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Owji H, Hajiebrahimi A, Seradj H, Hemmati S. Identification and functional prediction of stress responsive AP2/ERF transcription factors in Brassica napus by genome-wide analysis. Comput Biol Chem 2017; 71:32-56. [PMID: 28961511 DOI: 10.1016/j.compbiolchem.2017.09.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 09/12/2017] [Accepted: 09/12/2017] [Indexed: 01/08/2023]
Abstract
Using homology and domain authentication, 321 putative AP2/ERF transcription factors were identified in Brassica napus, called BnAP2/ERF TFs. BnAP2/ERF TFs were classified into five major subfamilies, including DREB, ERF, AP2, RAV, and BnSoloist. This classification is based on phylogenetic analysis, motif identification, gene structure analysis, and physiochemical characterization. These TFs were annotated based on phylogenetic relationship with Brassica rapa. BnAP2/ERF TFs were located on 19 chromosomes of B. napus. Orthologs and paralogs were identified using synteny-based methods Ks calculation within B. napus genome and between B. napus with other species such as B. rapa, Brassica oleracea, and Arabidopsis thaliana indicated that BnAP2/ERF TFs were formed through duplication events occurred before B. napus formation. Kn/Ks values were between 0 and 1, suggesting the purifying selection among BnAP2/ERF TFs. Gene ontology annotation, cis-regulatory elements and functional interaction networks suggested that BnAP2/ERF TFs participate in response to stressors, including drought, high salinity, heat and cold as well as developmental processes particularly organ specification and embryogenesis. The identified cis-regulatory elements in the upstream of BnAP2/ERF TFs were responsive to abscisic acid. Analysis of the expression data derived from Illumina Hiseq 2000 RNA sequencing revealed that BnAP2/ERF genes were highly expressed in the roots comparing to flower buds, leaves, and stems. Also, the ERF subfamily was over-expressed under salt and fungal treatments. BnERF039 and BnERF245 are candidates for salt-tolerant B. napus. BnERF253-256 and BnERF260-277 are potential cytokinin response factors. BnERF227, BnERF228, BnERF234, BnERF134, BnERF132, BnERF176, and BnERF235 were suggested for resistance against Leptosphaeria maculan and Leptosphaeria biglobosa.
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Affiliation(s)
- Hajar Owji
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Hajiebrahimi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hassan Seradj
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shiva Hemmati
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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152
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Noman A, Liu Z, Aqeel M, Zainab M, Khan MI, Hussain A, Ashraf MF, Li X, Weng Y, He S. Basic leucine zipper domain transcription factors: the vanguards in plant immunity. Biotechnol Lett 2017; 39:1779-1791. [DOI: 10.1007/s10529-017-2431-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/31/2017] [Indexed: 01/05/2023]
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153
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Rudnik R, Bulcha JT, Reifschneider E, Ellersiek U, Baier M. Specificity versus redundancy in the RAP2.4 transcription factor family of Arabidopsis thaliana: transcriptional regulation of genes for chloroplast peroxidases. BMC PLANT BIOLOGY 2017; 17:144. [PMID: 28835225 PMCID: PMC5569508 DOI: 10.1186/s12870-017-1092-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 08/14/2017] [Indexed: 05/07/2023]
Abstract
BACKGROUND The Arabidopsis ERFIb / RAP2.4 transcription factor family consists of eight members with highly conserved DNA binding domains. Selected members have been characterized individually, but a systematic comparison is pending. The redox-sensitive transcription factor RAP2.4a mediates chloroplast-to-nucleus redox signaling and controls induction of the three most prominent chloroplast peroxidases, namely 2-Cys peroxiredoxin A (2CPA) and thylakoid- and stromal ascorbate peroxidase (tAPx and sAPx). To test the specificity and redundancy of RAP2.4 transcription factors in the regulation of genes for chloroplast peroxidases, we compared the DNA-binding sites of the transcription factors in tertiary structure models, analyzed transcription factor and target gene regulation by qRT-PCR in RAP2.4, 2-Cys peroxiredoxin and ascorbate peroxidase T-DNA insertion lines and RAP2.4 overexpressing lines of Arabidopsis thaliana and performed promoter binding studies. RESULTS All RAP2.4 proteins bound the tAPx promoter, but only the four RAP2.4 proteins with identical DNA contact sites, namely RAP2.4a, RAP2.4b, RAP2.4d and RAP2.4h, interacted stably with the redox-sensitive part of the 2CPA promoter. Gene expression analysis in RAP2.4 knockout lines revealed that RAP2.4a is the only one supporting 2CPA and chloroplast APx expression. Rap2.4h binds to the same promoter region as Rap2.4a and antagonizes 2CPA expression. Like the other six RAP2.4 proteins, Rap2.4 h promotes APx mRNA accumulation. Chloroplast ROS signals induced RAP2.4b and RAP2.4d expression, but these two transcription factor genes are (in contrast to RAP2.4a) insensitive to low 2CP availability, and their expression decreased in APx knockout lines. RAP2.4e and RAP2.4f gradually responded to chloroplast APx availability and activated specifically APx expression. These transcription factors bound, like RAP2.4c and RAP2.4g, the tAPx promoter, but hardly the 2CPA promoter. CONCLUSIONS The RAP2.4 transcription factors form an environmentally and developmentally regulated transcription factor network, in which the various members affect the expression intensity of the others. Within the transcription factor family, RAP2.4a has a unique function as a general transcriptional activator of chloroplast peroxidase activity. The other RAP2.4 proteins mediate the fine-control and adjust the relative availability of 2CPA, sAPx and tAPx.
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Affiliation(s)
- Radoslaw Rudnik
- Dahlem Center of Plant Sciences, Plant Physiology, Freie Universität Berlin, Königin-Luise-Straße 12-16, 14195, Berlin, Germany
| | - Jote Tafese Bulcha
- Dahlem Center of Plant Sciences, Plant Physiology, Freie Universität Berlin, Königin-Luise-Straße 12-16, 14195, Berlin, Germany
| | - Elena Reifschneider
- Dahlem Center of Plant Sciences, Plant Physiology, Freie Universität Berlin, Königin-Luise-Straße 12-16, 14195, Berlin, Germany
| | - Ulrike Ellersiek
- Heinrich-Heine-Universität Düsseldorf, Plant Sciences, Universitätsstraße 25, 40225, Düsseldorf, Germany
| | - Margarete Baier
- Dahlem Center of Plant Sciences, Plant Physiology, Freie Universität Berlin, Königin-Luise-Straße 12-16, 14195, Berlin, Germany.
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154
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Ma L, Hu L, Fan J, Amombo E, Khaldun ABM, Zheng Y, Chen L. Cotton GhERF38 gene is involved in plant response to salt/drought and ABA. ECOTOXICOLOGY (LONDON, ENGLAND) 2017; 26:841-854. [PMID: 28536792 DOI: 10.1007/s10646-017-1815-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/05/2017] [Indexed: 05/06/2023]
Abstract
ERF (ethylene-responsive factor) transcription factors play important roles in plant stress signaling transduction pathways. However, their specific roles during diverse abiotic stresses tolerance in Gossypium hirsutum are largely unknown. Here, a novel ERF transcription factor, designated GhERF38, homologous to AtERF38 in Arabidopsis, was isolated from cotton (Gossypium hirsutum L). GhERF38 expression was up-regulated by salt, drought and ABA treatments. Subcellular localization results indicated that GhERF38 was localized in the cell nucleus. Over-expression of GhERF38 in Arabidopsis reduced plant tolerance to salt and drought stress as indicated by a decline of seed germination, plant greenness frequency, primary roots length and the survival rate in transgenic plants compared to those of wild type plants under salt or drought treatment. Besides, stress tolerance related physiological parameters such as proline content, relative water content, soluble sugar and chlorophyll content were all significantly lower in transgenic plants than those of wild type plants under salt or drought treatment. Furthermore, over-expression of GhERF38 in Arabidopsis resulted in ABA sensitivity in transgenic plants during both seed germination and seedling growth. Interestingly, the stomatal aperture of guard cells in the transgenic plants was larger than that in transgenic plant after ABA treatment, suggesting that GhERF38-overexpressing plants were insensitive to ABA in terms of stomatal closure. Furthermore, expressions of the stress-related genes were altered in the GhERF38 transgenic plants under high salinity, drought or ABA treatment. Together, our results revealed that GhERF38 functions as a novel regulator that is involved in response to salt/drought stress and ABA signaling during plant development.
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Affiliation(s)
- Liufeng Ma
- College of Biology and Geography Sciences, Kashgal University, Xinjiang, 844000, China
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Longxing Hu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Department of Turfgrass Sciences, College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Jibiao Fan
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Erick Amombo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - A B M Khaldun
- Oilseed Research Centre, Bangladesh Agricultural Research Institute (BARI), Gazipur, 1701, Bangladesh
| | - Yong Zheng
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China.
| | - Liang Chen
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China.
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155
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Liu D, Xin M, Zhou X, Wang C, Zhang Y, Qin Z. Expression and functional analysis of the transcription factor-encoding Gene CsERF004 in cucumber during Pseudoperonospora cubensis and Corynespora cassiicola infection. BMC PLANT BIOLOGY 2017; 17:96. [PMID: 28583084 PMCID: PMC5460474 DOI: 10.1186/s12870-017-1049-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 05/25/2017] [Indexed: 05/13/2023]
Abstract
BACKGROUND Cucumber downy mildew, caused by P. cubensis, is an important leaf disease that can severely affect cucumber production. In recent years, cucumber target spot, caused by C. cassiicola, has been reported in both Asia and Europe and is now considered as a major disease disrupting cucumber production. Single-disease-resistant cucumber varieties have been unable to satisfy production needs. To explore the molecular mechanisms of cucumber resistance to these two diseases, cucumber cultivars D9320 (resistant to downy mildew and target spot) and D0401 (susceptible to downy mildew and target spot) were used as experimental materials in this study. We used transcriptome sequencing technology to identify genes related to disease resistance and verified using transgenic technology. RESULTS We screened out the cucumber resistance-related gene CsERF004 using transcriptome sequencing technology. Induction by pathogens, salicylic acid (SA), and ethylene (ET) resulted in the up-regulation of CsERF004. Three treatments, namely, inoculation with C. cassiicola alone, inoculation with P. cubensis alone, and simultaneous inoculation with both pathogens, all resulted in the significant and sustained up-regulation of CsERF004 in the resistant cultivar D9320, during the early stage of infection. In the susceptible cultivar D0401, CsERF004 expression was also significantly up-regulated at the later stage of infection but to a lesser extent and for a shorter duration than in the resistant cultivar D9320. The CsERF004 gene encodes a protein localizes to the nucleus. The over-expression of CsERF004 in the susceptible cultivar D0401 resulted in the significant up-regulation of the CsPR1 and CsPR4 genes and increased the levels of SA and ET, which enhanced the resistance of cucumber to downy mildew and target spot. CONCLUSIONS Analyses of the CsERF004 expression pattern in disease-resistant and susceptible cucumber cultivars and transgenic validation indicate that CsERF004 confers resistance to P. cubensis and C. cassiicola. The findings of this study can help to better understanding of mechanisms of response to pathogens and in establishment the genetic basis for the development of cucumber broad-spectrum resistant cultivars.
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Affiliation(s)
- Dong Liu
- College of Horticulture and Landscape Architecture, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Northeast Agricultural University, Harbin, 150030, China
| | - Ming Xin
- College of Horticulture and Landscape Architecture, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Northeast Agricultural University, Harbin, 150030, China
| | - Xiuyan Zhou
- College of Horticulture and Landscape Architecture, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Northeast Agricultural University, Harbin, 150030, China
| | - Chunhua Wang
- College of Horticulture and Landscape Architecture, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Northeast Agricultural University, Harbin, 150030, China
| | - Yanju Zhang
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Zhiwei Qin
- College of Horticulture and Landscape Architecture, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Northeast Agricultural University, Harbin, 150030, China.
- Heilongjiang Bayi Agricultural University, Daqing, 163319, China.
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156
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Bi H, Luang S, Li Y, Bazanova N, Borisjuk N, Hrmova M, Lopato S. Wheat drought-responsive WXPL transcription factors regulate cuticle biosynthesis genes. PLANT MOLECULAR BIOLOGY 2017; 94:15-32. [PMID: 28161858 DOI: 10.1007/s11103-017-0585-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 01/15/2017] [Indexed: 06/06/2023]
Abstract
The cuticle forms a hydrophobic waxy layer that covers plant organs and provides protection from biotic and abiotic stresses. Transcription of genes responsible for cuticle formation is regulated by several types of transcription factors (TFs). Five orthologous to WAX PRODUCTION (WXP1 and WXP2) genes from Medicago truncatula were isolated from a cDNA library prepared from flag leaves and spikes of drought tolerant wheat (Triticum aestivum, breeding line RAC875) and designated TaWXP-like (TaWXPL) genes. Tissue-specific and drought-responsive expression of TaWXPL1D and TaWXPL2B was investigated by quantitative RT-PCR in two Australian wheat genotypes, RAC875 and Kukri, with contrasting glaucousness and drought tolerance. Rapid dehydration and/or slowly developing cyclic drought induced specific expression patterns of WXPL genes in flag leaves of the two cultivars RAC875 and Kukri. TaWXPL1D and TaWXPL2B proteins acted as transcriptional activators in yeast and in wheat cell cultures, and conserved sequences in their activation domains were localised at their C-termini. The involvement of wheat WXPL TFs in regulation of cuticle biosynthesis was confirmed by transient expression in wheat cells, using the promoters of wheat genes encoding two cuticle biosynthetic enzymes, the 3-ketoacyl-CoA-synthetase and the cytochrome P450 monooxygenase. Using the yeast 1-hybrid (Y1H) assay we also demonstrated the differential binding preferences of TaWXPL1D and TaWXPL2B towards three stress-related DNA cis-elements. Protein structural determinants underlying binding selectivity were revealed using comparative 3D molecular modelling of AP2 domains in complex with cis-elements. A scheme is proposed, which links the roles of WXPL and cuticle-related MYB TFs in regulation of genes responsible for the synthesis of cuticle components.
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Affiliation(s)
- Huihui Bi
- The University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Sukanya Luang
- The University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Yuan Li
- The University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Natalia Bazanova
- The University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Nikolai Borisjuk
- The University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
- School of Life Science, Huaiyin Normal University, Huaian, 223300, China
| | - Maria Hrmova
- The University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia.
| | - Sergiy Lopato
- The University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
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157
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Zhang C, Wu X, Zhang B, Chen Q, Liu M, Xin D, Qi Z, Li S, Ma Y, Wang L, Jin Y, Li W, Wu X, Su AY. Functional analysis of the GmESR1 gene associated with soybean regeneration. PLoS One 2017; 12:e0175656. [PMID: 28403182 PMCID: PMC5389854 DOI: 10.1371/journal.pone.0175656] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 03/29/2017] [Indexed: 11/19/2022] Open
Abstract
Plant regeneration can occur via in vitro tissue culture through somatic embryogenesis or de novo shoot organogenesis. Transformation of soybean (Glycine max) is difficult, hence optimization of the transformation system for soybean regeneration is required. This study investigated ENHANCER OF SHOOT REGENERATION 1 (GmESR1), a soybean transcription factor that targets regeneration-associated genes. Sequence analysis showed that GmESR1 contained a conserved 57 amino acid APETALA 2 (AP2)/ETHYLENE RESPONSE FACTOR (ERF) DNA-binding domain. The relative expression level of GmESR1 was highest in young embryos, flowers and stems in the soybean cultivar 'Dongnong 50'. To examine the function of GmESR1, transgenic Arabidopsis (Arabidopsis thaliana) and soybean plants overexpressing GmESR1 were generated. In Arabidopsis, overexpression of GmESR1 resulted in accelerated seed germination, and seedling shoot and root elongation. In soybean overexpression of GmESR1 also led to faster seed germination, and shoot and root elongation. GmESR1 specifically bound to the GCC-box. The results provide a foundation for the establishment of an efficient and stable transformation system for soybean.
