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      Molecular cloning and expression analysis of WRKY transcription factor genes in Salvia miltiorrhiza.

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          Abstract

          WRKY proteins comprise a large family of transcription factors and play important regulatory roles in plant development and defense response. The WRKY gene family in Salvia miltiorrhiza has not been characterized.

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          Codon-substitution models for heterogeneous selection pressure at amino acid sites.

          Shira N Goldman, Q. Z. Yang, Gloria A. Pedersen … (2000)
          Comparison of relative fixation rates of synonymous (silent) and nonsynonymous (amino acid-altering) mutations provides a means for understanding the mechanisms of molecular sequence evolution. The nonsynonymous/synonymous rate ratio (omega = d(N)d(S)) is an important indicator of selective pressure at the protein level, with omega = 1 meaning neutral mutations, omega 1 diversifying positive selection. Amino acid sites in a protein are expected to be under different selective pressures and have different underlying omega ratios. We develop models that account for heterogeneous omega ratios among amino acid sites and apply them to phylogenetic analyses of protein-coding DNA sequences. These models are useful for testing for adaptive molecular evolution and identifying amino acid sites under diversifying selection. Ten data sets of genes from nuclear, mitochondrial, and viral genomes are analyzed to estimate the distributions of omega among sites. In all data sets analyzed, the selective pressure indicated by the omega ratio is found to be highly heterogeneous among sites. Previously unsuspected Darwinian selection is detected in several genes in which the average omega ratio across sites is 1. Genes undergoing positive selection include the beta-globin gene from vertebrates, mitochondrial protein-coding genes from hominoids, the hemagglutinin (HA) gene from human influenza virus A, and HIV-1 env, vif, and pol genes. Tests for the presence of positively selected sites and their subsequent identification appear quite robust to the specific distributional form assumed for omega and can be achieved using any of several models we implement. However, we encountered difficulties in estimating the precise distribution of omega among sites from real data sets.
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            Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene.

            R Nielsen, Z. Yang (1998)
            Several codon-based models for the evolution of protein-coding DNA sequences are developed that account for varying selection intensity among amino acid sites. The "neutral model" assumes two categories of sites at which amino acid replacements are either neutral or deleterious. The "positive-selection model" assumes an additional category of positively selected sites at which nonsynonymous substitutions occur at a higher rate than synonymous ones. This model is also used to identify target sites for positive selection. The models are applied to a data set of the V3 region of the HIV-1 envelope gene, sequenced at different years after the infection of one patient. The results provide strong support for variable selection intensity among amino acid sites The neutral model is rejected in favor of the positive-selection model, indicating the operation of positive selection in the region. Positively selected sites are found in both the V3 region and the flanking regions.
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              Arabidopsis WRKY33 transcription factor is required for resistance to necrotrophic fungal pathogens.

              Zuyu Zheng, Synan Abu Qamar, Zhixiang Chen … (2006)
              Plant WRKY transcription factors are key regulatory components of plant responses to microbial infection. In addition to regulating the expression of defense-related genes, WRKY transcription factors have also been shown to regulate cross-talk between jasmonate- and salicylate-regulated disease response pathways. The two pathways mediate resistance against different types of microbial pathogens, and there are numerous reports of antagonistic interactions between them. Here we show that mutations of the Arabidopsis WRKY33 gene encoding a WRKY transcription factor cause enhanced susceptibility to the necrotrophic fungal pathogens Botrytis cinerea and Alternaria brassicicola concomitant with reduced expression of the jasmonate-regulated plant defensin PDF1.2 gene. Ectopic over-expression of WRKY33, on the other hand, increases resistance to the two necrotrophic fungal pathogens. The wrky33 mutants do not show altered responses to a virulent strain of the bacterial pathogen Pseudomonas syringae, although the ectopic expression of WRKY33 results in enhanced susceptibility to this pathogen. The susceptibility of WRKY33-over-expressing plants to P. syringae is associated with reduced expression of the salicylate-regulated PR-1 gene. The WRKY33 transcript is induced in response to pathogen infection, or treatment with salicylate or the paraquat herbicide that generates activated oxygen species in exposed cells. WRKY33 is localized to the nucleus of plant cells and recognizes DNA molecules containing the TTGACC W-box sequence. Together, these results indicate that pathogen-induced WRKY33 is an important transcription factor that regulates the antagonistic relationship between defense pathways mediating responses to P. syringae and necrotrophic pathogens.
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                Author and article information

                Journal
                Journal ID (iso-abbrev): BMC Genomics
                Title: BMC genomics
                Publisher: Springer Science and Business Media LLC
                ISSN (Electronic): 1471-2164
                ISSN (Print): 1471-2164
                Publication date (Electronic): Mar 17 2015
                Volume: 16
                Affiliations
                [1 ] Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No.151, Malianwa North Road, Haidian District, Beijing, 100193, China. licaili390@163.com.
                [2 ] Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No.151, Malianwa North Road, Haidian District, Beijing, 100193, China. butterfly_qiao@163.com.
                [3 ] Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No.151, Malianwa North Road, Haidian District, Beijing, 100193, China. sfjstar@126.com.
                [4 ] Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No.151, Malianwa North Road, Haidian District, Beijing, 100193, China. sflu@implad.ac.cn.
                Article
                Publisher Item ID: 10.1186/s12864-015-1411-x
                DOI: 10.1186/s12864-015-1411-x
                PMC ID: 4371873
                PubMed ID: 25881056
                SO-VID: e02bca49-65e4-4b79-8917-7703dc34b227
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