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Shen QJ, Xing GS, Liu ZY, Li EQ, Zhao BC, Zheng YC, Cao Q, Zhang T, Zhang JL. [Surgical treatment of the complex bicondylar tibial plateau fracture using a midline longitudinal incision]. Zhonghua Yi Xue Za Zhi 2020; 100:1260-1263. [PMID: 32344500 DOI: 10.3760/cma.j.cn112137-20190904-01962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To explore the outcomes after treatment of the complex bicondylar tibial plateau fracture through a midline longitudinal approach. Methods: A review of fifteen patients with an average age of (51.3±12.3) years old (range17-65yers;7 males, 8 females) surgically treated from October 2013 to Febuary 2018 were included. Sahatker Ⅴ in 10, Sahatker Ⅵ in 5; fractures of medial and lateral columns in 9, fractures of three columns in 6. All the patients were adopt a midline longitudinal approach combined with the posterior approach and bone grafting were conducted. Results: All cases were followed-up for (14.4±3.8) month, with an average of 12-24 month. All patients gained bone union during 12-16 weeks after operation, with an average of (15.2±1.3) weeks. There were significant differeces in both tibial plateau angle and posterior slope angle on radiography between preoperation and postoperation (P<0.05), there were no significant differeces in either tibial plateau angle or posterior slope angle on radiography between immediate postoperation and 12 months postoperation (P>0.05). At final follow-up,both the Lachman test and the Pivot-shift test were negative. All patients had complete knee extension, knee flexion angle 100°-135°, with an average of 117.7°±11.3°. The HSS (the Hospital for Special Surgery) score were 66-98, with an average of 85.1±9.3, six cases were excellent and seven cases were good, two cases was fair, the excellent and good rate was 86.7%. The Rasmussen radiological evaluationre were 9-18, with an average of 15.1±2.5, three cases were excellent and eleven cases were good, one cases was fair, the excellent and good rate was 93.3%. 1 patient had fat liquefactionof in antero incision, and got good outcomes after debridement dressing. Conclusion: The treatment of the complex bicondylar tibial plateau fracture through a midline longitudinal approach combined with the posterior approach can result in good exposure and satisfying knee function in short-term.
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Affiliation(s)
- Q J Shen
- Department of Orthopaedics, Tianjin Hospital, Tianjin 300211 China
| | - G S Xing
- Tianjin Institute of Orthopedics, Tianjin, 300050 China
| | - Z Y Liu
- Department of Orthopaedics, Tianjin Hospital, Tianjin 300211 China
| | - E Q Li
- Department of Orthopaedics, Tianjin Hospital, Tianjin 300211 China
| | - B C Zhao
- Department of Orthopaedics, Tianjin Hospital, Tianjin 300211 China
| | - Y C Zheng
- Department of Orthopaedics, Tianjin Hospital, Tianjin 300211 China
| | - Q Cao
- Department of Orthopaedics, Tianjin Hospital, Tianjin 300211 China
| | - T Zhang
- Department of Orthopaedics, Tianjin Hospital, Tianjin 300211 China
| | - J L Zhang
- Department of Orthopaedics, Tianjin Hospital, Tianjin 300211 China
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Jiang C, Shen QJ, Wang B, He B, Xiao S, Chen L, Yu T, Ke X, Zhong Q, Fu J, Chen Y, Wang L, Yin F, Zhang D, Ghidan W, Huang X, Cheng Z. Transcriptome analysis of WRKY gene family in Oryza officinalis Wall ex Watt and WRKY genes involved in responses to Xanthomonas oryzae pv. oryzae stress. PLoS One 2017; 12:e0188742. [PMID: 29190793 PMCID: PMC5708796 DOI: 10.1371/journal.pone.0188742] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 11/13/2017] [Indexed: 11/27/2022] Open
Abstract
Oryza officinalis Wall ex Watt, a very important and special wild rice species, shows abundant genetic diversity and disease resistance features, especially high resistance to bacterial blight. The molecular mechanisms of bacterial blight resistance in O. officinalis have not yet been elucidated. The WRKY transcription factor family is one of the largest gene families involved in plant growth, development and stress response. However, little is known about the numbers, structure, molecular phylogenetics, and expression of the WRKY genes under Xanthomonas oryzae pv. oryzae (Xoo) stress in O. officinalis due to lacking of O. officinalis genome. Therefore, based on the RNA-sequencing data of O. officinalis, we performed a comprehensive study of WRKY genes in O. officinalis and identified 89 OoWRKY genes. Then 89 OoWRKY genes were classified into three groups based on the WRKY domains and zinc finger motifs. Phylogenetic analysis strongly supported that the evolution of OoWRKY genes were consistent with previous studies of WRKYs, and subgroup IIc OoWRKY genes were the original ancestors of some group II and group III OoWRKYs. Among the 89 OoWRKY genes, eight OoWRKYs displayed significantly different expression (>2-fold, p<0.01) in the O. officinalis transcriptome under Xoo strains PXO99 and C5 stress 48 h, suggesting these genes might play important role in PXO99 and C5 stress responses in O. officinalis. QRT-PCR analysis and confirmation of