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Affiliation(s)
- Chao Zhang
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang province, People’s Republic of China
| | - Xiaodong Wu
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang province, People’s Republic of China
| | - Binbin Zhang
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang province, People’s Republic of China
| | - Qingshan Chen
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang province, People’s Republic of China
| | - Ming Liu
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang province, People’s Republic of China
| | - Dawei Xin
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang province, People’s Republic of China
| | - Zhaoming Qi
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang province, People’s Republic of China
| | - Sinan Li
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang province, People’s Republic of China
| | - Yanlong Ma
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang province, People’s Republic of China
| | - Lingshuang Wang
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang province, People’s Republic of China
| | - Yangmei Jin
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang province, People’s Republic of China
| | - Wenbin Li
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang province, People’s Republic of China
| | - Xiaoxia Wu
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang province, People’s Republic of China
| | - An-yu Su
- College of Resources and Environment, Northeast Agricultural University. Harbin, Heilongjiang province, People’s Republic of China
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158
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Kumar M, Choi J, An G, Kim SR. Ectopic Expression of OsSta2 Enhances Salt Stress Tolerance in Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:316. [PMID: 28344585 PMCID: PMC5344931 DOI: 10.3389/fpls.2017.00316] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 02/21/2017] [Indexed: 05/27/2023]
Abstract
Salt stress can severely reduce crop yields. To understand how rice (Oryza sativa) plants respond to this environmental challenge, we investigated the genes involved in conferring salt tolerance by screening T-DNA tagging lines and identified OsSta2-D (Oryza sativa Salt tolerance activation 2-Dominant). In that line, expression of OsSta2 was enhanced by approximately eightfold when compared with the non-transformed wild type (WT). This gene was highly expressed in the callus, roots, and panicles. To confirm its role in stress tolerance, we generated transgenic rice that over-expresses OsSta2 under a maize ubiquitin promoter. The OsSta2-Ox plants were salt-tolerant at the vegetative stage, based on our calculations of chlorophyll fluorescence (Fv/Fm), fresh and dry weights, chlorophyll concentrations, and survival rates. Under normal paddy field conditions, the Ox plants were somewhat shorter than the WT control but had improved agronomic traits such as higher total grain yield. They were also more tolerant to osmotic stress and hypersensitive to abscisic acid. Based on all of these results, we suggest that OsSta2 has important roles in determining yields as well as in conferring tolerance to salt stresses.
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Affiliation(s)
- Manu Kumar
- Department of Life Science, Sogang UniversitySeoul, South Korea
| | - Juyoung Choi
- Department of Life Science, Sogang UniversitySeoul, South Korea
| | - Gynheung An
- Department of Plant Molecular Systems Biotechnology, Kyung Hee UniversityYongin, South Korea
| | - Seong-Ryong Kim
- Department of Life Science, Sogang UniversitySeoul, South Korea
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159
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Sumoylation stabilizes RACK1B and enhance its interaction with RAP2.6 in the abscisic acid response. Sci Rep 2017; 7:44090. [PMID: 28272518 PMCID: PMC5341030 DOI: 10.1038/srep44090] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 02/01/2017] [Indexed: 12/16/2022] Open
Abstract
The highly conserved eukaryotic WD40 repeat protein, Receptor for Activated C Kinase 1 (RACK1), is involved in the abscisic acid (ABA) response in Arabidopsis. However, the regulation of RACK1 and the proteins with which it interacts are poorly understood. Here, we show that RACK1B is sumoylated at four residues, Lys50, Lys276, Lys281 and Lys291. Sumoylation increases RACK1B stability and its tolerance to ubiquitination-mediated degradation in ABA response. As a result, sumoylation leads to enhanced interaction between RACK1B and RAP2.6, an AP2/ERF family transcription factor. RACK1B binds directly to the AP2 domain of RAP2.6, which alters the affinity of RAP2.6 for CE1 and GCC cis-acting regulatory elements. Taken together, our findings illustrate that protein stability controlled by dynamic post-transcriptional modification is a critical regulatory mechanism for RACK1B, which functions as scaffold protein for RAP2.6 in ABA signaling.
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160
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Zhao Y, Chang X, Qi D, Dong L, Wang G, Fan S, Jiang L, Cheng Q, Chen X, Han D, Xu P, Zhang S. A Novel Soybean ERF Transcription Factor, GmERF113, Increases Resistance to Phytophthora sojae Infection in Soybean. FRONTIERS IN PLANT SCIENCE 2017; 8:299. [PMID: 28326092 PMCID: PMC5339286 DOI: 10.3389/fpls.2017.00299] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/20/2017] [Indexed: 05/18/2023]
Abstract
Phytophthora root and stem rot of soybean caused by the oomycete Phytophthora sojae, is a destructive disease worldwide. Ethylene response factors (ERFs) play important roles in regulating plant biotic and abiotic stress tolerance. In this study, a new ERF gene, GmERF113, was isolated from the highly resistant soybean 'Suinong 10.' Sequence analysis suggested that the protein encoded by GmERF113 contained a conserved AP2/ERF domain of 58 amino acid and belonged to the B-4 subgroup of the ERF subfamily. Expression of GmERF113 was significantly induced by P. sojae, ethylene, and methyl jasmonate. GmERF113 protein localized to the nucleus when transiently expressed in Arabidopsis protoplasts, could bind to the GCC-box, and acted as a transcription activator. In addition, a region of the full-length GmERF113, GmERF113-II, interacted with a basic helix-loop-helix transcription factor (GmbHLH) in yeast cells. Full-length GmERF113 also interacted with GmbHLH in planta. GmERF113-overexpressing transgenic plants in susceptible cultivar 'Dongnong 50' soybean exhibited increased resistance to P. sojae and positively regulated the expression of the pathogenesis-related genes, PR1 and PR10-1. These results indicate that GmERF113 may play a crucial role in the defense of soybean against P. sojae infection.
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Affiliation(s)
- Yuanling Zhao
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Xin Chang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
| | - Dongyue Qi
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
| | - Lidong Dong
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
| | - Guangjin Wang
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Sujie Fan
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
| | - Liangyu Jiang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
| | - Qun Cheng
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
| | - Xi Chen
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
| | - Dan Han
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
| | - Pengfei Xu
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
| | - Shuzhen Zhang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
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161
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Liu Y, Wei M, Hou C, Lu T, Liu L, Wei H, Cheng Y, Wei Z. Functional Characterization of Populus PsnSHN2 in Coordinated Regulation of Secondary Wall Components in Tobacco. Sci Rep 2017; 7:42. [PMID: 28246387 PMCID: PMC5428377 DOI: 10.1038/s41598-017-00093-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 02/03/2017] [Indexed: 11/13/2022] Open
Abstract
Wood formation is a biological process during which the most abundant lignocellulosic biomass on earth is produced. Although a number of transcription factors have been linked to the regulation of wood formation process, none of them has been demonstrated to be a higher hierarchical regulator that coordinately regulates secondary wall biosynthesis genes. Here, we identified a Populus gene, PsnSHN2, a counterpart of the Arabidopsis AP2/ERF type transcription factor, SHINE2. PsnSHN2 is predominantly expressed in xylem tissues and acted evidently as a high hierarchical transcriptional activator. Overexpression of PsnSHN2 in tobacco significantly altered the expression of both transcription factors and biosynthesis genes involved in secondary wall formation, leading to the thickened secondary walls and the changed cell wall composition. The most significant changes occurred in the contents of cellulose and hemicellulose that increased 37% and 28%, respectively, whereas the content of lignin that decreased 34%. Furthermore, PsnSHN2 activated or repressed the promoter activities of transcription factors involved in secondary wall biosynthesis and bound to five cis-acting elements enriched in the promoter regions of these transcription factors. Taken together, our results suggest PsnSHN2 coordinately regulate secondary wall formation through selective up/down-regulation of its downstream transcription factors that control secondary wall formation.
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Affiliation(s)
- Yingying Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin, 150040, P.R. China
| | - Minjing Wei
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin, 150040, P.R. China
| | - Cong Hou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin, 150040, P.R. China
| | - Tingting Lu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin, 150040, P.R. China
| | | | - Hairong Wei
- School of Forest Resource and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Yuxiang Cheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin, 150040, P.R. China.
| | - Zhigang Wei
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin, 150040, P.R. China.
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162
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Wang H, Lin J, Chang Y, Jiang CZ. Comparative Transcriptomic Analysis Reveals That Ethylene/H 2O 2-Mediated Hypersensitive Response and Programmed Cell Death Determine the Compatible Interaction of Sand Pear and Alternaria alternata. FRONTIERS IN PLANT SCIENCE 2017; 8:195. [PMID: 28261248 PMCID: PMC5309250 DOI: 10.3389/fpls.2017.00195] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 01/31/2017] [Indexed: 05/23/2023]
Abstract
A major restriction on sand pear (Pyrus pyrifolia) production is black spot disease caused by the necrotrophic fungus Alternaria alternata. However, the pear response mechanism to A. alternata is unknown at the molecular level. Here, host responses of a resistant cultivar Cuiguan (CG) and a susceptible cultivar Sucui1 (SC1) to A. alternata infection were investigated. We found that the primary necrotic lesion formed at 1 dpi and the expansion of lesions was aggressive in SC1. Data from transcriptomic profiles using RNA-Seq technology identified a large number of differentially expressed genes (DEGs) between CG and SC1 in the early phase of A. alternata infection. K-mean cluster and Mapman analysis revealed that genes involved in ethylene (ET) biosynthesis and ET signaling pathway, such as ACS, ACOs, and ERFs, and in hypersensitive response (HR) and programmed cell death (PCD) were significantly enriched and up-regulated in the susceptible cultivar SC1. Conversely, genes involved in response to hydrogen peroxide and superoxide were differentially up-regulated in the resistant cultivar CG after inoculation with the fungus. Furthermore, ET levels were highly accumulated in SC1, but not in CG. Higher activities of detoxifying enzymes such as catalases were detected in CG. Our results demonstrate that the ET-/H2O2-mediated PCD and detoxifying processes play a vital role in the interaction of pear and A. alternata.
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Affiliation(s)
- Hong Wang
- Institute of Horticulture, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic ImprovementNanjing, China
| | - Jing Lin
- Institute of Horticulture, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic ImprovementNanjing, China
| | - Youhong Chang
- Institute of Horticulture, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic ImprovementNanjing, China
| | - Cai-Zhong Jiang
- Department of Plant Sciences, University of California at DavisDavis, CA, USA
- Crops Pathology and Genetics Research Unit, United States Department of Agriculture, Agricultural Research ServiceDavis, CA, USA
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163
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Sun D, Li S, Niu L, Reid MS, Zhang Y, Jiang CZ. PhOBF1, a petunia ocs element binding factor, plays an important role in antiviral RNA silencing. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:915-930. [PMID: 28053190 PMCID: PMC6055658 DOI: 10.1093/jxb/erw490] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 12/09/2016] [Indexed: 05/09/2023]
Abstract
Virus-induced gene silencing (VIGS) is a common reverse genetics strategy for characterizing the function of genes in plants. The detailed mechanism governing RNA silencing efficiency triggered by viruses is largely unclear. Here, we reveal that a petunia (Petunia hybrida) ocs element binding factor, PhOBF1, one of the basic leucine zipper (bZIP) transcription factors, was up-regulated by Tobacco rattle virus (TRV) infection. Simultaneous silencing of PhOBF1 and a reporter gene, phytoene desaturase (PDS) or chalcone synthase (CHS), by TRV-based VIGS led to a failure of the development of leaf photobleaching or the white-corollas phenotype. PhOBF1 silencing caused down-regulation of RNA silencing-related genes, including RNA-dependent RNA polymerases (RDRs), Dicer-like RNase III enzymes (DCLs), and Argonautes (AGOs). After inoculation with the TRV-PhPDS, PhOBF1-RNAi lines exhibited a substantially impaired PDS silencing efficiency, whereas overexpression of PhOBF1 resulted in a recovery of the silencing phenotype (photobleaching) in systemic leaves. A compromised resistance to TRV and Tobacco mosaic virus was found in PhOBF1-RNAi lines, while PhOBF1-overexpressing lines displayed an enhanced resistance to their infections. Compared with wild-type plants, PhOBF1-silenced plants accumulated lower levels of free salicylic acid (SA), salicylic acid glucoside, and phenylalanine, contrarily to higher levels of those in plants overexpressing PhOBF1. Furthermore, transcripts of a number of genes associated with the shikimate and phenylpropanoid pathways were decreased or increased in PhOBF1-RNAi or PhOBF1-overexpressing lines, respectively. Taken together, the data suggest that PhOBF1 regulates TRV-induced RNA silencing efficiency through modulation of RDRs, DCLs, and AGOs mediated by the SA biosynthesis pathway.
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Affiliation(s)
- Daoyang Sun
- Department of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi, China
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Shaohua Li
- Department of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi, China
| | - Lixin Niu
- Department of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi, China
| | - Michael S Reid
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Yanlong Zhang
- Department of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi, China
| | - Cai-Zhong Jiang
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
- Crops Pathology and Genetic Research Unit, United States Department of Agriculture, Agricultural Research Service, Davis, CA, USA
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164
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Liu C, Zhang T. Expansion and stress responses of the AP2/EREBP superfamily in cotton. BMC Genomics 2017; 18:118. [PMID: 28143399 PMCID: PMC5282909 DOI: 10.1186/s12864-017-3517-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Accepted: 01/26/2017] [Indexed: 11/24/2022] Open
Abstract
Background The allotetraploid cotton originated from one hybridization event between an extant progenitor of Gosssypium herbaceum (A1) or G. arboreum (A2) and another progenitor, G. raimondii Ulbrich (D5) 1–1.5 million years ago (Mya). The APETALA2/ethylene-responsive element binding protein (AP2/EREBP) transcription factors constitute one of the largest and most conserved gene families in plants. They are characterized by their AP2 domain, which comprises 60–70 amino acids, and are classified into four main subfamilies: the APETALA2 (AP2), Related to ABI3/VP1 (RAV), Dehydration-Responsive Element Binding protein (DREB) and Ethylene-Responsive Factor (ERF) subfamilies. The AP2/EREBP genes play crucial roles in plant growth, development and biotic and abiotic stress responses. Hence, understanding the molecular characteristics of cotton stress tolerance and gene family expansion would undoubtedly facilitate cotton resistance breeding and evolution research. Results A total of 269 AP2/EREBP genes were identified in the G. raimondii (D5) cotton genome. The protein domain architecture and intron/exon structure are simple and relatively conserved within each subfamily. They are distributed throughout all chromosomes but are clustered on various chromosomes due to genomic tandem duplication. We identified 73 tandem duplicated genes and 221 segmental duplicated gene pairs which contributed to the expansion of AP2/EREBP superfamily. Of them, tandem duplication was the most important force of the expansion of the B3 group. Transcriptome analysis showed that 504 AP2/EREBP genes were expressed in at least one tested G. hirsutum TM-1 tissues. In G. hirsutum, 151 non-repeated genes of the DREB and ERF subfamily genes were responsive to different stresses: 132 genes were induced by cold, 63 genes by drought and 94 genes by heat. qRT-PCR confirmed that 13 GhDREB and 15 GhERF genes were induced by cold and/or drought. No transcripts detected for 53 of the 111 tandem duplicated genes in TM-1. In addition, some homoeologous genes showed biased expression toward either A-or D-subgenome. Conclusions The AP2/EREBP genes were obviously expanded in Gossypium. The GhDREB and GhERF genes play crucial roles in cotton stress responses. Our genome-wide analysis of AP2/EREBP genes in cotton provides valuable information for characterizing the molecular functions of AP2/EREBP genes and reveals insights into their evolution in polyploid plants. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3517-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chunxiao Liu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, People's Republic of China
| | - Tianzhen Zhang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, People's Republic of China.
