Transcriptome-wide analysis of AP2/ERF transcription factors involved in regulating Taxol biosynthesis in Taxus × media

Industrial Crops and Products - Tập 171 - Trang 113972 - 2021
Kaikai Zhang1,2, Luyuan Jiang1,2, Xu Wang3, Hua Han4, Duanfen Chen2, Deyou Qiu1, Yanfang Yang1
1State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
2College of Horticulture, Hebei Agricultural University, Baoding 071001, China
3Hebei Normal University of Science & Technology Qinhuangdao 066004,China
4State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China

Tài liệu tham khảo

Albrecht, 2001, The NAF domain defines a novel protein-protein interaction module conserved in Ca2+-regulated kinases, EMBO J., 20, 1051, 10.1093/emboj/20.5.1051 Alonso-Blanco, 2005, Genetic and molecular analyses of natural variation indicate CBF2 as a candidate gene for underlying a freezing tolerance quantitative trait locus in Arabidopsis, Plant Physiol., 139, 1304, 10.1104/pp.105.068510 Bailey, 2009, MEME SUITE: tools for motif discovery and searching, Nucleic Acids Res., 37, W202, 10.1093/nar/gkp335 Çevik, 2012, MEDIATOR25 acts as an integrative hub for the regulation of jasmonate-responsive gene expression in Arabidopsis, Plant Physiol., 160, 541, 10.1104/pp.112.202697 Chen, 2016, Expansion and stress responses of AP2/EREBP superfamily in Brachypodium distachyon, Sci. Rep., 6, 21623, 10.1038/srep21623 Chen, 2020, TBtools: an integrative toolkit developed for interactive analyses of big biological data, Mol. Plant, 13, 1194, 10.1016/j.molp.2020.06.009 Cheng, 2021, Chromosome-level genome of Himalayan yew provides insights into the origin and evolution of the paclitaxel biosynthetic pathway, Mol. Plant, S1674 Deokar, 2015, The CarERF genes in chickpea (Cicer arietinum L.) and the identification of CarERF116 as abiotic stress responsive transcription factor, Funct. Integr. Genomics, 15, 27, 10.1007/s10142-014-0399-7 Du, 2014, Genome-wide analysis of the AP2/ERF gene family in maize waterlogging stress response, Euphytica, 198, 115, 10.1007/s10681-014-1088-2 Feng, 2020, Advances in AP2/ERF super-family transcription factors in plant, Crit. Rev. Biotechnol., 40, 750, 10.1080/07388551.2020.1768509 Horton, 2007, WoLF PSORT: protein localization predictor, Nucleic Acids Res., 35, W585, 10.1093/nar/gkm259 Huang, 2010, CD-HIT Suite: a web server for clustering and comparing biological sequences, Bioinformatics, 26, 680, 10.1093/bioinformatics/btq003 Jiang, 2021, Characterization and expression analysis of genes encoding Taxol biosynthetic enzymes in Taxus spp, J. For. Res., 10.1007/s11676-021-01290-3 Kagale, 2011, EAR motif-mediated transcriptional repression in plants: an underlying mechanism for epigenetic regulation of gene expression, Epigenetics, 6, 141, 10.4161/epi.6.2.13627 Karanja, 2019, Genome-wide characterization of the AP2/ERF gene family in radish (Raphanus sativusL.): unveiling evolution and patterns in response to abiotic stresses, Gene, 718, 10.1016/j.gene.2019.144048 Kizis, 2001, Role of AP2/EREBP transcription factors in gene regulation during abiotic stress, FEBS Lett., 498, 187, 10.1016/S0014-5793(01)02460-7 Kumar, 2016, MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets, Mol. Biol. Evol., 33, 1870, 10.1093/molbev/msw054 Lata, 2014, Genome-wide investigation and expression profiling of AP2/ERF transcription factor superfamily in foxtail millet (Setaria italica L.), PLoS One, 9, 10.1371/journal.pone.0113092 Lee, 2004, Plant Mol. Biol., 55, 61, 10.1007/s11103-004-0417-6 Letunic, 2016, Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees, Nucleic Acids Res., 44, W242, 10.1093/nar/gkw290 Licausi, 2013, APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factors: mediators of stress responses and developmental programs, New Phytol., 199, 639, 10.1111/nph.12291 Liu, 1999, Transcription factors and their genes in higher plants functional domains, evolution and regulation, Eur. J. Biochem., 262, 247, 10.1046/j.1432-1327.1999.00349.x Liu, 2013, Genome-wide analysis of ZmDREB genes and their association with natural variation in drought tolerance at seedling stage of Zea mays L, PLoS Genet., 9, 10.1371/journal.pgen.1003790 Livak, 2001, Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method, Methods, 25, 402, 10.1006/meth.2001.1262 Lu, 2013, AaORA, a trichome-specific AP2/ERF transcription factor of Artemisia annua, is a positive regulator in the artemisinin biosynthetic pathway and in disease resistance to Botrytis cinerea, New Phytol., 198, 1191, 10.1111/nph.12207 Meng, 2017, Transcriptomic response of Chinese Yew (Taxus chinensis) to cold stress, Front. Plant Sci., 8, 468, 10.3389/fpls.2017.00468 Ming, 2020, The JA-responsive MYC2-BADH-like transcriptional regulatory module in Poncirus