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      Glutathione S-transferases and UDP-glycosyltransferases Are Involved in Response to Aluminum Stress in Flax

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          Abstract

          About 30% of the world's ice-free land area is occupied by acid soils. In soils with pH below 5, aluminum (Al) releases to the soil solution, and becomes highly toxic for plants. Therefore, breeding of varieties that are resistant to Al is needed. Flax ( Linum usitatissimum L.) is grown worldwide for fiber and seed production. Al toxicity in acid soils is a serious problem for flax cultivation. However, very little is known about mechanisms of flax resistance to Al and the genetics of this resistance. In the present work, we sequenced 16 transcriptomes of flax cultivars resistant (Hermes and TMP1919) and sensitive (Lira and Orshanskiy) to Al, which were exposed to control conditions and aluminum treatment for 4, 12, and 24 h. In total, 44.9–63.3 million paired-end 100-nucleotide reads were generated for each sequencing library. Based on the obtained high-throughput sequencing data, genes with differential expression under aluminum exposure were revealed in flax. The majority of the top 50 up-regulated genes were involved in transmembrane transport and transporter activity in both the Al-resistant and Al-sensitive cultivars. However, genes encoding proteins with glutathione transferase and UDP-glycosyltransferase activity were in the top 50 up-regulated genes only in the flax cultivars resistant to aluminum. For qPCR analysis in extended sampling, two UDP-glycosyltransferases (UGTs), and three glutathione S-transferases (GSTs) were selected. The general trend of alterations in the expression of the examined genes was the up-regulation under Al stress, especially after 4 h of Al exposure. Moreover, in the flax cultivars resistant to aluminum, the increase in expression was more pronounced than that in the sensitive cultivars. We speculate that the defense against the Al toxicity via GST antioxidant activity is the probable mechanism of the response of flax plants to aluminum stress. We also suggest that UGTs could be involved in cell wall modification and protection from reactive oxygen species (ROS) in response to Al stress in L. usitatissimum. Thus, GSTs and UGTs, probably, play an important role in the response of flax to Al via detoxification of ROS and cell wall modification.

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          Pathview: an R/Bioconductor package for pathway-based data integration and visualization

          Summary: Pathview is a novel tool set for pathway-based data integration and visualization. It maps and renders user data on relevant pathway graphs. Users only need to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps and integrates user data onto the pathway and renders pathway graphs with the mapped data. Although built as a stand-alone program, Pathview may seamlessly integrate with pathway and functional analysis tools for large-scale and fully automated analysis pipelines. Availability: The package is freely available under the GPLv3 license through Bioconductor and R-Forge. It is available at http://bioconductor.org/packages/release/bioc/html/pathview.html and at http://Pathview.r-forge.r-project.org/. Contact: luo_weijun@yahoo.com Supplementary information: Supplementary data are available at Bioinformatics online.
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            HMMER web server: 2015 update

            The HMMER website, available at http://www.ebi.ac.uk/Tools/hmmer/, provides access to the protein homology search algorithms found in the HMMER software suite. Since the first release of the website in 2011, the search repertoire has been expanded to include the iterative search algorithm, jackhmmer. The continued growth of the target sequence databases means that traditional tabular representations of significant sequence hits can be overwhelming to the user. Consequently, additional ways of presenting homology search results have been developed, allowing them to be summarised according to taxonomic distribution or domain architecture. The taxonomy and domain architecture representations can be used in combination to filter the results according to the needs of a user. Searches can also be restricted prior to submission using a new taxonomic filter, which not only ensures that the results are specific to the requested taxonomic group, but also improves search performance. The repertoire of profile hidden Markov model libraries, which are used for annotation of query sequences with protein families and domains, has been expanded to include the libraries from CATH-Gene3D, PIRSF, Superfamily and TIGRFAMs. Finally, we discuss the relocation of the HMMER webserver to the European Bioinformatics Institute and the potential impact that this will have.
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              THE FUNCTIONS AND REGULATION OF GLUTATHIONE S-TRANSFERASES IN PLANTS.

              Glutathione S-transferases (GSTs) play roles in both normal cellular metabolism as well as in the detoxification of a wide variety of xenobiotic compounds, and they have been intensively studied with regard to herbicide detoxification in plants. A newly discovered plant GST subclass has been implicated in numerous stress responses, including those arising from pathogen attack, oxidative stress, and heavy-metal toxicity. In addition, plant GSTs play a role in the cellular response to auxins and during the normal metabolism of plant secondary products like anthocyanins and cinnamic acid. This review presents the current knowledge about the functions of GSTs in regard to both herbicides and endogenous substrates. The catalytic mechanism of GST activity as well as the fate of glutathione S-conjugates are reviewed. Finally, a summary of what is known about the gene structure and regulation of plant GSTs is presented.
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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
                21 December 2016
                2016
                : 7
                : 1920
                Affiliations
                [1] 1Engelhardt Institute of Molecular Biology, Russian Academy of Sciences Moscow, Russia
                [2] 2All-Russian Research Institute for Flax Torzhok, Russia
                Author notes

                Edited by: Michael Deyholos, University of British Columbia, Canada

                Reviewed by: V. Mohan Murali Achary, International Centre for Genetic Engineering and Biotechnology (ICGEB), India; Alexandra De Sousa, Biosystems & Integrative Sciences Institute (BioISI), Portugal; Vladimir Zhukov, All-Russia Research Institute for Agricultural Microbiology, Russia

                *Correspondence: Nataliya V. Melnikova mnv-4529264@ 123456yandex.ru

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

                †These authors have contributed equally to this work.

                Article
                10.3389/fpls.2016.01920
                5174120
                16348f59-0c01-488d-bc97-e6fcdb89fac3
                Copyright © 2016 Dmitriev, Krasnov, Rozhmina, Kishlyan, Zyablitsin, Sadritdinova, Snezhkina, Fedorova, Yurkevich, Muravenko, Bolsheva, Kudryavtseva and Melnikova.

                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.

                History
                : 22 September 2016
                : 02 December 2016
                Page count
                Figures: 1, Tables: 2, Equations: 2, References: 106, Pages: 10, Words: 8485
                Funding
                Funded by: Russian Science Foundation 10.13039/501100006769
                Award ID: 16-16-00114
                Categories
                Plant Science
                Original Research

                Plant science & Botany
                linum usitatissimum,flax,aluminum stress,acid soil,transcriptome sequencing,gene expression,glutathione s-transferase,udp-glycosyltransferase

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