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165
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Bolt S, Zuther E, Zintl S, Hincha DK, Schmülling T. ERF105 is a transcription factor gene of Arabidopsis thaliana required for freezing tolerance and cold acclimation. PLANT, CELL & ENVIRONMENT 2017; 40:108-120. [PMID: 27723941 DOI: 10.1111/pce.12838] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 09/30/2016] [Accepted: 10/01/2016] [Indexed: 05/21/2023]
Abstract
Understanding the response to cold temperature stress is relevant for both basic biology and application. Here we report on ERF105, which is a novel cold-regulated transcription factor gene of Arabidopsis that makes a significant contribution to freezing tolerance and cold acclimation. The expression of cold-responsive genes in erf105 mutants suggests that its action is linked to the CBF regulon mediating cold responses.
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Affiliation(s)
- Sylvia Bolt
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Albrecht-Thaer-Weg 6, D-14195, Berlin, Germany
| | - Ellen Zuther
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476, Potsdam, Germany
| | - Stefanie Zintl
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Albrecht-Thaer-Weg 6, D-14195, Berlin, Germany
| | - Dirk K Hincha
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476, Potsdam, Germany
| | - Thomas Schmülling
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Albrecht-Thaer-Weg 6, D-14195, Berlin, Germany
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166
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Krishnan A, Gupta C, Ambavaram MMR, Pereira A. RECoN: Rice Environment Coexpression Network for Systems Level Analysis of Abiotic-Stress Response. FRONTIERS IN PLANT SCIENCE 2017; 8:1640. [PMID: 28979289 PMCID: PMC5611544 DOI: 10.3389/fpls.2017.01640] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 09/06/2017] [Indexed: 05/22/2023]
Abstract
Transcriptional profiling is a prevalent and powerful approach for capturing the response of crop plants to environmental stresses, e.g., response of rice to drought. However, functionally interpreting the resulting genome-wide gene expression changes is severely hampered by the large gaps in our genomic knowledge about which genes work together in cellular pathways/processes in rice. Here, we present a new web resource - RECoN - that relies on a network-based approach to go beyond currently limited annotations in delineating functional and regulatory perturbations in new rice transcriptome datasets generated by a researcher. To build RECoN, we first enumerated 1,744 abiotic stress-specific gene modules covering 28,421 rice genes (>72% of the genes in the genome). Each module contains a group of genes tightly coexpressed across a large number of environmental conditions and, thus, is likely to be functionally coherent. When a user provides a new differential expression profile, RECoN identifies modules substantially perturbed in their experiment and further suggests deregulated functional and regulatory mechanisms based on the enrichment of current annotations within the predefined modules. We demonstrate the utility of this resource by analyzing new drought transcriptomes of rice in three developmental stages, which revealed large-scale insights into the cellular processes and regulatory mechanisms involved in common and stage-specific drought responses. RECoN enables biologists to functionally explore new data from all abiotic stresses on a genome-scale and to uncover gene candidates, including those that are currently functionally uncharacterized, for engineering stress tolerance.
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Affiliation(s)
- Arjun Krishnan
- Virginia Bioinformatics Institute, Virginia Tech, BlacksburgVA, United States
| | - Chirag Gupta
- Crop, Soil, and Environmental Sciences, University of Arkansas, FayettevilleAR, United States
| | | | - Andy Pereira
- Virginia Bioinformatics Institute, Virginia Tech, BlacksburgVA, United States
- Crop, Soil, and Environmental Sciences, University of Arkansas, FayettevilleAR, United States
- *Correspondence: Andy Pereira,
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167
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Liu J, Wang Y, Zhao G, Zhao J, Du H, He X, Zhang H. A novel Gossypium barbadense ERF transcription factor, GbERFb, regulation host response and resistance to Verticillium dahliae in tobacco. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:125-134. [PMID: 28250589 PMCID: PMC5313406 DOI: 10.1007/s12298-016-0402-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 11/27/2016] [Indexed: 05/02/2023]
Abstract
Ethylene-responsive factors (ERFs) are commonly considered to play an important role in pathogen defense responses. However, only few of ERF members have been characterized in Sea island cotton (Gossypium barbadense). Here, we reported a novel AP2/ERF transcription factors gene, named GbERFb which was cloned and identified from Sea island cotton by RACE. The expression of GbERFb was significantly induced by treatments with ethylene, Methyl jasmonate, salicylic acid, wounding, H2O2 and Verticillium dahliae (V. dahliae) infection. Bioinformatics analysis showed that GbERFb protein containing a conserved ERF DNA binding domain and a nuclear localization signal sequence, belonged to IXb subgroup of the ERF family. Further experiments demonstrated that GbERFb could bind the GCC box cis-acting element and interact with GbMAPKb (MAP kinase) directly in yeast. Over-expression of GbERFb in tobacco could increase the disease resistance to V. dahliae. The results suggest that the GbERFb, a new AP2/ERF transcription factor, could enhance the resistance to V. dahliae and be useful in improvement of crop resistance to pathogenes.
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Affiliation(s)
- Jianguang Liu
- Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, No. 598 HePing West Road, Shi Jiazhuang, 050000 Hebei Province China
| | - Yongqiang Wang
- Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, No. 598 HePing West Road, Shi Jiazhuang, 050000 Hebei Province China
| | - Guiyuan Zhao
- Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, No. 598 HePing West Road, Shi Jiazhuang, 050000 Hebei Province China
| | - Junli Zhao
- Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, No. 598 HePing West Road, Shi Jiazhuang, 050000 Hebei Province China
| | - Haiying Du
- Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, No. 598 HePing West Road, Shi Jiazhuang, 050000 Hebei Province China
| | - Xiaoliang He
- School of Bioscience and Bioengineering, Hebei University of Science and Technology, Shi Jiazhuang, 050000 Hebei Province China
| | - Hanshuang Zhang
- Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, No. 598 HePing West Road, Shi Jiazhuang, 050000 Hebei Province China
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168
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Li H, Wang Y, Wu M, Li L, Li C, Han Z, Yuan J, Chen C, Song W, Wang C. Genome-Wide Identification of AP2/ERF Transcription Factors in Cauliflower and Expression Profiling of the ERF Family under Salt and Drought Stresses. FRONTIERS IN PLANT SCIENCE 2017; 8:946. [PMID: 28642765 PMCID: PMC5462956 DOI: 10.3389/fpls.2017.00946] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 05/22/2017] [Indexed: 05/18/2023]
Abstract
The AP2/ERF transcription factors (TFs) comprise one of the largest gene superfamilies in plants. These TFs perform vital roles in plant growth, development, and responses to biotic and abiotic stresses. In this study, 171 AP2/ERF TFs were identified in cauliflower (Brassica oleracea L. var. botrytis), one of the most important horticultural crops in Brassica. Among these TFs, 15, 9, and 1 TFs were classified into the AP2, RAV, and Soloist family, respectively. The other 146 TFs belong to ERF family, which were further divided into the ERF and DREB subfamilies. The ERF subfamily contained 91 TFs, while the DREB subfamily contained 55 TFs. Phylogenetic analysis results indicated that the AP2/ERF TFs can be classified into 13 groups, in which 25 conserved motifs were confirmed. Some motifs were group- or subgroup- specific, implying that they are significant to the functions of the AP2/ERF TFs of these clades. In addition, 35 AP2/ERF TFs from the 13 groups were selected randomly and then used for expression pattern analysis under salt and drought stresses. The majority of these AP2/ERF TFs exhibited positive responses to these stress conditions. In specific, Bra-botrytis-ERF054a, Bra-botrytis-ERF056, and Bra-botrytis-CRF2a demonstrated rapid responses. By contrast, six AP2/ERF TFs were showed to delay responses to both stresses. The AP2/ERF TFs exhibiting specific expression patterns under salt or drought stresses were also confirmed. Further functional analysis indicated that ectopic overexpression of Bra-botrytis-ERF056 could increase tolerance to both salt and drought treatments. These findings provide new insights into the AP2/ERF TFs present in cauliflower, and offer candidate AP2/ERF TFs for further studies on their roles in salt and drought stress tolerance.
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Affiliation(s)
- Hui Li
- College of Life Sciences, Nankai UniversityTianjin, China
- College of Horticulture and Landscape, Tianjin Agricultural UniversityTianjin, China
| | - Yu Wang
- College of Life Sciences, Nankai UniversityTianjin, China
| | - Mei Wu
- College of Life Sciences, Nankai UniversityTianjin, China
| | - Lihong Li
- College of Life Sciences, Nankai UniversityTianjin, China
| | - Cong Li
- College of Life Sciences, Nankai UniversityTianjin, China
| | - Zhanpin Han
- College of Horticulture and Landscape, Tianjin Agricultural UniversityTianjin, China
| | - Jiye Yuan
- College of Life Sciences, Nankai UniversityTianjin, China
| | - Chengbin Chen
- College of Life Sciences, Nankai UniversityTianjin, China
| | - Wenqin Song
- College of Life Sciences, Nankai UniversityTianjin, China
| | - Chunguo Wang
- College of Life Sciences, Nankai UniversityTianjin, China
- *Correspondence: Chunguo Wang
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169
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Iwase A, Harashima H, Ikeuchi M, Rymen B, Ohnuma M, Komaki S, Morohashi K, Kurata T, Nakata M, Ohme-Takagi M, Grotewold E, Sugimoto K. WIND1 Promotes Shoot Regeneration through Transcriptional Activation of ENHANCER OF SHOOT REGENERATION1 in Arabidopsis. THE PLANT CELL 2017; 29:54-69. [PMID: 28011694 PMCID: PMC5304349 DOI: 10.1105/tpc.16.00623] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 12/14/2016] [Accepted: 12/22/2016] [Indexed: 05/20/2023]
Abstract
Many plant species display remarkable developmental plasticity and regenerate new organs after injury. Local signals produced by wounding are thought to trigger organ regeneration but molecular mechanisms underlying this control remain largely unknown. We previously identified an AP2/ERF transcription factor WOUND INDUCED DEDIFFERENTIATION1 (WIND1) as a central regulator of wound-induced cellular reprogramming in plants. In this study, we demonstrate that WIND1 promotes callus formation and shoot regeneration by upregulating the expression of the ENHANCER OF SHOOT REGENERATION1 (ESR1) gene, which encodes another AP2/ERF transcription factor in Arabidopsis thaliana The esr1 mutants are defective in callus formation and shoot regeneration; conversely, its overexpression promotes both of these processes, indicating that ESR1 functions as a critical driver of cellular reprogramming. Our data show that WIND1 directly binds the vascular system-specific and wound-responsive cis-element-like motifs within the ESR1 promoter and activates its expression. The expression of ESR1 is strongly reduced in WIND1-SRDX dominant repressors, and ectopic overexpression of ESR1 bypasses defects in callus formation and shoot regeneration in WIND1-SRDX plants, supporting the notion that ESR1 acts downstream of WIND1. Together, our findings uncover a key molecular pathway that links wound signaling to shoot regeneration in plants.
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Affiliation(s)
- Akira Iwase
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | | | - Momoko Ikeuchi
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Bart Rymen
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Mariko Ohnuma
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Shinichiro Komaki
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Kengo Morohashi
- Center for Applied Plant Sciences and Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - Tetsuya Kurata
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Masaru Nakata
- National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8562, Japan
| | - Masaru Ohme-Takagi
- National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8562, Japan
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Erich Grotewold
- Center for Applied Plant Sciences and Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
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170
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Ma R, Xiao Y, Lv Z, Tan H, Chen R, Li Q, Chen J, Wang Y, Yin J, Zhang L, Chen W. AP2/ERF Transcription Factor, Ii049, Positively Regulates Lignan Biosynthesis in Isatis indigotica through Activating Salicylic Acid Signaling and Lignan/Lignin Pathway Genes. FRONTIERS IN PLANT SCIENCE 2017; 8:1361. [PMID: 28824690 PMCID: PMC5543283 DOI: 10.3389/fpls.2017.01361] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 07/20/2017] [Indexed: 05/15/2023]
Abstract
Lignans, such as lariciresinol and its derivatives, have been identified as effective antiviral ingredients in Isatis indigotica. Evidence suggests that the APETALA2/ethylene response factor (AP2/ERF) family might be related to the biosynthesis of lignans in I. indigotica. However, the special role played by the AP2/ERF family in the metabolism and its underlying putative mechanism still need to be elucidated. One novel AP2/ERF gene, named Ii049, was isolated and characterized from I. indigotica in this study. The quantitative real-time PCR analysis revealed that Ii049 was expressed highest in the root and responded to methyl jasmonate, salicylic acid (SA) and abscisic acid treatments to various degrees. Subcellular localization analysis indicated that Ii049 protein was localized in the nucleus. Knocking-down the expression of Ii049 caused a remarkable reduction of lignan/lignin contents and transcript levels of genes involved in the lignan/lignin biosynthetic pathway. Ii049 bound to the coupled element 1, RAV1AAT and CRTAREHVCBF2 motifs of genes IiPAL and IiCCR, the key structural genes in the lignan/lignin pathway. Furthermore, Ii049 was also essential for SA biosynthesis, and SA induced lignan accumulation in I. indigotica. Notably, the transgenic I. indigotica hairy roots overexpressing Ii049 showed high expression levels of lignan/lignin biosynthetic genes and SA content, resulting in significant accumulation of lignan/lignin. The best-engineered line (OVX049-10) produced 425.60 μg·g-1 lariciresinol, an 8.3-fold increase compared with the wild type production. This study revealed the function of Ii049 in regulating lignan/lignin biosynthesis, which had the potential to increase the content of valuable lignan/lignin in economically significant medicinal plants.
