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      Characterization and expression analysis of the WRKY gene family in moso bamboo

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          Abstract

          The WRKY family of transcription factors (TFs) is one of the ten largest families of TFs in higher plants and has been implicated in multiple biological processes. Here, we identified 121 WRKY TFs in moso bamboo, including five novel members that were not annotated in the Phyllostachys edulis genomic database. Estimation of the divergence time of paralogous gene pairs revealed an important role of the recent whole-genome duplication in the expansion of the WRKY family. Expression analysis based on quantitative reverse-transcription polymerase chain reaction (qRT-PCR) data revealed that a large number of PheWRKY genes varied significantly under cold or drought stress treatments, which could be defined as abiotic stress-responsive genes. The overexpression of PheWRKY72-2 in Arabidopsis resulted in a decreased sensitivity to drought stress during early seedling growth. PheWRKY72-2 may enhance plant tolerance to stress by functioning as a positive regulator of stoma closure. Our study provides a theoretical foundation and some experimental evidence for further functional verification of the PheWRKY family of TFs.

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          LEA (Late Embryogenesis Abundant) proteins and their encoding genes in Arabidopsis thaliana

          Michaela Hundertmark, Dirk Hincha (2008)
          Background LEA (late embryogenesis abundant) proteins have first been described about 25 years ago as accumulating late in plant seed development. They were later found in vegetative plant tissues following environmental stress and also in desiccation tolerant bacteria and invertebrates. Although they are widely assumed to play crucial roles in cellular dehydration tolerance, their physiological and biochemical functions are largely unknown. Results We present a genome-wide analysis of LEA proteins and their encoding genes in Arabidopsis thaliana. We identified 51 LEA protein encoding genes in the Arabidopsis genome that could be classified into nine distinct groups. Expression studies were performed on all genes at different developmental stages, in different plant organs and under different stress and hormone treatments using quantitative RT-PCR. We found evidence of expression for all 51 genes. There was only little overlap between genes expressed in vegetative tissues and in seeds and expression levels were generally higher in seeds. Most genes encoding LEA proteins had abscisic acid response (ABRE) and/or low temperature response (LTRE) elements in their promoters and many genes containing the respective promoter elements were induced by abscisic acid, cold or drought. We also found that 33% of all Arabidopsis LEA protein encoding genes are arranged in tandem repeats and that 43% are part of homeologous pairs. The majority of LEA proteins were predicted to be highly hydrophilic and natively unstructured, but some were predicted to be folded. Conclusion The analyses indicate a wide range of sequence diversity, intracellular localizations, and expression patterns. The high fraction of retained duplicate genes and the inferred functional diversification indicate that they confer an evolutionary advantage for an organism under varying stressful environmental conditions. This comprehensive analysis will be an important starting point for future efforts to elucidate the functional role of these enigmatic proteins.
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            [GSDS: a gene structure display server].

            An-Yuan Guo, Qi-Hui Zhu, Xin CHEN … (2007)
            We developed a web server GSDS (Gene Structure Display Server) for drawing gene structure schematic diagrams. Users can submit three types of dataCDS and genomic sequences, NCBI GenBank accession numbers or GIs, exon positions on a gene. GSDS uses this information to obtain the gene structure and draw diagram for it. Users can also designate some special regions to mark on the gene structure diagram. The output result will be PNG or SVG format picture. The corresponding sequence will be shown in a new window by clicking the picture in PNG format. A Chinese version for the main page is also built. The GSDS is available on http://gsds.cbi.pku.edu.cn/.
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              TRANSPARENT TESTA GLABRA2, a trichome and seed coat development gene of Arabidopsis, encodes a WRKY transcription factor.

              Cameron S Johnson, Ben Kolevski, David Smyth (2002)
              Mutants of a new gene, TRANSPARENT TESTA GLABRA2 (TTG2), show disruptions to trichome development and to tannin and mucilage production in the seed coat. The gene was tagged by the endogenous transposon Tag1 and shown to encode a WRKY transcription factor. It is the first member of this large, plant-specific family known to control morphogenesis. The functions of all other WRKY genes revealed to date involve responses to pathogen attack, mechanical stress, and senescence. TTG2 is strongly expressed in trichomes throughout their development, in the endothelium of developing seeds (in which tannin is later generated) and subsequently in other layers of the seed coat, and in the atrichoblasts of developing roots. TTG2 acts downstream of the trichome initiation genes TTG1 and GLABROUS1, although trichome expression of TTG2 continues to occur if they are inactivated. Later, TTG2 shares functions with GLABRA2 in controlling trichome outgrowth. In the seed coat, TTG2 expression requires TTG1 function in the production of tannin. Finally, TTG2 also may be involved in specifying atrichoblasts in roots redundantly with other gene(s) but independently of TTG1 and GLABRA2.
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                Author and article information

                Contributors
                Xueping Li: lxp@icbr.ac.cn
                Jian Gao: gaojian@icbr.ac.cn
                Journal
                Journal ID (nlm-ta): Sci Rep
                Journal ID (iso-abbrev): Sci Rep
                Title: Scientific Reports
                Publisher: Nature Publishing Group UK (London )
                ISSN (Electronic): 2045-2322
                Publication date (Electronic): 27 July 2017
                Publication date PMC-release: 27 July 2017
                Publication date Collection: 2017
                Volume: 7
                Electronic Location Identifier: 6675
                Affiliations
                [1 ]ISNI 0000 0004 0596 3180, GRID grid.454880.5, International Center for Bamboo and Rattan, , Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, ; Beijing, 100102 People’s Republic of China
                [2 ]ISNI 0000 0004 1760 4150, GRID grid.144022.1, College of Forestry, , Northwest Agriculture & Forestry University, ; Yangling, Shaanxi 712100 People’s Republic of China
                [3 ]ISNI 0000 0004 1760 2876, GRID grid.256111.0, Center for Molecular Cell and Systems Biology, , College of Life Sciences, Fujian Agriculture and Forestry University, ; Fuzhou, 350002 People’s Republic of China
                [4 ]ISNI 0000 0004 0368 505X, GRID grid.253663.7, Department of Microbiology, , College of Life Science, Capital Normal University, ; Beijing, 100048 People’s Republic of China
                Article
                Publisher ID: 6701
                DOI: 10.1038/s41598-017-06701-2
                PMC ID: 5532226
                PubMed ID: 28751687
                SO-VID: e824fd82-5393-42d2-9a96-9c0314e328cb
                Copyright © © The Author(s) 2017
                License:

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                Date received : 1 July 2016
                Date accepted : 16 June 2017
                Categories
                Subject: Article
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                issue-copyright-statement © The Author(s) 2017

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