eight OoWRKYs expression patterns revealed that they responded strongly to PXO99 and C5 stress 24 h, 48 h, and 72 h, and the trends of these genes displaying marked changes were consistent with the 48 h RNA-sequencing data, demonstrated these genes played important roles in response to biotic stress and might even involved in the bacterial blight resistance. Tissue expression profiles of eight OoWRKY genes revealed that they were highly expressed in root, stem, leaf, and flower, especially in leaf (except OoWRKY71), suggesting these genes might be also important for plant growth and organ development. In this study, we analyzed the WRKY family of transcription factors in O.officinalis. Insight was gained into the classification, evolution, and function of the OoWRKY genes, revealing the putative roles of eight significantly different expression OoWRKYs in Xoo strains PXO99 and C5 stress responses in O.officinalis. This study provided a better understanding of the evolution and functions of O. officinalis WRKY genes, and suggested that manipulating eight significantly different expression OoWRKYs would enhance resistance to bacterial blight.
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Affiliation(s)
- Chunmiao Jiang
- Biotechnology & Genetic Germplasm Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, P.R. China
- School of Life Sciences, Yunnan University, Kunming, Yunnan, P.R. China
| | - Qingxi J. Shen
- School of Life Sciences, University of Nevada, Las Vegas, USA
| | - Bo Wang
- Biotechnology & Genetic Germplasm Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, P.R. China
| | - Bin He
- Jiangxi Science & Technology Normal University, Nanchang, Jiangxi, P.R. China
| | - Suqin Xiao
- Biotechnology & Genetic Germplasm Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, P.R. China
| | - Ling Chen
- Biotechnology & Genetic Germplasm Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, P.R. China
| | - Tengqiong Yu
- Biotechnology & Genetic Germplasm Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, P.R. China
| | - Xue Ke
- Biotechnology & Genetic Germplasm Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, P.R. China
| | - Qiaofang Zhong
- Biotechnology & Genetic Germplasm Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, P.R. China
| | - Jian Fu
- Biotechnology & Genetic Germplasm Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, P.R. China
| | - Yue Chen
- Biotechnology & Genetic Germplasm Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, P.R. China
| | - Lingxian Wang
- Biotechnology & Genetic Germplasm Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, P.R. China
| | - Fuyou Yin
- Biotechnology & Genetic Germplasm Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, P.R. China
| | - Dunyu Zhang
- Biotechnology & Genetic Germplasm Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, P.R. China
| | - Walid Ghidan
- Rice Research & Training Center, Field Crops Research Institute, Agricultural Research Center (ARC), Sakha, Kafr Elsheikh, Egypt
| | - Xingqi Huang
- Biotechnology & Genetic Germplasm Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, P.R. China
- School of Life Sciences, Yunnan University, Kunming, Yunnan, P.R. China
- * E-mail: (XH); (ZC)
| | - Zaiquan Cheng
- Biotechnology & Genetic Germplasm Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, P.R. China
- * E-mail: (XH); (ZC)
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Ji LD, Hu SP, Li JY, Yao BB, Shen QJ, Xu J. Shared genetic etiology of hypertension and stroke: evidence from bioinformatics analysis of genome-wide association studies. J Hum Hypertens 2017; 32:34-39. [PMID: 29176593 DOI: 10.1038/s41371-017-0012-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/11/2017] [Accepted: 10/04/2017] [Indexed: 12/18/2022]
Abstract
Hypertension is the most significant modifiable risk factor for cerebrovascular disease. It has been estimated that about 54% of strokes worldwide can be attributed to hypertension. However, there has not been a systematic study assessing the shared genetic susceptibility to hypertension and stroke on a genome-wide level. In this study, SNPs associated with essential hypertension and stroke were collected from the NHGRI-EBI GWAS catalog, and genotype imputation were conducted using information from the 1000 Genomes Project. Subsequently, the SNPs and the mapped genes were compared between the two diseases. Finally, functional clustering was performed, and the enriched GO terms and KEGG pathways were further compared between hypertension and stroke. Comparison of these two groups of SNPs and genes identified only one shared SNP (rs3184504) and 11 shared genes. After genotype imputation, 129 shared SNPs and 16 shared genes were identified. These genes were significantly enriched in 10 GO terms, which were mainly involved in lipoprotein and triglyceride metabolism. Additionally, KEGG analysis identified one pathway, glycerolipid metabolism, as being significantly enriched in both diseases. The present study strongly suggests that the gene network regulating lipid metabolism and blood circulation is the major shared genetic etiology of hypertension and stroke.