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Affiliation(s)
- Ruifang Ma
- Department of Pharmacy, Changzheng Hospital, Second Military Medical UniversityShanghai, China
| | - Ying Xiao
- Department of Pharmacy, Changzheng Hospital, Second Military Medical UniversityShanghai, China
| | - Zongyou Lv
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical UniversityShanghai, China
| | - Hexin Tan
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical UniversityShanghai, China
| | - Ruibing Chen
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical UniversityShanghai, China
| | - Qing Li
- Department of Pharmacy, Changzheng Hospital, Second Military Medical UniversityShanghai, China
| | - Junfeng Chen
- Department of Pharmacy, Changzheng Hospital, Second Military Medical UniversityShanghai, China
| | - Yun Wang
- Department of Pharmacy, Changzheng Hospital, Second Military Medical UniversityShanghai, China
| | - Jun Yin
- Development and Utilization Key Laboratory of Northeast Plant Materials, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical UniversityShenyang, China
- *Correspondence: Jun Yin
| | - Lei Zhang
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical UniversityShanghai, China
- Lei Zhang
| | - Wansheng Chen
- Department of Pharmacy, Changzheng Hospital, Second Military Medical UniversityShanghai, China
- Wansheng Chen
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171
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Wang RH, Yuan XY, Meng LH, Zhu BZ, Zhu HL, Luo YB, Fu DQ. Transcriptome Analysis Provides a Preliminary Regulation Route of the Ethylene Signal Transduction Component, SlEIN2, during Tomato Ripening. PLoS One 2016; 11:e0168287. [PMID: 27973616 PMCID: PMC5156437 DOI: 10.1371/journal.pone.0168287] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 11/29/2016] [Indexed: 11/18/2022] Open
Abstract
Ethylene is crucial in climacteric fruit ripening. The ethylene signal pathway regulates several physiological alterations such as softening, carotenoid accumulation and sugar level reduction, and production of volatile compounds. All these physiological processes are controlled by numerous genes and their expression simultaneously changes at the onset of ripening. Ethylene insensitive 2 (EIN2) is a key component for ethylene signal transduction, and its mutation causes ethylene insensitivity. In tomato, silencing SlEIN2 resulted in a non-ripening phenotype and low ethylene production. RNA sequencing of SlEIN2-silenced and wild type tomato, and differential gene expression analyses, indicated that silencing SlEIN2 caused changes in more than 4,000 genes, including those related to photosynthesis, defense, and secondary metabolism. The relative expression level of 28 genes covering ripening-associated transcription factors, ethylene biosynthesis, ethylene signal pathway, chlorophyll binding proteins, lycopene and aroma biosynthesis, and defense pathway, showed that SlEIN2 influences ripening inhibitor (RIN) in a feedback loop, thus controlling the expression of several other genes. SlEIN2 regulates many aspects of fruit ripening, and is a key factor in the ethylene signal transduction pathway. Silencing SlEIN2 ultimately results in lycopene biosynthesis inhibition, which is the reason why tomato does not turn red, and this gene also affects the expression of several defense-associated genes. Although SlEIN2-silenced and green wild type fruits are similar in appearance, their metabolism is significantly different at the molecular level.
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Affiliation(s)
- Rui-Heng Wang
- Laboratory of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Haidian District, Beijing, China
| | - Xin-Yu Yuan
- Laboratory of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Haidian District, Beijing, China
| | - Lan-Huan Meng
- Laboratory of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Haidian District, Beijing, China
| | - Ben-Zhong Zhu
- Laboratory of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Haidian District, Beijing, China
| | - Hong-liang Zhu
- Laboratory of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Haidian District, Beijing, China
| | - Yun-Bo Luo
- Laboratory of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Haidian District, Beijing, China
| | - Da-Qi Fu
- Laboratory of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Haidian District, Beijing, China
- * E-mail:
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172
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Santa Brigida AB, Rojas CA, Grativol C, de Armas EM, Entenza JOP, Thiebaut F, Lima MDF, Farrinelli L, Hemerly AS, Lifschitz S, Ferreira PCG. Sugarcane transcriptome analysis in response to infection caused by Acidovorax avenae subsp. avenae. PLoS One 2016; 11:e0166473. [PMID: 27936012 PMCID: PMC5147822 DOI: 10.1371/journal.pone.0166473] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 10/28/2016] [Indexed: 12/22/2022] Open
Abstract
Sugarcane is an important tropical crop mainly cultivated to produce ethanol and sugar. Crop productivity is negatively affected by Acidovorax avenae subsp avenae (Aaa), which causes the red stripe disease. Little is known about the molecular mechanisms triggered in response to the infection. We have investigated the molecular mechanism activated in sugarcane using a RNA-seq approach. We have produced a de novo transcriptome assembly (TR7) from sugarcane RNA-seq libraries submitted to drought and infection with Aaa. Together, these libraries present 247 million of raw reads and resulted in 168,767 reference transcripts. Mapping in TR7 of reads obtained from infected libraries, revealed 798 differentially expressed transcripts, of which 723 were annotated, corresponding to 467 genes. GO and KEGG enrichment analysis showed that several metabolic pathways, such as code for proteins response to stress, metabolism of carbohydrates, processes of transcription and translation of proteins, amino acid metabolism and biosynthesis of secondary metabolites were significantly regulated in sugarcane. Differential analysis revealed that genes in the biosynthetic pathways of ET and JA PRRs, oxidative burst genes, NBS-LRR genes, cell wall fortification genes, SAR induced genes and pathogenesis-related genes (PR) were upregulated. In addition, 20 genes were validated by RT-qPCR. Together, these data contribute to a better understanding of the molecular mechanisms triggered by the Aaa in sugarcane and opens the opportunity for the development of molecular markers associated with disease tolerance in breeding programs.
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Affiliation(s)
- Ailton B. Santa Brigida
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brasil
| | - Cristian A. Rojas
- Instituto Latino-Americano de Ciências da Vida e da Natureza, Universidade Federal da Integração Latino-Americana, Foz do Iguaçu, Paraná, Brasil
| | - Clícia Grativol
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro, Brasil
| | - Elvismary M. de Armas
- Departamento de Informática, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brasil
| | - Júlio O. P. Entenza
- Departamento de Informática, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brasil
| | - Flávia Thiebaut
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brasil
| | - Marcelo de F. Lima
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, Brasil
| | | | - Adriana S. Hemerly
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brasil
| | - Sérgio Lifschitz
- Departamento de Informática, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brasil
| | - Paulo C. G. Ferreira
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brasil
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173
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Wang N, Zhong X, Cong Y, Wang T, Yang S, Li Y, Gai J. Genome-wide Analysis of Phosphoenolpyruvate Carboxylase Gene Family and Their Response to Abiotic Stresses in Soybean. Sci Rep 2016; 6:38448. [PMID: 27924923 PMCID: PMC5141416 DOI: 10.1038/srep38448] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 11/07/2016] [Indexed: 11/09/2022] Open
Abstract
Phosphoenolpyruvate carboxylase (PEPC) plays an important role in assimilating atmospheric CO2 during C4 and crassulacean acid metabolism photosynthesis, and also participates in various non-photosynthetic processes, including fruit ripening, stomatal opening, supporting carbon-nitrogen interactions, seed formation and germination, and regulation of plant tolerance to stresses. However, a comprehensive analysis of PEPC family in Glycine max has not been reported. Here, a total of ten PEPC genes were identified in soybean and denominated as GmPEPC1-GmPEPC10. Based on the phylogenetic analysis of the PEPC proteins from 13 higher plant species including soybean, PEPC family could be classified into two subfamilies, which was further supported by analyses of their conserved motifs and gene structures. Nineteen cis-regulatory elements related to phytohormones, abiotic and biotic stresses were identified in the promoter regions of GmPEPC genes, indicating their roles in soybean development and stress responses. GmPEPC genes were expressed in various soybean tissues and most of them responded to the exogenously applied phytohormones. GmPEPC6, GmPEPC8 and GmPEPC9 were significantly induced by aluminum toxicity, cold, osmotic and salt stresses. In addition, the enzyme activities of soybean PEPCs were also up-regulated by these treatments, suggesting their potential roles in soybean response to abiotic stresses.
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Affiliation(s)
- Ning Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement/National Center for Soybean Improvement/Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Xiujuan Zhong
- National Key Laboratory of Crop Genetics and Germplasm Enhancement/National Center for Soybean Improvement/Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Yahui Cong
- National Key Laboratory of Crop Genetics and Germplasm Enhancement/National Center for Soybean Improvement/Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Tingting Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement/National Center for Soybean Improvement/Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Songnan Yang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement/National Center for Soybean Improvement/Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Yan Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement/National Center for Soybean Improvement/Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Junyi Gai
- National Key Laboratory of Crop Genetics and Germplasm Enhancement/National Center for Soybean Improvement/Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture)/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
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174
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Divergent Expression Patterns in Two Vernicia Species Revealed the Potential Role of the Hub Gene VmAP2/ERF036 in Resistance to Fusarium oxysporum in Vernicia montana. Genes (Basel) 2016; 7:genes7120109. [PMID: 27916924 PMCID: PMC5192485 DOI: 10.3390/genes7120109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Revised: 11/09/2016] [Accepted: 11/14/2016] [Indexed: 12/14/2022] Open
Abstract
Tung oil tree (Vernicia fordii) is a promising industrial oil crop; however, this tree is highly susceptible to Fusarium wilt disease. Conversely, Vernicia montana is resistant to the pathogen. The APETALA2/ethylene-responsive element binding factor (AP2/ERF) transcription factor superfamily has been reported to play a significant role in resistance to Fusarium oxysporum. In this study, comprehensive analysis identified 75 and 81 putative Vf/VmAP2/ERF transcription factor-encoding genes in V. fordii and V. montana, respectively, which were divided into AP2, ERF, related to ABI3 and VP1 (RAV) and Soloist families. After F. oxysporum infection, a majority of AP2/ERF superfamily genes showed strong patterns of repression in both V. fordii and V. montana. We then identified 53 pairs of one-to-one orthologs in V. fordii and V. montana, with most pairs of orthologous genes exhibiting similar expression in response to the pathogen. Further investigation of Vf/VmAP2/ERF gene expression in plant tissues indicated that the pairs of genes with different expression patterns in response to F. oxysporum tended to exhibit different tissue profiles in the two species. In addition, VmAP2/ERF036, showing the strongest interactions with 666 genes, was identified as a core hub gene mediating resistance. Moreover, qRT-PCR results indicated VmAP2/ERF036 showed repressed expression while its orthologous gene VfAP2/ERF036 had the opposite expression pattern during pathogen infection. Overall, comparative analysis of the Vf/VmAP2/ERF superfamily and indication of a potential hub resistance gene in resistant and susceptible Vernicia species provides valuable information for understanding the molecular basis and selection of essential functional genes for V. fordii genetic engineering to control Fusarium wilt disease.
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175
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Li T, Jiang Z, Zhang L, Tan D, Wei Y, Yuan H, Li T, Wang A. Apple (Malus domestica) MdERF2 negatively affects ethylene biosynthesis during fruit ripening by suppressing MdACS1 transcription. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:735-748. [PMID: 27476697 DOI: 10.1111/tpj.13289] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 07/21/2016] [Accepted: 07/26/2016] [Indexed: 05/08/2023]
Abstract
Ripening in climacteric fruit requires the gaseous phytohormone ethylene. Although ethylene signaling has been well studied, knowledge of the transcriptional regulation of ethylene biosynthesis is still limited. Here we show that an apple (Malus domestica) ethylene response factor, MdERF2, negatively affects ethylene biosynthesis and fruit ripening by suppressing the transcription of MdACS1, a gene that is critical for biosynthesis of ripening-related ethylene. Expression of MdERF2 was suppressed by ethylene during ripening of apple fruit, and we observed that MdERF2 bound to the promoter of MdACS1 and directly suppressed its transcription. Moreover, MdERF2 suppressed the activity of the promoter of MdERF3, a transcription factor that we found to bind to the MdACS1 promoter, thereby increasing MdACS1 transcription. We determined that the MdERF2 and MdERF3 proteins directly interact, and this interaction suppresses the binding of MdERF3 to the MdACS1 promoter. Moreover, apple fruit with transiently downregulated MdERF2 expression showed higher ethylene production and faster ripening. Our results indicate that MdERF2 negatively affects ethylene biosynthesis and fruit ripening in apple by suppressing the transcription of MdACS1 via multiple mechanisms, thereby acting as an antagonist of positive ripening regulators. Our findings offer a deep understanding of the transcriptional regulation of ethylene biosynthesis during climacteric fruit ripening.
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Affiliation(s)
- Tong Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhongyu Jiang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Lichao Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Dongmei Tan
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yun Wei
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Hui Yuan
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Tianlai Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Aide Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
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176
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Imran QM, Falak N, Hussain A, Mun BG, Sharma A, Lee SU, Kim KM, Yun BW. Nitric Oxide Responsive Heavy Metal-Associated Gene AtHMAD1 Contributes to Development and Disease Resistance in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2016; 7:1712. [PMID: 27917181 PMCID: PMC5116471 DOI: 10.3389/fpls.2016.01712] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 10/31/2016] [Indexed: 05/29/2023]
Abstract
Exposure of plants to different biotic and abiotic stress condition instigates significant change in the cellular redox status; resulting in the elevation of reactive nitrogen species that play signaling role in mediating defense responses. Heavy metal associated (HMA) domain containing genes are required for spatio-temporal transportation of metal ions that bind with various enzymes and co-factors within the cell. To uncover the underlying mechanisms mediated by AtHMA genes, we identified 14 Arabidopsis HMA genes that were differentially expressed in response to nitrosative stress through RNA-seq analysis. Of those 14 genes, the expression of eight HMA genes was significantly increased, whereas that of six genes was significantly reduced. We further validated the RNA-seq results through quantitative real-time PCR analysis. Gene ontology analysis revealed the involvement of these genes in biological processes such as hemostasis and transport. The majority of these nitric oxide (NO)-responsive AtHMA gene products are carrier/transport proteins. AtHMAD1 (At1g51090) showed the highest fold change to S-nitrosocystein. We therefore, further investigated its role in oxidative and nitrosative mediated stress conditions and found that AtHMAD1 has antagonistic role in shoot and root growth. Characterization of AtHMAD1 through functional genomics showed that the knock out mutant athmad1 plants were resistant to virulent Pseudomonas syringae (DC3000) and showed early induction and high transcript accumulation of pathogenesis related gene. Furthermore, inoculation of athamd1 with avirulent strain of the same bacteria showed negative regulation of R-gene mediated resistance. These results were supported by hypersensitive cell death response and cell death induced electrolyte leakage. AtHMAD1 was also observed to negatively regulate systemic acquired resistance SAR as the KO mutant showed induction of SAR marker genes. Overall, these results imply that NO-responsive AtHMA domain containing genes may play an important role in plant development and immunity.
