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      Transcriptome- Assisted Label-Free Quantitative Proteomics Analysis Reveals Novel Insights into Piper nigrumPhytophthora capsici Phytopathosystem

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          Abstract

          Black pepper ( Piper nigrum L.), a tropical spice crop of global acclaim, is susceptible to Phytophthora capsici, an oomycete pathogen which causes the highly destructive foot rot disease. A systematic understanding of this phytopathosystem has not been possible owing to lack of genome or proteome information. In this study, we explain an integrated transcriptome-assisted label-free quantitative proteomics pipeline to study the basal immune components of black pepper when challenged with P. capsici. We report a global identification of 532 novel leaf proteins from black pepper, of which 518 proteins were functionally annotated using BLAST2GO tool. A label-free quantitation of the protein datasets revealed 194 proteins common to diseased and control protein datasets of which 22 proteins showed significant up-regulation and 134 showed significant down-regulation. Ninety-three proteins were identified exclusively on P. capsici infected leaf tissues and 245 were expressed only in mock (control) infected samples. In-depth analysis of our data gives novel insights into the regulatory pathways of black pepper which are compromised during the infection. Differential down-regulation was observed in a number of critical pathways like carbon fixation in photosynthetic organism, cyano-amino acid metabolism, fructose, and mannose metabolism, glutathione metabolism, and phenylpropanoid biosynthesis. The proteomics results were validated with real-time qRT-PCR analysis. We were also able to identify the complete coding sequences for all the proteins of which few selected genes were cloned and sequence characterized for further confirmation. Our study is the first report of a quantitative proteomics dataset in black pepper which provides convincing evidence on the effectiveness of a transcriptome-based label-free proteomics approach for elucidating the host response to biotic stress in a non-model spice crop like P. nigrum, for which genome information is unavailable. Our dataset will serve as a useful resource for future studies in this plant. Data are available via ProteomeXchange with identifier PXD003887.

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          Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

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            Primer3Plus, an enhanced web interface to Primer3

            Here we present Primer3Plus, a new web interface to the popular Primer3 primer design program as an enhanced alternative for the CGI- scripts that come with Primer3. Primer3 consists of a command line program and a web interface. The web interface is one large form showing all of the possible options. This makes the interface powerful, but at the same time confusing for occasional users. Primer3Plus provides an intuitive user interface using present-day web technologies and has been developed in close collaboration with molecular biologists and technicians regularly designing primers. It focuses on the task at hand, and hides detailed settings from the user until these are needed. We also added functionality to automate specific tasks like designing primers for cloning or step-wise sequencing. Settings and designed primer sequences can be stored locally for later use. Primer3Plus supports a range of common sequence formats, such as FASTA. Finally, primers selected by Primer3Plus can be sent to an order form, allowing tight integration into laboratory ordering systems. Moreover, the open architecture of Primer3Plus allows easy expansion or integration of external software packages. The Primer3Plus Perl source code is available under GPL license from SourceForge. Primer3Plus is available at http://www.bioinformatics.nl/primer3plus.
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              Laccase: new functions for an old enzyme

               A. Mayer (2002)
              Laccases occur widely in fungi; they have been characterized less frequently in higher plants. Here we have focused on more recent reports on the occurrence of laccase and its functions in physiological development and industrial utility. The reports of molecular weights, pH optima, and substrate specificity are extremely diverse. Conclusive proof of the occurrence of laccase in a tissue must demonstrate that the enzyme be able to oxidize quinol with concomitant uptake of oxygen. Laccase is involved in the pigmentation process of fungal spores, the regeneration of tobacco protoplasts, as fungal virulence factors, and in lignification of cell walls and delignification during white rot of wood. Commercially, laccases have been used to delignify woody tissues, produce ethanol, and to distinguish between morphine and codeine. A very wide variety of bioremediation processes employ laccase in order to protect the environment from damage caused by industrial effluents. Research in recent years has been intense, much of it elicited by the wide diversity of laccases, their utility and their very interesting enzymology.
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                Author and article information

                Contributors
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                20 June 2016
                2016
                : 7
                Affiliations
                1Division of Plant Molecular Biology, Rajiv Gandhi Center for Biotechnology Thiruvananthapuram, India
                2Proteomics Core Facility, Rajiv Gandhi Center for Biotechnology Thiruvananthapuram, India
                Author notes

                Edited by: Swarup Kumar Parida, National Institute of Plant Genome Research, India

                Reviewed by: Stanley Roux, The University of Texas at Austin, USA; Xun Xu, Beijing Genomics Institute-Shenzhen, China

                *Correspondence: Manjula Sakuntala smanjula@ 123456rgcb.res.in

                This article was submitted to Plant Genetics and Genomics, a section of the journal Frontiers in Plant Science

                Article
                10.3389/fpls.2016.00785
                4913111
                27379110
                Copyright © 2016 Mahadevan, Krishnan, Saraswathy, Surendran, Jaleel and Sakuntala.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                Page count
                Figures: 14, Tables: 0, Equations: 0, References: 78, Pages: 17, Words: 10997
                Categories
                Plant Science
                Original Research

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