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Affiliation(s)
- L D Ji
- Department of Biochemistry, School of Medicine, Ningbo University, Ningbo, China.,Zhejiang Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China
| | - S P Hu
- Department of Research and Teaching, Ningbo No. 2 Hospital, Ningbo, China
| | - J Y Li
- Department of of Clinical Medicine, School of Medicine, Ningbo University, Ningbo, China
| | - B B Yao
- Department of Preventive Medicine, School of Medicine, Ningbo University, 818 Fenghua Road, Jiangbei District, 315211, Ningbo, Zhejiang Province, China
| | - Q J Shen
- Zhejiang Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China. .,Department of Preventive Medicine, School of Medicine, Ningbo University, 818 Fenghua Road, Jiangbei District, 315211, Ningbo, Zhejiang Province, China.
| | - J Xu
- Zhejiang Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China. .,Department of Preventive Medicine, School of Medicine, Ningbo University, 818 Fenghua Road, Jiangbei District, 315211, Ningbo, Zhejiang Province, China.
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Watanabe KA, Homayouni A, Gu L, Huang KY, Ho THD, Shen QJ. Transcriptomic analysis of rice aleurone cells identified a novel abscisic acid response element. Plant Cell Environ 2017. [PMID: 28626890 DOI: 10.1111/pce.13006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Seeds serve as a great model to study plant responses to drought stress, which is largely mediated by abscisic acid (ABA). The ABA responsive element (ABRE) is a key cis-regulatory element in ABA signalling. However, its consensus sequence (ACGTG(G/T)C) is present in the promoters of only about 40% of ABA-induced genes in rice aleurone cells, suggesting other ABREs may exist. To identify novel ABREs, RNA sequencing was performed on aleurone cells of rice seeds treated with 20 μM ABA. Gibbs sampling was used to identify enriched elements, and particle bombardment-mediated transient expression studies were performed to verify the function. Gene ontology analysis was performed to predict the roles of genes containing the novel ABREs. This study revealed 2443 ABA-inducible genes and a novel ABRE, designated as ABREN, which was experimentally verified to mediate ABA signalling in rice aleurone cells. Many of the ABREN-containing genes are predicted to be involved in stress responses and transcription. Analysis of other species suggests that the ABREN may be monocot specific. This study also revealed interesting expression patterns of genes involved in ABA metabolism and signalling. Collectively, this study advanced our understanding of diverse cis-regulatory sequences and the transcriptomes underlying ABA responses in rice aleurone cells.