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Affiliation(s)
- Q. Muhammad Imran
- Laboratory of Plant Functional Genomics, School of Applied Biosciences, Kyungpook National UniversityDaegu, South Korea
| | - Noreen Falak
- Laboratory of Plant Functional Genomics, School of Applied Biosciences, Kyungpook National UniversityDaegu, South Korea
| | - Adil Hussain
- Department of Agriculture, Abdul Wali Khan UniversityMardan, Pakistan
| | - Bong-Gyu Mun
- Laboratory of Plant Functional Genomics, School of Applied Biosciences, Kyungpook National UniversityDaegu, South Korea
| | - Arti Sharma
- Laboratory of Plant Functional Genomics, School of Applied Biosciences, Kyungpook National UniversityDaegu, South Korea
| | - Sang-Uk Lee
- Laboratory of Plant Functional Genomics, School of Applied Biosciences, Kyungpook National UniversityDaegu, South Korea
| | - Kyung-Min Kim
- Laboratory of Plant Molecular Breeding, School of Applied Biosciences, Kyungpook National UniversityDaegu, South Korea
| | - Byung-Wook Yun
- Laboratory of Plant Functional Genomics, School of Applied Biosciences, Kyungpook National UniversityDaegu, South Korea
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177
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Agarwal P, Kumar R, Pareek A, Sharma AK. Fruit preferential activity of the tomato RIP1 gene promoter in transgenic tomato and Arabidopsis. Mol Genet Genomics 2016; 292:145-156. [PMID: 27796641 DOI: 10.1007/s00438-016-1262-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 10/17/2016] [Indexed: 01/21/2023]
Abstract
Isolation and functional characterization of tissue- and stage-specific gene promoters is beneficial for genetic improvement of economically important crops. Here, we have characterized a putative promoter of a ripening-induced gene RIP1 (Ripening induced protein 1) in tomato. Quantification of the transcript level of RIP1 showed that its expression is fruit preferential, with maximum accumulation in red ripe fruits. To test the promoter activity, we made a reporter construct by cloning 1450 bp putative RIP1 promoter driving the GUS (ß-glucuronidase) gene expression and generated stable transgenic lines in tomato and Arabidopsis. Histochemical and fluorometric assays validated the fruit-specific expression of RIP1 as the highest GUS activity was found in red ripe tomatoes. Similarly, we detected high levels of GUS activity in the siliques of Arabidopsis. On the contrary, weak GUS activity was found in the flower buds in both tomato and Arabidopsis. To characterize the specific regions of the RIP1 promoter that might be essential for its maximum activity and specificity in fruits, we made stable transgenic lines of tomato and Arabidopsis with 5'-deletion constructs. Characterization of these transgenic plants showed that the full length promoter is essential for its function. Overall, we report the identification and characterization of a ripening-induced promoter of tomato, which would be useful for the controlled manipulation of the ripening-related agronomic traits in genetic manipulation studies in future.
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Affiliation(s)
- Priyanka Agarwal
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Rahul Kumar
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.,Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Amit Pareek
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Arun K Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.
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178
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Fu CC, Han YC, Qi XY, Shan W, Chen JY, Lu WJ, Kuang JF. Papaya CpERF9 acts as a transcriptional repressor of cell-wall-modifying genes CpPME1/2 and CpPG5 involved in fruit ripening. PLANT CELL REPORTS 2016; 35:2341-2352. [PMID: 27502602 DOI: 10.1007/s00299-016-2038-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 08/04/2016] [Indexed: 05/18/2023]
Abstract
KEY MESSAGE CpERF9 controls papaya fruit ripening through transcriptional repression of cell-wall-modifying genes CpPME1/2 and CpPG5 by directly binding to their promoters. Papaya fruit ripening is an intricate and highly coordinated developmental process which is controlled by the action of ethylene and expression of numerous ethylene-responsive genes. Ethylene response factors (ERFs) representing the last regulators of ethylene-signaling pathway determine the specificities of ethylene response. However, knowledge concerning the transcriptional controlling mechanism of ERF-mediated papaya fruit ripening is limited. In the present work, a gene-encoding AP2/ERF protein with two ERF-associated amphiphilic repression (EAR) motifs, named CpERF9, was characterized from papaya fruit. CpERF9 was found to localize in nucleus, and possess transcriptional repression ability. CpERF9 expression steadily decreased during papaya fruit ripening, while several genes encoding pectin methylesterases (PMEs) and polygalacturonases (PGs), such as CpPME1/2 and CpPG5, were gradually increased, paralleling the decline of fruit firmness. Electrophoretic mobility shift assay (EMSA) demonstrated a specific binding of CpERF9 to promoters of CpPME1/2 and CpPG5, via the GCC-box motif. Transient expression of CpERF9 in tobacco repressed CpPME1/2 and CpPG5 promoter activities, which was depended on two EAR motifs of CpERF9 protein. Taken together, these findings suggest that papaya CpERF9 may act as a transcriptional repressor of several cell-wall modifying genes, such as CpPME1/2 and CpPG5, via directly binding to their promoters.
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Affiliation(s)
- Chang-Chun Fu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Yan-Chao Han
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Xiu-Ye Qi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Wei Shan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Jian-Ye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Wang-Jin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Jian-Fei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China.
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179
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Yang Y, Dong C, Li X, Du J, Qian M, Sun X, Yang Y. A novel Ap2/ERF transcription factor from Stipa purpurea leads to enhanced drought tolerance in Arabidopsis thaliana. PLANT CELL REPORTS 2016; 35:2227-2239. [PMID: 27443644 DOI: 10.1007/s00299-016-2030-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 07/19/2016] [Indexed: 05/10/2023]
Abstract
SpERF1 acts as a positive regulator, contributing to drought stress tolerance in A. thaliana through activating DRE/CRT elements in the promoters of abiotic stress-responsive genes. Stipa purpurea is an endemic perennial grass species in alpine arid and semi-arid meadows on the Qinghai-Xizang Plateau, which is highly tolerant against drought and cold. ERF transcription factors are known to regulate gene expression under abiotic and biotic treatments. Herein, we isolated a full-length ERF gene CDS from S. purpurea named SpERF1, which was induced by drought, cold, and jasmonic acid stresses. Subcellular localization revealed that SpERF1 is a nuclear protein, consistent with its roles as a transcription factor. Overexpression of SpERF1 enhanced drought tolerance of transgenic Arabidopsis thaliana via the activation of DRE/CRT elements in the promoters of abiotic stress-responsive genes. Furthermore, increased accumulation of proline indicated that SpERF1 might be involved in proline synthesis in the transgenic lines, allowing them to have a better buffering capacity and membrane protection under drought stress. This study indicated that SpERF1 might be an attractive target in the genetic engineering for improving stress tolerance in other crops. Moreover, SpERF1 protein function analysis increased our understanding of S. purpurea's ability to adapt to the adverse conditions of the Qinghai-Xizang Plateau.
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Affiliation(s)
- Yunqiang Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650204, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Chao Dong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650204, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiong Li
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650204, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jiancan Du
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650204, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Min Qian
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650204, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Xudong Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650204, China.
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Yongping Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650204, China.
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
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180
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Zhuang J, Li MY, Wu B, Liu YJ, Xiong AS. Arg156 in the AP2-Domain Exhibits the Highest Binding Activity among the 20 Individuals to the GCC Box in BnaERF-B3-hy15, a Mutant ERF Transcription Factor from Brassica napus. FRONTIERS IN PLANT SCIENCE 2016; 7:1603. [PMID: 27833627 PMCID: PMC5081391 DOI: 10.3389/fpls.2016.01603] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/11/2016] [Indexed: 05/29/2023]
Abstract
To develop mutants of the ERF factor with more binding activities to the GCC box, we performed in vitro directed evolution by using DNA shuffling and screened mutants through yeast one-hybrid assay. Here, a series of mutants were obtained and used to reveal key amino acids that induce changes in the DNA binding activity of the BnaERF-B3 protein. With the BnaERF-B3-hy15 as the template, we produced 12 mutants which host individual mutation of potential key residues. We found that amino acid 156 is the key site, and the other 18 mutants host the 18 corresponding individual amino acid residues at site 156. Among the 20 individuals comprising WT (Gly156), Mu3 (Arg156), and 18 mutants with other 18 amino acid residues, Arg156 in the AP2-domain is the amino acid residue with the highest binding activity to the GCC box. The structure of the α-helix in the AP2-domain affects the binding activity. Other residues within AP2-domain modulated binding activity of ERF protein, suggesting that these positions are important for binding activity. Comparison of the mutant and wild-type transcription factors revealed the relationship of protein function and sequence modification. Our result provides a potential useful resource for understanding the trans-activation of ERF proteins.
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181
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Bahieldin A, Atef A, Edris S, Gadalla NO, Ali HM, Hassan SM, Al-Kordy MA, Ramadan AM, Makki RM, Al-Hajar ASM, El-Domyati FM. Ethylene responsive transcription factor ERF109 retards PCD and improves salt tolerance in plant. BMC PLANT BIOLOGY 2016; 16:216. [PMID: 27716054 PMCID: PMC5053207 DOI: 10.1186/s12870-016-0908-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 09/27/2016] [Indexed: 05/21/2023]
Abstract
BACKGROUND The ultimate goal of this work was to detect the role of transcription factors (TFs) concordantly expressed with genes related to programmed cell death (PCD) during PCD and salt stress. This work was based on the hypothesis that TFs and their driven genes likely co-express under different stimuli. The conserved superfamily ethylene responsive factor (AP2/ERF) draw attention of the present study as it participates in the response to biotic and abiotic stimuli as well as to program cell death (PCD). RESULTS RNA-Seq analysis was done for tobacco (N. benthamiana) leaves exposed to oxalic acid (OA) at 20 mM for 0, 2, 6, 12 and 24 h to induce PCD. Genes up-regulated after 2 h of OA treatment with known function during PCD were utilized as landmarks to select TFs with concordant expression. Knockdown mutants of these TFs were generated in tobacco via virus induced gene silencing (VIGS) in order to detect their roles during PCD. Based on the results of PCD assay, knockout (KO) T-DNA insertion mutants of Arabidopsis as well as over-expression lines of two selected TFs, namely ERF109 and TFIID5, analogs to those in tobacco, were tested under salt stress (0, 100, 150 and 200 mM NaCl). CONCLUSIONS Results of knockdown mutant tobacco cells confirmed the influence of these two TFs during PCD. Knockout insertion mutants and over-expression lines indicated the role of ERF109 in conferring salt tolerance in Arabidopsis.
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Affiliation(s)
- Ahmed Bahieldin
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
| | - Ahmed Atef
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
| | - Sherif Edris
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
- Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Nour O. Gadalla
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
| | - Hani M. Ali
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
| | - Sabah M. Hassan
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
| | - Magdy A. Al-Kordy
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
| | - Ahmed M. Ramadan
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
| | - Rania M. Makki
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
| | - Abdulrahman S. M. Al-Hajar
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
| | - Fotouh M. El-Domyati
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
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182
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Ma H, Wang F, Wang W, Yin G, Zhang D, Ding Y, Timko MP, Zhang H. Alternative splicing of basic chitinase gene PR3b in the low-nicotine mutants of Nicotiana tabacum L. cv. Burley 21. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:5799-5809. [PMID: 27664270 PMCID: PMC5066497 DOI: 10.1093/jxb/erw345] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Two unlinked semi-dominant loci, A (NIC1) and B (NIC2), control nicotine and related alkaloid biosynthesis in Burley tobaccos. Mutations in either or both loci (nic1 and nic2) lead to low nicotine phenotypes with altered environmental stress responses. Here we show that the transcripts derived from the pathogenesis-related (PR) protein gene PR3b are alternatively spliced to a greater extent in the nic1 and nic2 mutants of Burley 21 tobacco and the nic1nic2 double mutant. The alternative splicing results in a deletion of 65 nucleotides and introduces a premature stop codon into the coding region of PR3b that leads to a significant reduction of PR3b specific chitinase activity. Assays of PR3b splicing in F2 individuals derived from crosses between nic1 and nic2 mutants and wild-type plants showed that the splicing phenotype is controlled by the NIC1 and NIC2 loci, even though NIC1 and NIC2 are unlinked loci. Moreover, the transcriptional analyses showed that the splicing patterns of PR3b in the low-nicotine mutants were differentially regulated by jasmonate (JA) and ethylene (ET). These data suggest that the NIC1 and NIC2 loci display differential roles in regulating the alternative splicing of PR3b in Burley 21. The findings in this study have provided valuable information for extending our understanding of the broader effects of the low-nicotine mutants of Burley 21 and the mechanism by which JA and ET signalling pathways post-transcriptionally regulate the activity of PR3b protein.
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Affiliation(s)
- Haoran Ma
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Feng Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Wenjing Wang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Guoying Yin
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Dingyu Zhang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Yongqiang Ding
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Hongbo Zhang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
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183
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De Zio E, Trupiano D, Montagnoli A, Terzaghi M, Chiatante D, Grosso A, Marra M, Scaloni A, Scippa GS. Poplar woody taproot under bending stress: the asymmetric response of the convex and concave sides. ANNALS OF BOTANY 2016; 118:865-883. [PMID: 27558889 PMCID: PMC5055640 DOI: 10.1093/aob/mcw159] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 07/03/2016] [Accepted: 07/20/2016] [Indexed: 05/09/2023]
Abstract
Background and Aims Progress has been made in understanding the physiological and molecular basis of root response to mechanical stress, especially in the model plant Arabidopsis thaliana, in which bending causes the initiation of lateral root primordia toward the convex side of the bent root. In the case of woody roots, it has been reported that mechanical stress induces an asymmetric distribution of lateral roots and reaction wood formation, but the mechanisms underlying these responses are largely unknown. In the present work, the hypothesis was tested that bending could determine an asymmetric response in the two sides of the main root axis as cells are stretched on the convex side and compressed on the concave side. Methods Woody taproots of 20 seedlings were bent to an angle of 90° using a steel net. Changes in the anatomy, lignin and phytohormone content and proteome expression in the two sides of the bent root were analysed; anatomical changes, including dissimilarities and similarities to those found in poplar bent woody stem, were also considered. Key Results Compression forces at the concave side of poplar root induced the formation of reaction wood which presented a high lignin content and was associated with the induction of cambium cell activity. Auxin seemed to be the main hormone triggering lignin deposition and cell wall strengthening in the concave sides. Abscisic acid appeared to function in the water stress response induced by xylem structures and/or osmotic alterations in the compression sides, whereas gibberellins may control cell elongation and gravitropisms. Conclusions Poplar root reaction wood showed characteristics different from those produced in bent stem. Besides providing biomechanical functions, a bent root ensures water uptake and transport in the deforming condition induced by tension and compression forces by two different strategies: an increase in xylem thickness in the compressed side, and lateral root formation in the tension side.
