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      Transcriptome-Based Analysis of Dof Family Transcription Factors and Their Responses to Abiotic Stress in Tea Plant ( Camellia sinensis)

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          Abstract

          Tea plant ( Camellia sinensis (L.) O. Kuntze) is affected by abiotic stress during its growth and development. DNA-binding with one finger (Dof) transcription factors (TFs) play important roles in abiotic stress tolerance of plants. In this study, a total of 29 putative Dof TFs were identified based on transcriptome of tea plant, and the conserved domains and common motifs of these CsDof TFs were predicted and analyzed. The 29 CsDof proteins were divided into 7 groups (A, B1, B2, C1, C2.1, C2.2, and D2), and the interaction networks of Dof proteins in C. sinensis were established according to the data in Arabidopsis. Gene expression was analyzed in “Yingshuang” and “Huangjinya” under four experimental stresses by qRT-PCR. CsDof genes were expressed differentially and related to different abiotic stress conditions. In total, our results might suggest that there is a potential relationship between CsDof factors and tea plant stress resistance.

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          Multiple sequence alignment with the Clustal series of programs.

          R Chenna (2003)
          The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees. The popularity of the programs depends on a number of factors, including not only the accuracy of the results, but also the robustness, portability and user-friendliness of the programs. New features include NEXUS and FASTA format output, printing range numbers and faster tree calculation. Although, Clustal was originally developed to run on a local computer, numerous Web servers have been set up, notably at the EBI (European Bioinformatics Institute) (http://www.ebi.ac.uk/clustalw/).
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            FKF1 F-box protein mediates cyclic degradation of a repressor of CONSTANS in Arabidopsis.

            Takato Imaizumi, Thomas Schultz, Frank G Harmon … (2005)
            The temporal control of CONSTANS (CO) expression and activity is a key mechanism in photoperiodic flowering in Arabidopsis. FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (FKF1) protein regulates CO transcription, although the molecular mechanism is unknown. We demonstrate here that FKF1 controls the stability of a Dof transcription factor, CYCLING DOF FACTOR 1 (CDF1). FKF1 physically interacts with CDF1, and CDF1 protein is more stable in fkf1 mutants. Plants with elevated levels of CDF1 flower late and have reduced expression of CO. CDF1 and CO are expressed in the same tissues, and CDF1 binds to the CO promoter. Thus, FKF1 controls daily CO expression in part by degrading CDF1, a repressor of CO transcription.
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              PlnTFDB: an integrative plant transcription factor database

              Diego Mauricio Riaño-Pachón, Slobodan Ruzicic, Ingo Dreyer … (2007)
              Background Transcription factors (TFs) are key regulatory proteins that enhance or repress the transcriptional rate of their target genes by binding to specific promoter regions (i.e. cis-acting elements) upon activation or de-activation of upstream signaling cascades. TFs thus constitute master control elements of dynamic transcriptional networks. TFs have fundamental roles in almost all biological processes (development, growth and response to environmental factors) and it is assumed that they play immensely important functions in the evolution of species. In plants, TFs have been employed to manipulate various types of metabolic, developmental and stress response pathways. Cross-species comparison and identification of regulatory modules and hence TFs is thought to become increasingly important for the rational design of new plant biomass. Up to now, however, no computational repository is available that provides access to the largely complete sets of transcription factors of sequenced plant genomes. Description PlnTFDB is an integrative plant transcription factor database that provides a web interface to access large (close to complete) sets of transcription factors of several plant species, currently encompassing Arabidopsis thaliana (thale cress), Populus trichocarpa (poplar), Oryza sativa (rice), Chlamydomonas reinhardtii and Ostreococcus tauri. It also provides an access point to its daughter databases of a species-centered representation of transcription factors (OstreoTFDB, ChlamyTFDB, ArabTFDB, PoplarTFDB and RiceTFDB). Information including protein sequences, coding regions, genomic sequences, expressed sequence tags (ESTs), domain architecture and scientific literature is provided for each family. Conclusion We have created lists of putatively complete sets of transcription factors and other transcriptional regulators for five plant genomes. They are publicly available through . Further data will be included in the future when the sequences of other plant genomes become available.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Int J Genomics
                Journal ID (iso-abbrev): Int J Genomics
                Journal ID (publisher-id): IJG
                Title: International Journal of Genomics
                Publisher: Hindawi Publishing Corporation
                ISSN (Print): 2314-436X
                ISSN (Electronic): 2314-4378
                Publication date (Print): 2016
                Publication date (Electronic): 31 October 2016
                Volume: 2016
                Electronic Location Identifier: 5614142
                Affiliations
                1Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
                2State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
                Author notes

                Academic Editor: Margarita Hadzopoulou-Cladaras

                Author information
                http://orcid.org/0000-0001-6960-5217
                Article
                DOI: 10.1155/2016/5614142
                PMC ID: 5107859
                SO-VID: d8133b67-df28-484c-9e98-afed121f170b
                Copyright © Copyright © 2016 Hui Li et al.
                License:

                This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 19 May 2016
                Date accepted : 6 September 2016
                Funding
                Funded by: National Natural Science Foundation of China
                Award ID: 31570691
                Categories
                Subject: Research Article

                Data availability:

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