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Affiliation(s)
- Kenneth A Watanabe
- School of Life Sciences, University of Nevada Las Vegas, 4505 South Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Arielle Homayouni
- School of Life Sciences, University of Nevada Las Vegas, 4505 South Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Lingkun Gu
- School of Life Sciences, University of Nevada Las Vegas, 4505 South Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Kuan-Ying Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Tuan-Hua David Ho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Department of Biology, Washington University, St. Louis, MO, 63130, USA
| | - Qingxi J Shen
- School of Life Sciences, University of Nevada Las Vegas, 4505 South Maryland Parkway, Las Vegas, NV, 89154, USA
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Hu LJ, Ren WY, Shen QJ, Ji HY, Zhu L. Inflammation in lung after acute myocardial infarction is induced by dendritic cell-mediated immune response. J BIOL REG HOMEOS AG 2017; 31:29-40. [PMID: 28337868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The present study was performed to describe the changes of lung tissues in mice with acute myocardial infarction (AMI) and also explain the cell mechanism involved in inflammation in lung. AMI was established by left coronary ligation in mice. Then mice were divided into three groups: control group, MW1 group (sampling after surgery for one week) and MW2 group (sampling after surgery for two weeks). Afterwards, measurement of lung weight and lung histology, cell sorting in bronchoalveolar lavage (BAL) fluid and detection of several adhesive molecules, inflammatory molecules as well as enzyme associated with inflammation were performed. Moreover, dendritic cells (DCs) were isolated from bone marrow of C57B/L6 mice. After incubating with necrotic myocardium, the expression of antigen presenting molecules, co-stimulatory molecules and inflammatory molecules were detected by flow cytometry or immunohistochemistry in DCs. We also detected T-cell proliferation after incubating with necrotic myocardium-treated DCs. AMI induced pathological changes of lung tissue and increased inflammatory cell amount in BAL fluid. AMI also increased the expression of several inflammatory factors, adhesive molecules and enzymes associated with inflammation. CD11c and TLR9, which are DC surface markers, showed a significantly increased expression in mice with AMI. Additionally, necrotic myocardium significantly increased the expression of co-stimulatory factors including CD83 and CD80, inflammatory cytokines including TNF-α, IFN-γ and NF-κB in DCs. Furthermore, DCs treated with necrotic myocardium also significantly promoted T-cell proliferation. AMI induced inflammation in lung and these pathological changes were mediated by DC-associated immune response.
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Affiliation(s)
- L J Hu
- Department of Pulmonary Medicine, Research Institute of Respiratory Disease, Zhongshan Hospital, Fudan University, Shanghai, China
| | - W Y Ren
- Department of Geriatrics, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Q J Shen
- Department of Pulmonary Medicine, Research Institute of Respiratory Disease, Zhongshan Hospital, Fudan University, Shanghai, China
| | - H Y Ji
- Department of Pulmonary Medicine, Research Institute of Respiratory Disease, Zhongshan Hospital, Fudan University, Shanghai, China
| | - L Zhu
- Department of Pulmonary Medicine, Research Institute of Respiratory Disease, Zhongshan Hospital, Fudan University, Shanghai, China
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Watanabe KA, Ma K, Homayouni A, Rushton PJ, Shen QJ. Transcript structure and domain display: a customizable transcript visualization tool. Bioinformatics 2016; 32:2024-5. [PMID: 27153680 DOI: 10.1093/bioinformatics/btw095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 02/12/2016] [Indexed: 11/14/2022] Open
Abstract
UNLABELLED Transcript Structure and Domain Display (TSDD) is a publicly available, web-based program that provides publication quality images of transcript structures and domains. TSDD is capable of producing transcript structures from GFF/GFF3 and BED files. Alternatively, the GFF files of several model organisms have been pre-loaded so that users only needs to enter the locus IDs of the transcripts to be displayed. Visualization of transcripts provides many benefits to researchers, ranging from evolutionary analysis of DNA-binding domains to predictive function modeling. AVAILABILITY AND IMPLEMENTATION TSDD is freely available for non-commercial users at http://shenlab.sols.unlv.edu/shenlab/software/TSD/transcript_display.html CONTACT : jeffery.shen@unlv.nevada.edu.
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Affiliation(s)
- Kenneth A Watanabe
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Kaiwang Ma
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA School of Medical Technology & Engineering, Henan University of Science & Technology, Luoyang, 471003, China
| | - Arielle Homayouni
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | | | - Qingxi J Shen
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
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Abstract
The WRKY transcription factor family is one of the largest gene families involved in plant development and stress response. Although many WRKY genes have been studied in cultivated rice (Oryza sativa), the WRKY genes in the wild rice species Oryza nivara, the direct progenitor of O. sativa, have not been studied. O. nivara shows abundant genetic diversity and elite drought and disease resistance features. Herein, a total of 97 O. nivara WRKY (OnWRKY) genes were identified. RNA-sequencing demonstrates that OnWRKY genes were generally expressed at higher levels in the roots of 30-day-old plants. Bioinformatic analyses suggest that most of OnWRKY genes could be induced by salicylic acid, abscisic acid, and drought. Abundant potential MAPK phosphorylation sites in OnWRKYs suggest that activities of most OnWRKYs can be regulated by phosphorylation. Phylogenetic analyses of OnWRKYs support a novel hypothesis that ancient group IIc OnWRKYs were the original ancestors of only some group IIc and group III WRKYs. The analyses also offer strong support that group IIc OnWRKYs containing the HVE sequence in their zinc finger motifs were derived from group Ia WRKYs. This study provides a solid foundation for the study of the evolution and functions of WRKY genes in O. nivara.