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Affiliation(s)
- Elena De Zio
- Dipartimento di Bioscienze e Territorio, University of Molise, 86090 Pesche (IS), Italy
| | - Dalila Trupiano
- Dipartimento di Bioscienze e Territorio, University of Molise, 86090 Pesche (IS), Italy
| | - Antonio Montagnoli
- Dipartimento di Biotecnologie e Scienze della Vita, University of Insubria, 21100 Varese, Italy
| | - Mattia Terzaghi
- Dipartimento di Biotecnologie e Scienze della Vita, University of Insubria, 21100 Varese, Italy
| | - Donato Chiatante
- Dipartimento di Biotecnologie e Scienze della Vita, University of Insubria, 21100 Varese, Italy
| | - Alessandro Grosso
- Dipartimento di Biologia, University of Rome ‘Tor Vergata’, 00133 Rome, Italy
| | - Mauro Marra
- Dipartimento di Biologia, University of Rome ‘Tor Vergata’, 00133 Rome, Italy
| | - Andrea Scaloni
- Proteomics and Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Napoli, Italy
| | - Gabriella S. Scippa
- Dipartimento di Bioscienze e Territorio, University of Molise, 86090 Pesche (IS), Italy
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Park CS, Go YS, Suh MC. Cuticular wax biosynthesis is positively regulated by WRINKLED4, an AP2/ERF-type transcription factor, in Arabidopsis stems. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:257-270. [PMID: 27337244 DOI: 10.1111/tpj.13248] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 06/20/2016] [Accepted: 06/21/2016] [Indexed: 05/06/2023]
Abstract
The aerial surfaces of terrestrial plants are covered by a cuticular wax layer, which protects the plants from environmental stresses such as desiccation, high irradiance, and UV radiation. Cuticular wax deposition is regulated in an organ-specific manner; Arabidopsis stems have more than 10-fold higher wax loads than leaves. In this study, we found that WRINKLED4 (WRI4), encoding an AP2/ERF (ethylene-responsive factor) transcription factor (TF), is predominantly expressed in stem epidermis, is upregulated by salt stress, and is involved in activating cuticular wax biosynthesis in Arabidopsis stems. WRI4 harbors a transcriptional activation domain at its N-terminus, and fluorescent signals from a WRI4:eYFP construct were localized to the nuclei of tobacco leaf protoplasts. Deposition of epicuticular wax crystals on stems was reduced in wri4-1 and wri4-3 knockout mutants. Total wax loads were reduced by ~28% in wri4 stems but were not altered in wri4 siliques or leaves compared to the wild type. The levels of 29-carbon long alkanes, ketones, and secondary alcohols, which are the most abundant components of stem waxes, were significantly reduced in wri4 stems relative to the wild type. A transactivation assay in tobacco protoplasts and a chromatin immunoprecipitation (ChIP) assay showed that the expression of long-chain acyl-CoA synthetase1 (LACS1), β-ketoacyl CoA reductase1 (KCR1), PASTICCINO2 (PAS2), trans-2,3-enoyl-CoA reductase (ECR), and bifunctional wax synthase/acyl-CoA: diacylglycerol acyltransferase (WSD1) is positively regulated by direct binding of WRI4 to their promoters. Taken together, these results suggest that WRI4 is a transcriptional activator that specifically controls cuticular wax biosynthesis in Arabidopsis stems.
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Affiliation(s)
- Chan Song Park
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, 61186, Korea
| | - Young Sam Go
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, 61186, Korea
| | - Mi Chung Suh
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, 61186, Korea
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185
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Cui L, Feng K, Wang M, Wang M, Deng P, Song W, Nie X. Genome-wide identification, phylogeny and expression analysis of AP2/ERF transcription factors family in Brachypodium distachyon. BMC Genomics 2016; 17:636. [PMID: 27527343 PMCID: PMC4986339 DOI: 10.1186/s12864-016-2968-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 07/26/2016] [Indexed: 11/20/2022] Open
Abstract
Background The AP2/ERF transcription factor is one of the most important gene families in plants, which plays the vital role in regulating plant growth and development as well as in response to diverse stresses. Although AP2/ERFs have been thoroughly characterized in many plant species, little is known about this family in the model plant Brachypodium distachyon, especially those involved in the regulatory network of stress processes. Results In this study, a comprehensive genome-wide search was performed to identify AP2/ERF gene family in Brachypodium and a total of 141 BdAP2/ERFs were obtained. Phylogenetic analysis classified them into four subfamilies, of which 112 belonged to ERF, four to RAV and 24 to AP2 as well as one to soloist subfamily respectively, which was in accordance with the number of AP2 domains and gene structure analysis. Chromosomal localization, gene structure, conserved protein motif and cis-regulatory elements as well as gene duplication events analysis were further performed to systematically investigate the evolutionary features of these BdAP2/ERF genes. Furthermore, the regulatory network between BdAP2/ERF and other genes were constructed using the orthology-based method, and 39 BdAP2/ERFs were found to be involved in the regulatory network and 517 network branches were identified. The expression profiles of BdAP2/ERF during development and under diverse stresses were investigated using the available RNA-seq and microarray data and ten tissue-specific and several stress-responsive BdAP2/ERF genes were identified. Finally, 11 AP2/ERF genes were selected to validate their expressions in different tissues and under different stress treatments using RT-PCR method and results verified that these AP2/ERFs were involved in various developmental and physiological processes. Conclusions This study for the first time reported the characteristics of the BdAP2/ERF family, which will provide the invaluable information for further evolutionary and functional studies of AP2/ERF in Brachypodium, and also contribute to better understanding the molecular basis for development and stresses tolerance in this model species and beyond. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2968-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Licao Cui
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Kewei Feng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Mengxing Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Meng Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Pingchuan Deng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Weining Song
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, 712100, Shaanxi, China. .,Australia-China Joint Research Centre for Abiotic and Biotic Stress Management in Agriculture, Horticulture and Forestry, Yangling, 712100, Shaanxi, China.
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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186
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Zhou X, Zhang ZL, Park J, Tyler L, Yusuke J, Qiu K, Nam EA, Lumba S, Desveaux D, McCourt P, Kamiya Y, Sun TP. The ERF11 Transcription Factor Promotes Internode Elongation by Activating Gibberellin Biosynthesis and Signaling. PLANT PHYSIOLOGY 2016; 171:2760-70. [PMID: 27255484 PMCID: PMC4972265 DOI: 10.1104/pp.16.00154] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/30/2016] [Indexed: 05/18/2023]
Abstract
The phytohormone gibberellin (GA) plays a key role in promoting stem elongation in plants. Previous studies show that GA activates its signaling pathway by inducing rapid degradation of DELLA proteins, GA signaling repressors. Using an activation-tagging screen in a reduced-GA mutant ga1-6 background, we identified AtERF11 to be a novel positive regulator of both GA biosynthesis and GA signaling for internode elongation. Overexpression of AtERF11 partially rescued the dwarf phenotype of ga1-6 AtERF11 is a member of the ERF (ETHYLENE RESPONSE FACTOR) subfamily VIII-B-1a of ERF/AP2 transcription factors in Arabidopsis (Arabidopsis thaliana). Overexpression of AtERF11 resulted in elevated bioactive GA levels by up-regulating expression of GA3ox1 and GA20ox genes. Hypocotyl elongation assays further showed that overexpression of AtERF11 conferred elevated GA response, whereas loss-of-function erf11 and erf11 erf4 mutants displayed reduced GA response. In addition, yeast two-hybrid, coimmunoprecipitation, and transient expression assays showed that AtERF11 enhances GA signaling by antagonizing the function of DELLA proteins via direct protein-protein interaction. Interestingly, AtERF11 overexpression also caused a reduction in the levels of another phytohormone ethylene in the growing stem, consistent with recent finding showing that AtERF11 represses transcription of ethylene biosynthesis ACS genes. The effect of AtERF11 on promoting GA biosynthesis gene expression is likely via its repressive function on ethylene biosynthesis. These results suggest that AtERF11 plays a dual role in promoting internode elongation by inhibiting ethylene biosynthesis and activating GA biosynthesis and signaling pathways.
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Affiliation(s)
- Xin Zhou
- Department of Biology, Duke University, Durham, North Carolina 27705 (X.Z., Z.-L.Z., L.T., J.P., E.A.N., T.-p.S.); RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan (J.Y., Y.K.); Department of Cell and Systems Biology, University of Toronto, Ontario M5S 3B2, Canada (S.L., D.D., P.M.); Centre for the Analysis of Genome Evolution and Function, University of Toronto, Ontario M5S 3B2, Canada (D.D.); andState Key Laboratory of Genetic Engineering and Fudan Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China (K.Q.)
| | - Zhong-Lin Zhang
- Department of Biology, Duke University, Durham, North Carolina 27705 (X.Z., Z.-L.Z., L.T., J.P., E.A.N., T.-p.S.); RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan (J.Y., Y.K.); Department of Cell and Systems Biology, University of Toronto, Ontario M5S 3B2, Canada (S.L., D.D., P.M.); Centre for the Analysis of Genome Evolution and Function, University of Toronto, Ontario M5S 3B2, Canada (D.D.); andState Key Laboratory of Genetic Engineering and Fudan Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China (K.Q.)
| | - Jeongmoo Park
- Department of Biology, Duke University, Durham, North Carolina 27705 (X.Z., Z.-L.Z., L.T., J.P., E.A.N., T.-p.S.); RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan (J.Y., Y.K.); Department of Cell and Systems Biology, University of Toronto, Ontario M5S 3B2, Canada (S.L., D.D., P.M.); Centre for the Analysis of Genome Evolution and Function, University of Toronto, Ontario M5S 3B2, Canada (D.D.); andState Key Laboratory of Genetic Engineering and Fudan Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China (K.Q.)
| | - Ludmila Tyler
- Department of Biology, Duke University, Durham, North Carolina 27705 (X.Z., Z.-L.Z., L.T., J.P., E.A.N., T.-p.S.); RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan (J.Y., Y.K.); Department of Cell and Systems Biology, University of Toronto, Ontario M5S 3B2, Canada (S.L., D.D., P.M.); Centre for the Analysis of Genome Evolution and Function, University of Toronto, Ontario M5S 3B2, Canada (D.D.); andState Key Laboratory of Genetic Engineering and Fudan Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China (K.Q.)
| | - Jikumaru Yusuke
- Department of Biology, Duke University, Durham, North Carolina 27705 (X.Z., Z.-L.Z., L.T., J.P., E.A.N., T.-p.S.); RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan (J.Y., Y.K.); Department of Cell and Systems Biology, University of Toronto, Ontario M5S 3B2, Canada (S.L., D.D., P.M.); Centre for the Analysis of Genome Evolution and Function, University of Toronto, Ontario M5S 3B2, Canada (D.D.); andState Key Laboratory of Genetic Engineering and Fudan Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China (K.Q.)
| | - Kai Qiu
- Department of Biology, Duke University, Durham, North Carolina 27705 (X.Z., Z.-L.Z., L.T., J.P., E.A.N., T.-p.S.); RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan (J.Y., Y.K.); Department of Cell and Systems Biology, University of Toronto, Ontario M5S 3B2, Canada (S.L., D.D., P.M.); Centre for the Analysis of Genome Evolution and Function, University of Toronto, Ontario M5S 3B2, Canada (D.D.); andState Key Laboratory of Genetic Engineering and Fudan Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China (K.Q.)
| | - Edward A Nam
- Department of Biology, Duke University, Durham, North Carolina 27705 (X.Z., Z.-L.Z., L.T., J.P., E.A.N., T.-p.S.); RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan (J.Y., Y.K.); Department of Cell and Systems Biology, University of Toronto, Ontario M5S 3B2, Canada (S.L., D.D., P.M.); Centre for the Analysis of Genome Evolution and Function, University of Toronto, Ontario M5S 3B2, Canada (D.D.); andState Key Laboratory of Genetic Engineering and Fudan Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China (K.Q.)
| | - Shelley Lumba
- Department of Biology, Duke University, Durham, North Carolina 27705 (X.Z., Z.-L.Z., L.T., J.P., E.A.N., T.-p.S.); RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan (J.Y., Y.K.); Department of Cell and Systems Biology, University of Toronto, Ontario M5S 3B2, Canada (S.L., D.D., P.M.); Centre for the Analysis of Genome Evolution and Function, University of Toronto, Ontario M5S 3B2, Canada (D.D.); andState Key Laboratory of Genetic Engineering and Fudan Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China (K.Q.)
| | - Darrell Desveaux
- Department of Biology, Duke University, Durham, North Carolina 27705 (X.Z., Z.-L.Z., L.T., J.P., E.A.N., T.-p.S.); RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan (J.Y., Y.K.); Department of Cell and Systems Biology, University of Toronto, Ontario M5S 3B2, Canada (S.L., D.D., P.M.); Centre for the Analysis of Genome Evolution and Function, University of Toronto, Ontario M5S 3B2, Canada (D.D.); andState Key Laboratory of Genetic Engineering and Fudan Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China (K.Q.)
| | - Peter McCourt
- Department of Biology, Duke University, Durham, North Carolina 27705 (X.Z., Z.-L.Z., L.T., J.P., E.A.N., T.-p.S.); RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan (J.Y., Y.K.); Department of Cell and Systems Biology, University of Toronto, Ontario M5S 3B2, Canada (S.L., D.D., P.M.); Centre for the Analysis of Genome Evolution and Function, University of Toronto, Ontario M5S 3B2, Canada (D.D.); andState Key Laboratory of Genetic Engineering and Fudan Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China (K.Q.)
| | - Yuji Kamiya
- Department of Biology, Duke University, Durham, North Carolina 27705 (X.Z., Z.-L.Z., L.T., J.P., E.A.N., T.-p.S.); RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan (J.Y., Y.K.); Department of Cell and Systems Biology, University of Toronto, Ontario M5S 3B2, Canada (S.L., D.D., P.M.); Centre for the Analysis of Genome Evolution and Function, University of Toronto, Ontario M5S 3B2, Canada (D.D.); andState Key Laboratory of Genetic Engineering and Fudan Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China (K.Q.)
| | - Tai-Ping Sun
- Department of Biology, Duke University, Durham, North Carolina 27705 (X.Z., Z.-L.Z., L.T., J.P., E.A.N., T.-p.S.); RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan (J.Y., Y.K.); Department of Cell and Systems Biology, University of Toronto, Ontario M5S 3B2, Canada (S.L., D.D., P.M.); Centre for the Analysis of Genome Evolution and Function, University of Toronto, Ontario M5S 3B2, Canada (D.D.); andState Key Laboratory of Genetic Engineering and Fudan Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China (K.Q.)
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Chaabouni S, Pirrello J, Liu M, El-Sharkawy I, Roustan JP, Bouzayen M. Identification and functional characterization of two HOOKLESS genes in Tomato (Solanum lycopersicum). JOURNAL OF PLANT PHYSIOLOGY 2016; 200:76-81. [PMID: 27343715 DOI: 10.1016/j.jplph.2016.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 05/27/2016] [Accepted: 05/30/2016] [Indexed: 06/06/2023]
Abstract
The apical hook of dark-grown dicotyledonous plants results from asymmetric growth of the inner and outer sides of the upper part of the hypocotyl. This protective structure prevents damage of the shoot apical meristem and the young leaves as the seedling pushes through the soil. HOOKLESS (HLS1) of Arabidopsis was recognised as an ethylene response gene whose product is required for hook formation. We cloned two cDNAs from tomato, Sl-HLS1 and Sl-HLS2, and showed through the complementation of the Arabidopsis hls1 mutant that the encoded proteins are functional orthologs of At-HLS1. The genomic clones of Sl-HLS1 and Sl-HLS2 showed similar structure with two introns and three exons. While the data indicate complete functional redundancy between the two tomato HLS genes, only the expression of Sl-HLS2 is regulated by ethylene and auxin and the ethylene-induced expression of Sl-HLS2 is localised in the outer side of the hook while the auxin-responsive expression is not restricted to a specific side of the hook. 1-MCP, an inhibitor of ethylene signalling, inhibited auxin-enhanced accumulation of Sl-HLS2 mRNA in the apical hook suggesting that regulation of Sl-HLS2 by auxin is ethylene-dependent. The overexpression of tomato Sl-HLS1 and Sl-HLS2 in Arabidopsis confers hypersensitivity to ethylene. The data presented bring further insight into the complex ethylene-auxin interplay in hook formation.
