2016

Cited by 37 | Viewed by 7242

Abstract

The tapetum is a single layer of secretory cells which encloses the anther locule and sustains pollen development and maturation. Upon apoptosis, the remnants of the tapetal cells, consisting mostly of lipids and proteins, fill the pits of the sculpted exine to form the bulk of the pollen coat. This extracellular matrix forms an impermeable barrier that protects the male gametophyte from water loss and UV light. It also aids pollen adhesion and hydration and retains small signaling compounds involved in pollen–stigma communication. In this study, we have updated the list of the pollen coat’s protein components and also discussed their functions in the context of sexual reproduction Full article

(This article belongs to the Special Issue Advances in Plant Proteomics: Methodology to Biology)

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