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Affiliation(s)
- Hengjian Xu
- School of Life Sciences, Shandong University of Technology, Zibo 255000, Shandong Province, People's Republic of China School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Kenneth A Watanabe
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Liyuan Zhang
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Qingxi J Shen
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
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Tripathi P, Rabara RC, Reese RN, Miller MA, Rohila JS, Subramanian S, Shen QJ, Morandi D, Bücking H, Shulaev V, Rushton PJ. A toolbox of genes, proteins, metabolites and promoters for improving drought tolerance in soybean includes the metabolite coumestrol and stomatal development genes. BMC Genomics 2016; 17:102. [PMID: 26861168 PMCID: PMC4746818 DOI: 10.1186/s12864-016-2420-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 01/26/2016] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The purpose of this project was to identify metabolites, proteins, genes, and promoters associated with water stress responses in soybean. A number of these may serve as new targets for the biotechnological improvement of drought responses in soybean (Glycine max). RESULTS We identified metabolites, proteins, and genes that are strongly up or down regulated during rapid water stress following removal from a hydroponics system. 163 metabolites showed significant changes during water stress in roots and 93 in leaves. The largest change was a root-specific 160-fold increase in the coumestan coumestrol making it a potential biomarker for drought and a promising target for improving drought responses. Previous reports suggest that coumestrol stimulates mycorrhizal colonization and under certain conditions mycorrhizal plants have improved drought tolerance. This suggests that coumestrol may be part of a call for help to the rhizobiome during stress. About 3,000 genes were strongly up-regulated by drought and we identified regulators such as ERF, MYB, NAC, bHLH, and WRKY transcription factors, receptor-like kinases, and calcium signaling components as potential targets for soybean improvement as well as the jasmonate and abscisic acid biosynthetic genes JMT, LOX1, and ABA1. Drought stressed soybean leaves show reduced mRNA levels of stomatal development genes including FAMA-like, MUTE-like and SPEECHLESS-like bHLH transcription factors and leaves formed after drought stress had a reduction in stomatal density of 22.34 % and stomatal index of 17.56 %. This suggests that reducing stomatal density may improve drought tolerance. MEME analyses suggest that ABRE (CACGT/CG), CRT/DRE (CCGAC) and a novel GTGCnTGC/G element play roles in transcriptional activation and these could form components of synthetic promoters to drive expression of transgenes. Using transformed hairy roots, we validated the increase in promoter activity of GmWRKY17 and GmWRKY67 during dehydration and after 20 μM ABA treatment. CONCLUSIONS Our toolbox provides new targets and strategies for improving soybean drought tolerance and includes the coumestan coumestrol, transcription factors that regulate stomatal density, water stress-responsive WRKY gene promoters and a novel DNA element that appears to be enriched in water stress responsive promoters.
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Affiliation(s)
- Prateek Tripathi
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD57007, USA.
- Current address, Molecular and Computational Biology, Dana & David Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
| | - Roel C Rabara
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD57007, USA.
- Current address: Texas A&M AgriLife Research and Extension Center, Dallas, TX, 75252, USA.
| | - R Neil Reese
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD57007, USA.
| | - Marissa A Miller
- Texas A&M AgriLife Research and Extension Center, Dallas, TX, 75252, USA.
| | - Jai S Rohila
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD57007, USA.
| | - Senthil Subramanian
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD57007, USA.
| | - Qingxi J Shen
- School of Life Sciences, University of Nevada, Las Vegas, 89154, USA.
| | - Dominique Morandi
- INRA, UMR 1347 Agroécologie, 17 rue Sully, BP 86510, 21065, Dijon, CEDEX, France.
| | - Heike Bücking
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD57007, USA.
| | - Vladimir Shulaev
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA.
| | - Paul J Rushton
- Texas A&M AgriLife Research and Extension Center, Dallas, TX, 75252, USA.
- Current address, 22nd Century Group Inc., 9530 Main Street Clarence, New York, 14031, USA.