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Affiliation(s)
- Salma Chaabouni
- University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruits, Avenue de l'Agrobiopole BP 32607, Castanet-Tolosan F-31326, France; INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan F-31326, France.
| | - Julien Pirrello
- University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruits, Avenue de l'Agrobiopole BP 32607, Castanet-Tolosan F-31326, France; INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan F-31326, France
| | - Mingchun Liu
- University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruits, Avenue de l'Agrobiopole BP 32607, Castanet-Tolosan F-31326, France; INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan F-31326, France
| | - Islam El-Sharkawy
- University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruits, Avenue de l'Agrobiopole BP 32607, Castanet-Tolosan F-31326, France; INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan F-31326, France
| | - Jean-Paul Roustan
- University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruits, Avenue de l'Agrobiopole BP 32607, Castanet-Tolosan F-31326, France; INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan F-31326, France
| | - Mondher Bouzayen
- University of Toulouse, INPT, Laboratory of Genomics and Biotechnology of Fruits, Avenue de l'Agrobiopole BP 32607, Castanet-Tolosan F-31326, France; INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan F-31326, France
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Murphy E, Vu LD, Van den Broeck L, Lin Z, Ramakrishna P, van de Cotte B, Gaudinier A, Goh T, Slane D, Beeckman T, Inzé D, Brady SM, Fukaki H, De Smet I. RALFL34 regulates formative cell divisions in Arabidopsis pericycle during lateral root initiation. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4863-75. [PMID: 27521602 PMCID: PMC4983113 DOI: 10.1093/jxb/erw281] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In plants, many signalling molecules, such as phytohormones, miRNAs, transcription factors, and small signalling peptides, drive growth and development. However, very few small signalling peptides have been shown to be necessary for lateral root development. Here, we describe the role of the peptide RALFL34 during early events in lateral root development, and demonstrate its specific importance in orchestrating formative cell divisions in the pericycle. Our results further suggest that this small signalling peptide acts on the transcriptional cascade leading to a new lateral root upstream of GATA23, an important player in lateral root formation. In addition, we describe a role for ETHYLENE RESPONSE FACTORs (ERFs) in regulating RALFL34 expression. Taken together, we put forward RALFL34 as a new, important player in lateral root initiation.
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Affiliation(s)
- Evan Murphy
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
| | - Lam Dai Vu
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium Department of Medical Protein Research, VIB, 9000 Ghent, Belgium Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Lisa Van den Broeck
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Zhefeng Lin
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
| | - Priya Ramakrishna
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
| | - Brigitte van de Cotte
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Allison Gaudinier
- Department of Plant Biology and Genome Center, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Tatsuaki Goh
- Department of Biology, Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Daniel Slane
- Department of Cell Biology, Max Planck Institute for Developmental Biology, D- 72076 Tübingen, Germany
| | - Tom Beeckman
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Hidehiro Fukaki
- Department of Biology, Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Ive De Smet
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium Centre for Plant Integrative Biology, University of Nottingham, Loughborough LE12 5RD, UK
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189
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Zhang H, Hong Y, Huang L, Li D, Song F. Arabidopsis AtERF014 acts as a dual regulator that differentially modulates immunity against Pseudomonas syringae pv. tomato and Botrytis cinerea. Sci Rep 2016; 6:30251. [PMID: 27445230 PMCID: PMC4957219 DOI: 10.1038/srep30251] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 07/01/2016] [Indexed: 11/09/2022] Open
Abstract
ERF transcription factors play critical roles in plant immune responses. Here, we report the function of AtERF014, a nucleus-localized transcriptional activator, in Arabidopsis immunity. Expression of AtERF014 was induced by Pseudomonas syringae pv. tomato (Pst) and Botrytis cinerea (Bc). AtERF014-overexpressing (OE) plants displayed increased Pst resistance but decreased Bc resistance, whereas AtERF014-RNAi plants exhibited decreased Pst resistance but increased Bc resistance. After Pst infection, expression of salicylic acid (SA)-responsive genes AtPR1 and AtPR5 in AtERF014-OE plants and of a jasmonic acid/ethylene-responsive gene AtPDF1.2 in AtERF014-RNAi plants was intensified but expression of AtPDF1.2 in AtERF014-OE plants and of AtPR1 and AtPR5 in AtERF014-RNAi plants was weakened. After Bc infection, expression of AtPR1 and AtPR5 in AtERF014-OE plants was attenuated but expression of AtPR1, AtPR5 and AtPDF1.2 in AtERF014-RNAi plants was strengthened. Pathogen- and flg22-induced ROS burst, expression of PTI genes and SA-induced defense were partially suppressed in AtERF014-RNAi plants, whereas pathogen-induced ROS and flg22-induced immune response were strengthened in AtER014-OE plants. Altered expression of AtERR014 affected expression of pectin biosynthetic genes and pectin content in AtERF014-RNAi plants was decreased. These data demonstrate that AtERF014 acts as a dual regulator that differentially modulates immunity against Pst and Bc in Arabidopsis.
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Affiliation(s)
- Huijuan Zhang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, P.R. China
| | - Yongbo Hong
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, P.R. China
| | - Lei Huang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, P.R. China
| | - Dayong Li
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, P.R. China
| | - Fengming Song
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, P.R. China
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Zhang H, Li A, Zhang Z, Huang Z, Lu P, Zhang D, Liu X, Zhang ZF, Huang R. Ethylene Response Factor TERF1, Regulated by ETHYLENE-INSENSITIVE3-like Factors, Functions in Reactive Oxygen Species (ROS) Scavenging in Tobacco (Nicotiana tabacum L.). Sci Rep 2016; 6:29948. [PMID: 27435661 PMCID: PMC4951782 DOI: 10.1038/srep29948] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 06/27/2016] [Indexed: 12/13/2022] Open
Abstract
The phytohormone ethylene plays a crucial role in the production and accumulation of reactive oxygen species (ROS) in plants under stress conditions. Ethylene response factors (ERFs) are important ethylene-signaling regulators functioning in plant defense responses against biotic and abiotic stresses. However, the roles of ERFs during plant adapting to ROS stress have not yet been well documented. Our studies previously reported that a tomato ERF transcription factor TERF1 functions in the regulation of plant ethylene responses and stress tolerance. Here, we report our findings regarding the roles of TERF1 in ROS scavenging. In this study, we revealed that the transcription of TERF1 is regulated by upstream EIN3-like (EIN3, ethylene-insensitive 3) regulators LeEIL3 and LeEIL4 in tomato (Solanum lycopersicum), and is also inducible by exogenous applied ROS-generating reagents. Ectopic expression of TERF1 in tobacco promoted the expression of genes involved in oxidative stress responses, including carbonic anhydrase functioning in hypersensitive defense, catalase and glutathione peroxidase catalyzing oxidative reactions, and GDP-D-mannose pyrophosphorylase functioning in ascorbic acid biosynthesis, reduced the ROS content induced by ethylene treatment, and enhanced stress tolerance of tobacco seedlings to hydrogen peroxide (H2O2). Cumulatively, these findings suggest that TERF1 is an ethylene inducible factor regulating ROS scavenging during stress responses.
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Affiliation(s)
- Hongbo Zhang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Ang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhijin Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zejun Huang
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Pingli Lu
- Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Dingyu Zhang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Xinmin Liu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Zhong-Feng Zhang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Rongfeng Huang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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191
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Zhang Y, Barthe G, Grosser JW, Wang N. Transcriptome analysis of root response to citrus blight based on the newly assembled Swingle citrumelo draft genome. BMC Genomics 2016; 17:485. [PMID: 27391971 PMCID: PMC4938905 DOI: 10.1186/s12864-016-2779-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 05/26/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Citrus blight is a citrus tree overall decline disease and causes serious losses in the citrus industry worldwide. Although it was described more than one hundred years ago, its causal agent remains unknown and its pathophysiology is not well determined, which hampers our understanding of the disease and design of suitable disease management. RESULTS In this study, we sequenced and assembled the draft genome for Swingle citrumelo, one important citrus rootstock. The draft genome is approximately 280 Mb, which covers 74 % of the estimated Swingle citrumelo genome and the average coverage is around 15X. The draft genome of Swingle citrumelo enabled us to conduct transcriptome analysis of roots of blight and healthy Swingle citrumelo using RNA-seq. The RNA-seq was reliable as evidenced by the high consistence of RNA-seq analysis and quantitative reverse transcription PCR results (R(2) = 0.966). Comparison of the gene expression profiles between blight and healthy root samples revealed the molecular mechanism underneath the characteristic blight phenotypes including decline, starch accumulation, and drought stress. The JA and ET biosynthesis and signaling pathways showed decreased transcript abundance, whereas SA-mediated defense-related genes showed increased transcript abundance in blight trees, suggesting unclassified biotrophic pathogen was involved in this disease. CONCLUSIONS Overall, the Swingle citrumelo draft genome generated in this study will advance our understanding of plant biology and contribute to the citrus breeding. Transcriptome analysis of blight and healthy trees deepened our understanding of the pathophysiology of citrus blight.
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Affiliation(s)
- Yunzeng Zhang
- />Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL USA
| | - Gary Barthe
- />Citrus Research and Education Center, Department of Horticultural Sciences, University of Florida, Lake Alfred, FL USA
| | - Jude W. Grosser
- />Citrus Research and Education Center, Department of Horticultural Sciences, University of Florida, Lake Alfred, FL USA
| | - Nian Wang
- />Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL USA
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192
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Ji AJ, Luo HM, Xu ZC, Zhang X, Zhu YJ, Liao BS, Yao H, Song JY, Chen SL. Genome-Wide Identification of the AP2/ERF Gene Family Involved in Active Constituent Biosynthesis in. THE PLANT GENOME 2016; 9. [PMID: 27898817 DOI: 10.3835/plantgenome2015.08.0077] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Tanshinones and phenolic acids are the major bioactive constituents in the traditional medicinal crop ; however, transcription factors (TFs) are seldom investigated with regard to their regulation of the biosynthesis of these compounds. Here a complete overview of the APETALA2/ethylene-responsive factor (AP2/ERF) transcription factor family in is provided, including phylogeny, gene structure, conserved motifs, and gene expression profiles of different organs (root, stem, leaf, flower) and root tissues (periderm, phloem, xylem). In total, 170 AP2/ERF genes were identified and divided into five relatively conserved subfamilies, including AP2 (25 genes), DREB (61 genes), ethylene responsive factor (ERF; 79 genes), RAV (4 genes), and Soloist (1 gene). According to the distribution of bioactive constituents and the expression patterns of AP2/ERF genes in different organs and root tissues, the genes related to the biosynthesis of bioactive constituents were selected. On the basis of quantitative real-time polymerase chain reaction (qRT-PCR) analysis, coexpression analysis, and the prediction of -regulatory elements in the promoters, we propose that two genes ( and ) regulate tanshinone biosynthesis and two genes ( and ) participate in controlling phenolic acid biosynthesis. The genes related to tanshinone biosynthesis belong to the ERF-B3 subgroup. In contrast, the genes predicted to regulate phenolic acid biosynthesis belong to the ERF-B1 and ERF-B4 subgroups. These results provide a foundation for future functional characterization of AP2/ERF genes to enhance the biosynthesis of the bioactive compounds of .
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193
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Huang Y, Zhang BL, Sun S, Xing GM, Wang F, Li MY, Tian YS, Xiong AS. AP2/ERF Transcription Factors Involved in Response to Tomato Yellow Leaf Curly Virus in Tomato. THE PLANT GENOME 2016; 9. [PMID: 27898839 DOI: 10.3835/plantgenome2015.09.0082] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Tomato yellow leaf curly virus (TYLCV), transmitted by the whitefly (), causes leaf curling and yellowing, plant dwarfism, and growth inhibition in tomato ( L.). The APETALA2 (AP2) and ethylene response factor (ERF) transcription factor (TF) family, the largest plant-specific TF family, was identified to function in plant development and pathogen defense. Our study aimed to analyze the mechanism underlying the function of ERF (SlERF) TFs in response to TYLCV infection and improve useful information to increase the resistance to TYLCV in tomato. A total of 22 tomato AP2/ERF TFs in response to TYLCV were identified according to transcriptome database. Five ERF-B3 TFs were identified in cultivars Hongbeibei (highly resistant), Zheza-301, Zhefen-702 (both resistant), Jinpeng-1, and Xianke-6 (both susceptible). Interaction network indicated that SlERF TFs could interact with mitogen-activated protein kinase (MAPK). Expression profiles of five ERF-B3 genes (, , , , and ) were detected by quantitative real-time-polymerase chain reaction (qRT-PCR) after TYLCV infection in five tomato cultivars. expression was upregulated in five tomato cultivars. The expressions of three genes (, , and ) were upregulated in Zheza-301 and Zhefen-702. and expressions were downregulated in Hongbeibei and Xianke-6, respectively. Yeast one-hybrid showed that the GCC-box binding ability of ERF-B3 TFs differed in resistant and susceptible tomato cultivars. Expression profiles were related to the GCC-box binding ability of SlERF TFs in resistant and susceptible tomato cultivars. The defense mechanism underlying the tomato's response to TYLCV involved a complicated network, which provided important information for us in breeding and genetic analysis.
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Han YC, Kuang JF, Chen JY, Liu XC, Xiao YY, Fu CC, Wang JN, Wu KQ, Lu WJ. Banana Transcription Factor MaERF11 Recruits Histone Deacetylase MaHDA1 and Represses the Expression of MaACO1 and Expansins during Fruit Ripening. PLANT PHYSIOLOGY 2016; 171:1070-84. [PMID: 27208241 PMCID: PMC4902611 DOI: 10.1104/pp.16.00301] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 04/02/2016] [Indexed: 05/18/2023]
Abstract
Phytohormone ethylene controls diverse developmental and physiological processes such as fruit ripening via modulation of ethylene signaling pathway. Our previous study identified that ETHYLENE RESPONSE FACTOR11 (MaERF11), a transcription factor in the ethylene signaling pathway, negatively regulates the ripening of banana, but the mechanism for the MaERF11-mediated transcriptional regulation remains largely unknown. Here we showed that MaERF11 has intrinsic transcriptional repression activity in planta. Electrophoretic mobility shift assay and chromatin immunoprecipitation analyses demonstrated that MaERF11 binds to promoters of three ripening-related Expansin genes, MaEXP2, MaEXP7 and MaEXP8, as well as an ethylene biosynthetic gene MaACO1, via the GCC-box motif. Furthermore, expression patterns of MaACO1, MaEXP2, MaEXP7, and MaEXP8 genes are correlated with the changes of histone H3 and H4 acetylation level during fruit ripening. Moreover, we found that MaERF11 physically interacts with a histone deacetylase, MaHDA1, which has histone deacetylase activity, and the interaction significantly strengthens the MaERF11-mediated transcriptional repression of MaACO1 and Expansins Taken together, these findings suggest that MaERF11 may recruit MaHDA1 to its target genes and repress their expression via histone deacetylation.