trifoliata contributes to cold tolerance by modulation of glycine betaine biosynthesis, New Phytol., 229, 2730, 10.1111/nph.17063 Nakano, 2006, Genome-wide analysis of the ERF gene family in Arabidopsis and rice, Plant Physiol., 140, 411, 10.1104/pp.105.073783 Ohta, 2001, Repression domains of class II ERF transcriptional repressors share an essential motif for active repression, Plant Cell, 13, 1959, 10.1105/TPC.010127 Okamuro, 1997, The AP2 domain of APETALA2 defines a large new family of DNA binding proteins in Arabidopsis, Proc. Natl. Acad. Sci. U. S. A., 94, 7076, 10.1073/pnas.94.13.7076 Park, 2001, Overexpression of the tobacco Tsi1 gene encoding an EREBP/AP2-type transcription factor enhances resistance against pathogen attack and osmotic stress in tobacco, Plant Cell, 13, 1035 Qu, 2006, Transcription factor families in Arabidopsis: major progress and outstanding issues for future research, Curr. Opin. Plant Biol., 9, 544, 10.1016/j.pbi.2006.07.005 Rashid, 2012, AP2/ERF transcription factor in rice: genome-wide canvas and syntenic relationships between monocots and eudicots, Evol. Bioinform. Online, 8, 321, 10.4137/EBO.S9369 Rashotte, 2006, A subset of Arabidopsis AP2 transcription factors mediates cytokinin responses in concert with a two-component pathway, Proc. Natl. Acad. Sci. U. S. A., 103, 11081, 10.1073/pnas.0602038103 Riechmann, 1998, The AP2/EREBP family of plant transcription factors, Biol. Chem., 379, 633 Sakuma, 2002, DNA-binding specificity of the ERF/AP2 domain of Arabidopsis DREBs, transcription factors involved in dehydration- and cold-inducible gene expression, Biochem. Biophys. Res. Commun., 290, 998, 10.1006/bbrc.2001.6299 Song, 2013, Genome-wide analysis of the AP2/ERF transcription factor superfamily in Chinese cabbage (Brassica rapa ssp. pekinensis), BMC Genomics, 14, 573, 10.1186/1471-2164-14-573 Sun, 2013, Deep sequencing reveals transcriptome re-programming of Taxus × media cells to the elicitation with methyl jasmonate, PLoS One, 8, 10.1371/journal.pone.0062865 Tiwari, 2012, The EDLL motif: a potent plant transcriptional activation domain from AP2/ERF transcription factors, Plant J., 70, 855, 10.1111/j.1365-313X.2012.04935.x Van der Fits, 2000, ORCA3, a jasmonate-responsive transcriptional regulator of plant primary and secondary metabolism, Science, 289, 295, 10.1126/science.289.5477.295 Wilkins, 1999, Protein identification and analysis tools in the ExPASy server, Methods Mol. Biol., 112, 531 Xiong, 2021, The Taxus genome provides insights into paclitaxel biosynthesis, Nat. Plants, 7, 1026, 10.1038/s41477-021-00963-5 Xu, 2006, Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice, Nature, 442, 705, 10.1038/nature04920 Yang, 2018, Identification and characterization of MYC transcription factors in Taxus sp, Gene, 675, 1, 10.1016/j.gene.2018.06.065 Yu, 2002, High stable production of taxol in elicited synchronous cultures of Taxus chinensis cells, Process Biochem., 38, 207, 10.1016/S0032-9592(02)00069-9 Zhang, 2008, Phylogeny, gene structures, and expression patterns of the ERF gene family in soybean (Glycine max L.), J. Exp. Bot., 59, 4095, 10.1093/jxb/ern248 Zhang, 2009, Overexpression of the soybean GmERF3 gene, an AP2/ERF type transcription factor for increased tolerances to salt, drought, and diseases in transgenic tobacco, J. Exp. Bot., 60, 3781, 10.1093/jxb/erp214 Zhang, 2012, Genome-wide analysis of the AP2/ERF superfamily in peach (Prunus persica), Genet. Mol. Res., 11, 4789 Zhang, 2015, Two jasmonate-responsive factors, TcERF12 and TcERF15, respectively act as repressor and activator of tasy gene of taxol biosynthesis in Taxus chinensis, Plant Mol. Biol., 89, 463, 10.1007/s11103-015-0382-2 Zhang, 2019, New different origins and evolutionary processes of AP2/EREBP transcription factors in Taxus chinensis, BMC Plant Biol., 19, 413, 10.1186/s12870-019-2044-z Zhang, 2020, Selection and validation of reference genes for quantitative gene expression normalization in Taxus spp, Sci. Rep., 10, 10.1038/s41598-020-79213-1 Zhang, 2020, Genome-wide identification, molecular evolution, and expression analysis provide new insights into the APETALA2/ethylene responsive factor (AP2/ERF) superfamily in Dimocarpus longan Lour, BMC Genomics, 21, 62, 10.1186/s12864-020-6469-4 Zhao, 2018, Cloning and expression analysis of BpERF1 and BpERF2 genes from Betula platyphylla, J. Sichuan Agric. Univ., 3, 329 Zhou, 1997, The Pto kinase conferring resistance to tomato bacterial speck disease interacts with proteins that bind a cis-element of pathogenesis-related genes, EMBO J., 16, 3207, 10.1093/emboj/16.11.3207 Zhuang, 2008, Genome-wide analysis of the AP2/ERF gene family in Populus trichocarpa, Biochem. Biophys. Res. Commun., 371, 468, 10.1016/j.bbrc.2008.04.087