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Tripathi P, Rabara RC, Shulaev V, Shen QJ, Rushton PJ. Understanding Water-Stress Responses in Soybean Using Hydroponics System-A Systems Biology Perspective. Front Plant Sci 2015; 6:1145. [PMID: 26734044 PMCID: PMC4685135 DOI: 10.3389/fpls.2015.01145] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 12/02/2015] [Indexed: 05/26/2023]
Abstract
The deleterious changes in environmental conditions such as water stress bring physiological and biochemical changes in plants, which results in crop loss. Thus, combating water stress is important for crop improvement to manage the needs of growing population. Utilization of hydroponics system in growing plants is questionable to some researchers, as it does not represent an actual field condition. However, trying to address a complex problem like water stress we have to utilize a simpler growing condition like the hydroponics system wherein every input given to the plants can be controlled. With the advent of high-throughput technologies, it is still challenging to address all levels of the genetic machinery whether a gene, protein, metabolite, and promoter. Thus, using a system of reduced complexity like hydroponics can certainly direct us toward the right candidates, if not completely help us to resolve the issue.
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Affiliation(s)
- Prateek Tripathi
- Department of Biology and Microbiology, South Dakota State University Brookings, SD, USA
| | - Roel C Rabara
- Department of Biology and Microbiology, South Dakota State University Brookings, SD, USA
| | - Vladimir Shulaev
- Department of Biological Sciences, University of North Texas Denton, TX, USA
| | - Qingxi J Shen
- School of Life Sciences, University of Nevada Las Vegas Las Vegas, NV, USA
| | - Paul J Rushton
- Texas A&M AgriLife Research & Extension Center Dallas, TX, USA
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Rinerson CI, Scully ED, Palmer NA, Donze-Reiner T, Rabara RC, Tripathi P, Shen QJ, Sattler SE, Rohila JS, Sarath G, Rushton PJ. The WRKY transcription factor family and senescence in switchgrass. BMC Genomics 2015; 16:912. [PMID: 26552372 PMCID: PMC4640240 DOI: 10.1186/s12864-015-2057-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 10/13/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Early aerial senescence in switchgrass (Panicum virgatum) can significantly limit biomass yields. WRKY transcription factors that can regulate senescence could be used to reprogram senescence and enhance biomass yields. METHODS All potential WRKY genes present in the version 1.0 of the switchgrass genome were identified and curated using manual and bioinformatic methods. Expression profiles of WRKY genes in switchgrass flag leaf RNA-Seq datasets were analyzed using clustering and network analyses tools to identify both WRKY and WRKY-associated gene co-expression networks during leaf development and senescence onset. RESULTS We identified 240 switchgrass WRKY genes including members of the RW5 and RW6 families of resistance proteins. Weighted gene co-expression network analysis of the flag leaf transcriptomes across development readily separated clusters of co-expressed genes into thirteen modules. A visualization highlighted separation of modules associated with the early and senescence-onset phases of flag leaf growth. The senescence-associated module contained 3000 genes including 23 WRKYs. Putative promoter regions of senescence-associated WRKY genes contained several cis-element-like sequences suggestive of responsiveness to both senescence and stress signaling pathways. A phylogenetic comparison of senescence-associated WRKY genes from switchgrass flag leaf with senescence-associated WRKY genes from other plants revealed notable hotspots in Group I, IIb, and IIe of the phylogenetic tree. CONCLUSIONS We have identified and named 240 WRKY genes in the switchgrass genome. Twenty three of these genes show elevated mRNA levels during the onset of flag leaf senescence. Eleven of the WRKY genes were found in hotspots of related senescence-associated genes from multiple species and thus represent promising targets for future switchgrass genetic improvement. Overall, individual WRKY gene expression profiles could be readily linked to developmental stages of flag leaves.
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Affiliation(s)
- Charles I Rinerson
- Texas A&M AgriLife Research and Extension Center, Dallas, TX, 75252, USA.
| | - Erin D Scully
- Grain, Forage and Bioenergy Research Unit USDA-ARS UNL, Lincoln, NE, 68583-0937, USA.
| | - Nathan A Palmer
- Grain, Forage and Bioenergy Research Unit USDA-ARS UNL, Lincoln, NE, 68583-0937, USA.
| | - Teresa Donze-Reiner
- Department of Biology, West Chester University of Pennsylvania, West Chester, PA, 19382, USA.
| | - Roel C Rabara
- Texas A&M AgriLife Research and Extension Center, Dallas, TX, 75252, USA.
| | - Prateek Tripathi
- Molecular and Computational Biology Section, Dana & David Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, USA.
| | - Qingxi J Shen
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
| | - Scott E Sattler
- Grain, Forage and Bioenergy Research Unit USDA-ARS UNL, Lincoln, NE, 68583-0937, USA.
| | - Jai S Rohila
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57007, USA.
| | - Gautam Sarath
- Grain, Forage and Bioenergy Research Unit USDA-ARS UNL, Lincoln, NE, 68583-0937, USA.
| | - Paul J Rushton
- Texas A&M AgriLife Research and Extension Center, Dallas, TX, 75252, USA.