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Affiliation(s)
- Yan-Chao Han
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China (Y.-C.H., J.-F.K., J.-Y.C., Y.-Y.X., C.-C.F., J.-N.W., W.-J.L.); Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China (X.-C.L.); and Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan (K.-Q.W.)
| | - Jian-Fei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China (Y.-C.H., J.-F.K., J.-Y.C., Y.-Y.X., C.-C.F., J.-N.W., W.-J.L.); Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China (X.-C.L.); and Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan (K.-Q.W.)
| | - Jian-Ye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China (Y.-C.H., J.-F.K., J.-Y.C., Y.-Y.X., C.-C.F., J.-N.W., W.-J.L.); Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China (X.-C.L.); and Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan (K.-Q.W.)
| | - Xun-Cheng Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China (Y.-C.H., J.-F.K., J.-Y.C., Y.-Y.X., C.-C.F., J.-N.W., W.-J.L.); Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China (X.-C.L.); and Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan (K.-Q.W.)
| | - Yun-Yi Xiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China (Y.-C.H., J.-F.K., J.-Y.C., Y.-Y.X., C.-C.F., J.-N.W., W.-J.L.); Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China (X.-C.L.); and Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan (K.-Q.W.)
| | - Chang-Chun Fu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China (Y.-C.H., J.-F.K., J.-Y.C., Y.-Y.X., C.-C.F., J.-N.W., W.-J.L.); Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China (X.-C.L.); and Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan (K.-Q.W.)
| | - Jun-Ning Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China (Y.-C.H., J.-F.K., J.-Y.C., Y.-Y.X., C.-C.F., J.-N.W., W.-J.L.); Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China (X.-C.L.); and Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan (K.-Q.W.)
| | - Ke-Qiang Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China (Y.-C.H., J.-F.K., J.-Y.C., Y.-Y.X., C.-C.F., J.-N.W., W.-J.L.); Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China (X.-C.L.); and Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan (K.-Q.W.)
| | - Wang-Jin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China (Y.-C.H., J.-F.K., J.-Y.C., Y.-Y.X., C.-C.F., J.-N.W., W.-J.L.); Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China (X.-C.L.); and Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan (K.-Q.W.)
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Rahimi M, Kordrostami M, Maleki M, ModaresKia M. Investigating the effect of drought stress on expression of WRKY1 and EREBP1 genes and antioxidant enzyme activities in lemon balm (Melissa Officinalis L.). 3 Biotech 2016; 6:99. [PMID: 28330169 PMCID: PMC4826382 DOI: 10.1007/s13205-016-0416-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Accepted: 03/21/2016] [Indexed: 11/30/2022] Open
Abstract
Drought stress is a severe environmental constraint to plant productivity. In this study, gene expression of WRKY1 and EREBP1 genes and activity of two enzymes were investigated in two genotypes, G9 (as resistance) and G12 (as susceptible) of 10 days-old lemon balm seedlings. Experiments were done according to factorial design on the base of completely randomized design with three replications for expression analysis and enzyme assays. Seedlings were cultured in MS medium suspensions, including 0, 3, 6, 12 and 15 % w/v PEG 6000. Leaf samples were subsequently collected at 0, 3, 6, 24, 48, 72 h after culture. According to the results of the enzyme assay, SOD activity in resistant genotype was more than in sensitive one. POD activity was high in G9 in severe drought condition and in G12 this activity was increased at initial times of drought stress. The survey results revealed that the expression levels of both genes, EREBP1 and WRKY1, in G9 variety were more than G12, and in this respect we can say that the G9 variety is more resistant to drought.
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Affiliation(s)
- Mehdi Rahimi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, End of Haft Bagh-e-Alavi Highway Knowledge Paradise, P.O. Box 76315-117, Kerman, 7631133131 Iran
| | - Mojtaba Kordrostami
- Department of Biotechnology, Faculty of Agricultural Sciences, University of Guilan, P.O. Box 41635-1314, Rasht, Iran
| | - Mahmood Maleki
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, End of Haft Bagh-e-Alavi Highway Knowledge Paradise, P.O. Box 76315-117, Kerman, 7631133131 Iran
| | - Mohsen ModaresKia
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, End of Haft Bagh-e-Alavi Highway Knowledge Paradise, P.O. Box 76315-117, Kerman, 7631133131 Iran
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196
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Discriminative gene co-expression network analysis uncovers novel modules involved in the formation of phosphate deficiency-induced root hairs in Arabidopsis. Sci Rep 2016; 6:26820. [PMID: 27220366 PMCID: PMC4879556 DOI: 10.1038/srep26820] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 05/10/2016] [Indexed: 12/22/2022] Open
Abstract
Cell fate and differentiation in the Arabidopsis root epidermis are genetically defined but remain plastic to environmental signals such as limited availability of inorganic phosphate (Pi). Root hairs of Pi-deficient plants are more frequent and longer than those of plants grown under Pi-replete conditions. To dissect genes involved in Pi deficiency-induced root hair morphogenesis, we constructed a co-expression network of Pi-responsive genes against a customized database that was assembled from experiments in which differentially expressed genes that encode proteins with validated functions in root hair development were over-represented. To further filter out less relevant genes, we combined this procedure with a search for common cis-regulatory elements in the promoters of the selected genes. In addition to well-described players and processes such as auxin signalling and modifications of primary cell walls, we discovered several novel aspects in the biology of root hairs induced by Pi deficiency, including cell cycle control, putative plastid-to-nucleus signalling, pathogen defence, reprogramming of cell wall-related carbohydrate metabolism, and chromatin remodelling. This approach allows the discovery of novel of aspects of a biological process from transcriptional profiles with high sensitivity and accuracy.
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197
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Hopper DW, Ghan R, Schlauch KA, Cramer GR. Transcriptomic network analyses of leaf dehydration responses identify highly connected ABA and ethylene signaling hubs in three grapevine species differing in drought tolerance. BMC PLANT BIOLOGY 2016; 16:118. [PMID: 27215785 PMCID: PMC4877820 DOI: 10.1186/s12870-016-0804-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 05/17/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND Grapevine is a major food crop that is affected by global climate change. Consistent with field studies, dehydration assays of grapevine leaves can reveal valuable information of the plant's response at physiological, transcript, and protein levels. There are well-known differences in grapevine rootstocks responses to dehydration. We used time-series transcriptomic approaches combined with network analyses to elucidate and identify important physiological processes and network hubs that responded to dehydration in three different grapevine species differing in their drought tolerance. RESULTS Transcriptomic analyses of the leaves of Cabernet Sauvignon, Riparia Gloire, and Ramsey were evaluated at different times during a 24-h controlled dehydration. Analysis of variance (ANOVA) revealed that approximately 11,000 transcripts changed significantly with respect to the genotype x treatment interaction term and approximately 6000 transcripts changed significantly according to the genotype x treatment x time interaction term indicating massive differential changes in gene expression over time. Standard analyses determined substantial effects on the transcript abundance of genes involved in the metabolism and signaling of two known plant stress hormones, abscisic acid (ABA) and ethylene. ABA and ethylene signaling maps were constructed and revealed specific changes in transcript abundance that were associated with the known drought tolerance of the genotypes including genes such as VviABI5, VviABF2, VviACS2, and VviWRKY22. Weighted-gene coexpression network analysis (WGCNA) confirmed these results. In particular, WGCNA identified 30 different modules, some of which had highly enriched gene ontology (GO) categories for photosynthesis, phenylpropanoid metabolism, ABA and ethylene signaling. The ABA signaling transcription factors, VviABI5 and VviABF2, were highly connected hubs in two modules, one being enriched in gaseous transport and the other in ethylene signaling. VviABI5 was distinctly correlated with an early response and high expression for the drought tolerant Ramsey and with little response from the drought sensitive Riparia Gloire. These ABA signaling transcription factors were highly connected to VviSnRK1 and other gene hubs associated with sugar, ethylene and ABA signaling. CONCLUSION A leaf dehydration assay provided transcriptomic evidence for differential leaf responses to dehydration between genotypes differing in their drought tolerance. WGCNA proved to be a powerful network analysis approach; it identified 30 distinct modules (networks) with highly enriched GO categories and enabled the identification of gene hubs in these modules. Some of these genes were highly connected hubs in both the ABA and ethylene signaling pathways, supporting the hypothesis that there is substantial crosstalk between the two hormone pathways. This study identifies solid gene candidates for future investigations of drought tolerance in grapevine.
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Affiliation(s)
- Daniel W Hopper
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Ryan Ghan
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Karen A Schlauch
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Grant R Cramer
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA.
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198
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Anh Tuan P, Bai S, Saito T, Imai T, Ito A, Moriguchi T. Involvement of EARLY BUD-BREAK, an AP2/ERF Transcription Factor Gene, in Bud Break in Japanese Pear (Pyrus pyrifolia Nakai) Lateral Flower Buds: Expression, Histone Modifications and Possible Target Genes. PLANT & CELL PHYSIOLOGY 2016; 57:1038-47. [PMID: 26940832 DOI: 10.1093/pcp/pcw041] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 02/19/2016] [Indexed: 05/05/2023]
Abstract
In the Japanese pear (Pyrus pyrifolia Nakai) 'Kosui', three developmental stages of lateral flower buds have been proposed to occur during ecodormancy to the flowering phase, i.e. rapid enlargement, sprouting and flowering. Here, we report an APETALA2/ethylene-responsive factor (AP2/ERF) transcription factor gene, named pear EARLY BUD-BREAK (PpEBB), which was highly expressed during the rapid enlargement stage occurring prior to the onset of bud break in flower buds. Gene expression analysis revealed that PpEBB expression was dramatically increased during the rapid enlargement stage in three successive growing seasons. PpEBB transcript levels peaked 1 week prior to onset of bud break in 'Kosui' potted plants treated with hydrogen cyanamide or water under forcing conditions. Chromatin immunoprecipitation-quantitative PCR showed that higher levels of active histone modifications (trimethylation of the histone H3 tail at Lys4) in the 5'-upstream and start codon regions of the PpEBB gene were associated with the induced expression level of PpEBB during the rapid enlargement stage. In addition, we provide evidence that PpEBB may interact with and regulate pear four D-type cyclin (PpCYCD3) genes during bud break in 'Kosui' lateral flower buds. PpEBB significantly increased the promoter activities of four PpCYCD3 genes in a dual-luciferase assay using tobacco leaves. Taken together, our findings uncovered aspects of the bud break regulatory mechanism in the Japanese pear and provided further evidence that the EBB family plays an important role in bud break in perennial plants.
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Affiliation(s)
- Pham Anh Tuan
- NARO Institute of Fruit Tree Science, Tsukuba, Ibaraki, 305-8605 Japan
| | - Songling Bai
- NARO Institute of Fruit Tree Science, Tsukuba, Ibaraki, 305-8605 Japan Present address: Institute of Fruit Science, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Takanori Saito
- NARO Institute of Fruit Tree Science, Tsukuba, Ibaraki, 305-8605 Japan Present address: Graduate School of Horticulture, Chiba University, Matsudo, Chiba, 271-8510 Japan
| | - Tsuyoshi Imai
- NARO Institute of Fruit Tree Science, Tsukuba, Ibaraki, 305-8605 Japan
| | - Akiko Ito
- NARO Institute of Fruit Tree Science, Tsukuba, Ibaraki, 305-8605 Japan
| | - Takaya Moriguchi
- NARO Institute of Fruit Tree Science, Tsukuba, Ibaraki, 305-8605 Japan
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199
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Sun D, Nandety RS, Zhang Y, Reid MS, Niu L, Jiang CZ. A petunia ethylene-responsive element binding factor, PhERF2, plays an important role in antiviral RNA silencing. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3353-65. [PMID: 27099376 PMCID: PMC4892726 DOI: 10.1093/jxb/erw155] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Virus-induced RNA silencing is involved in plant antiviral defense and requires key enzyme components, including RNA-dependent RNA polymerases (RDRs), Dicer-like RNase III enzymes (DCLs), and Argonaute proteins (AGOs). However, the transcriptional regulation of these critical components is largely unknown. In petunia (Petunia hybrida), an ethylene-responsive element binding factor, PhERF2, is induced by Tobacco rattle virus (TRV) infection. Inclusion of a PhERF2 fragment in a TRV silencing construct containing reporter fragments of phytoene desaturase (PDS) or chalcone synthase (CHS) substantially impaired silencing efficiency of both the PDS and CHS reporters. Silencing was also impaired in PhERF2- RNAi lines, where TRV-PhPDS infection did not show the expected silencing phenotype (photobleaching). In contrast, photobleaching in response to infiltration with the TRV-PhPDS construct was enhanced in plants overexpressing PhERF2 Transcript abundance of the RNA silencing-related genes RDR2, RDR6, DCL2, and AGO2 was lower in PhERF2-silenced plants but higher in PhERF2-overexpressing plants. Moreover, PhERF2-silenced lines showed higher susceptibility to Cucumber mosaic virus (CMV) than wild-type (WT) plants, while plants overexpressing PhERF2 exhibited increased resistance. Interestingly, growth and development of PhERF2-RNAi lines were substantially slower, whereas the overexpressing lines were more vigorous than the controls. Taken together, our results indicate that PhERF2 functions as a positive regulator in antiviral RNA silencing.
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Affiliation(s)
- Daoyang Sun
- Department of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi 712100, China Department of Plant Sciences, University of California Davis, Davis, CA 95616, USA
| | - Raja Sekhar Nandety
- Department of Plant Pathology, University of California Davis, Davis, CA 95616, USA
| | - Yanlong Zhang
- Department of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Michael S Reid
- Department of Plant Sciences, University of California Davis, Davis, CA 95616, USA
| | - Lixin Niu
- Department of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Cai-Zhong Jiang
- Crops Pathology and Genetic Research Unit, United States Department of Agriculture, Agricultural Research Service, Davis, CA 95616, USA
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200
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Chialva C, Eichler E, Grissi C, Muñoz C, Gomez-Talquenca S, Martínez-Zapater JM, Lijavetzky D. Expression of grapevine AINTEGUMENTA-like genes is associated with variation in ovary and berry size. PLANT MOLECULAR BIOLOGY 2016; 91:67-80. [PMID: 26843119 DOI: 10.1007/s11103-016-0443-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 01/23/2016] [Indexed: 06/05/2023]
Abstract
Fruit size is a highly important trait for most fruit and vegetable crops. This trait has been a main selection target and could be involved in divergent selection processes leading to the differentiation between modern table and wine cultivars. Even though its determination is highly influenced by cultural practices, several regions within the grapevine genome have been identified affecting berry size, either directly or indirectly through their effect on seed content. Using grapevine seeded cultivars, we have analyzed the relationship between ovary cell number and the final size of ovaries and berry fruits. We also performed the characterization of the grapevine AINTEGUMENTA-LIKE family, since it is well reported in Arabidopsis that AINTEGUMENTA (ANT) regulates cell proliferation and organ growth in flower organ primordia by maintaining the meristematic competence of cells during organogenesis. Here we show that orthologous grapevine gene expression associate with flower developmental stages suggesting a similar biological role for this gene family in this species. Moreover, we detected a correlation between those organs size and the level of expression of VviANT1 the grapevine homolog of AtANT. This grapevine gene also co-localizes in linkage group 18 with the confidence interval of a previously detected QTL for berry size. Thus our results suggest the involvement of ANT in the regulation of berry size in grapevine.
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Affiliation(s)
- Constanza Chialva
- Instituto de Biología Agrícola de Mendoza (IBAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (FCA-UNCuyo), Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina
| | - Estefanía Eichler
- Instituto de Biología Agrícola de Mendoza (IBAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (FCA-UNCuyo), Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina
| | - Cecilia Grissi
- Instituto de Biología Agrícola de Mendoza (IBAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (FCA-UNCuyo), Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina
| | - Claudio Muñoz
- Instituto de Biología Agrícola de Mendoza (IBAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (FCA-UNCuyo), Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina
| | | | - José M Martínez-Zapater
- Instituto de Ciencias de la Vid y del Vino (CSIC-Universidad de La Rioja-Gobierno de La Rioja), Logroño, Spain
| | - Diego Lijavetzky
- Instituto de Biología Agrícola de Mendoza (IBAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (FCA-UNCuyo), Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina.
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