- Current address: 22nd Century Group Inc., Clarence, 14031, New York.
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11
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Watanabe KA, Homayouni A, Tufano T, Lopez J, Ringler P, Rushton P, Shen QJ. Tiling Assembly: a new tool for reference annotation-independent transcript assembly and novel gene identification by RNA-sequencing. DNA Res 2015; 22:319-29. [PMID: 26341416 PMCID: PMC4596398 DOI: 10.1093/dnares/dsv015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 07/12/2015] [Indexed: 11/28/2022] Open
Abstract
Annotation of the rice (Oryza sativa) genome has evolved significantly since release of its draft sequence, but it is far from complete. Several published transcript assembly programmes were tested on RNA-sequencing (RNA-seq) data to determine their effectiveness in identifying novel genes to improve the rice genome annotation. Cufflinks, a popular assembly software, did not identify all transcripts suggested by the RNA-seq data. Other assembly software was CPU intensive, lacked documentation, or lacked software updates. To overcome these shortcomings, a heuristic ab initio transcript assembly algorithm, Tiling Assembly, was developed to identify genes based on short read and junction alignment. Tiling Assembly was compared with Cufflinks to evaluate its gene-finding capabilities. Additionally, a pipeline was developed to eliminate false-positive gene identification due to noise or repetitive regions in the genome. By combining Tiling Assembly and Cufflinks, 767 unannotated genes were identified in the rice genome, demonstrating that combining both programmes proved highly efficient for novel gene identification. We also demonstrated that Tiling Assembly can accurately determine transcription start sites by comparing the Tiling Assembly genes with their corresponding full-length cDNA. We applied our pipeline to additional organisms and identified numerous unannotated genes, demonstrating that Tiling Assembly is an organism-independent tool for genome annotation.
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Affiliation(s)
- Kenneth A Watanabe
- School of Life Sciences, University of Nevada Las Vegas, 4505 South Maryland Parkway, Las Vegas, NV 89154, USA
| | - Arielle Homayouni
- School of Life Sciences, University of Nevada Las Vegas, 4505 South Maryland Parkway, Las Vegas, NV 89154, USA
| | - Tara Tufano
- School of Life Sciences, University of Nevada Las Vegas, 4505 South Maryland Parkway, Las Vegas, NV 89154, USA
| | - Jennifer Lopez
- School of Life Sciences, University of Nevada Las Vegas, 4505 South Maryland Parkway, Las Vegas, NV 89154, USA
| | - Patricia Ringler
- School of Life Sciences, University of Nevada Las Vegas, 4505 South Maryland Parkway, Las Vegas, NV 89154, USA
| | - Paul Rushton
- Texas A&M AgriLife Research, 17360 Coit Road, Dallas, TX 75252, USA
| | - Qingxi J Shen
- School of Life Sciences, University of Nevada Las Vegas, 4505 South Maryland Parkway, Las Vegas, NV 89154, USA
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12
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Zhang L, Gu L, Ringler P, Smith S, Rushton PJ, Shen QJ. Three WRKY transcription factors additively repress abscisic acid and gibberellin signaling in aleurone cells. Plant Sci 2015; 236:214-22. [PMID: 26025535 DOI: 10.1016/j.plantsci.2015.04.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 04/14/2015] [Accepted: 04/19/2015] [Indexed: 05/06/2023]
Abstract
Members of the WRKY transcription factor superfamily are essential for the regulation of many plant pathways. Functional redundancy due to duplications of WRKY transcription factors, however, complicates genetic analysis by allowing single-mutant plants to maintain wild-type phenotypes. Our analyses indicate that three group I WRKY genes, OsWRKY24, -53, and -70, act in a partially redundant manner. All three showed characteristics of typical WRKY transcription factors: each localized to nuclei and yeast one-hybrid assays indicated that they all bind to W-boxes, including those present in their own promoters. Quantitative real time-PCR (qRT-PCR) analyses indicated that the expression levels of the three WRKY genes varied in the different tissues tested. Particle bombardment-mediated transient expression analyses indicated that all three genes repress the GA and ABA signaling in a dosage-dependent manner. Combination of all three WRKY genes showed additive antagonism of ABA and GA signaling. These results suggest that these WRKY proteins function as negative transcriptional regulators of GA and ABA signaling. However, different combinations of these WRKY genes can lead to varied strengths in suppression of their targets.
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Affiliation(s)
- Liyuan Zhang
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA
| | - Lingkun Gu
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA
| | - Patricia Ringler
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA
| | - Stanley Smith
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA
| | - Paul J Rushton
- Texas A&M AgriLife Research and Extension Center, Dallas, TX 75252, USA
| | - Qingxi J Shen
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA.
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13
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Rabara RC, Tripathi P, Reese RN, Rushton DL, Alexander D, Timko MP, Shen QJ, Rushton PJ. Tobacco drought stress responses reveal new targets for Solanaceae crop improvement. BMC Genomics 2015; 16:484. [PMID: 26123791 PMCID: PMC4485875 DOI: 10.1186/s12864-015-1575-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 04/24/2015] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The Solanaceae are an economically important family of plants that include tobacco (Nicotiana tabacum L.), tomato, and potato. Drought is a major cause of crop losses. RESULTS We have identified major changes in physiology, metabolites, mRNA levels, and promoter activities during the tobacco response to drought. We have classified these as potential components of core responses that may be common to many plant species or responses that may be family/species-specific features of the drought stress response in tobacco or the Solanaceae. In tobacco the largest increase in any metabolite was a striking 70-fold increase in 4-hydroxy-2-oxoglutaric acid (KHG) in roots that appears to be tobacco/Solanaceae specific. KHG is poorly characterized in plants but is broken down to pyruvate and glyoxylate after the E. coli SOS response to facilitate the resumption of respiration. A similar process in tobacco would represent a mechanism to restart respiration upon water availability after drought. At the mRNA level, transcription factor gene induction by drought also showed both core and species/family specific responses. Many Group IX Subgroup 3 AP2/ERF transcription factors in tobacco appear to play roles in nicotine biosynthesis as a response to herbivory, whereas their counterparts in legume species appear to play roles in drought responses. We observed apparent Solanaceae-specific drought induction of several Group IId WRKY genes. One of these, NtWRKY69, showed ABA-independent drought stress-inducible promoter activity that moved into the leaf through the vascular tissue and then eventually into the surrounding leaf cells. CONCLUSIONS We propose components of a core metabolic response to drought stress in plants and also show that some major responses to drought stress at the metabolome and transcriptome levels are family specific. We therefore propose that the observed family-specific changes in metabolism are regulated, at least in part, by family-specific changes in transcription factor activity. We also present a list of potential targets for the improvement of Solanaceae drought responses.
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Affiliation(s)
- Roel C Rabara
- Texas A&M AgriLife Research and Extension Center, Dallas, Texas, 75252, USA.
| | - Prateek Tripathi
- Molecular and Computational Biology Section, Dana & David Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, USA.
| | - R Neil Reese
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57007, USA.
| | - Deena L Rushton
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA.
| | | | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, Virginia, 22904, USA.
| | - Qingxi J Shen
- School of Life Sciences, University of Nevada, Las Vegas, 89154, USA.
| | - Paul J Rushton
- Texas A&M AgriLife Research and Extension Center, Dallas, Texas, 75252, USA.
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Tripathi P, Rabara RC, Shen QJ, Rushton PJ. Transcriptomics analyses of soybean leaf and root samples during water-deficit. Genom Data 2015; 5:164-6. [PMID: 26484247 PMCID: PMC4583655 DOI: 10.1016/j.gdata.2015.05.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 05/25/2015] [Indexed: 11/26/2022]
Abstract
Drought being a major challenge for crop productivity and yield affects multigenic and quantitative traits. It is also well documented that water stress shows a cross talk with other abiotic stresses such as high temperature and high light intensities (Tripathi et al., 2013) [1]. In this report, we documented the details of the methods and quality controls used and considered in our time course-based transcriptome profile of soybean plants under water deficit conditions using microarray technology. The findings of this study are recently published by the Rushton lab in BMC Genomics for a comparative study of tobacco and Soybean (Rabara et al., 2015) [2]. The raw microarray data set is deposited in GEO database with accession number GSE49537.
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Affiliation(s)
- Prateek Tripathi
- Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90089, USA
| | - Roel C Rabara
- Texas A&M AgriLife Research & Extension Center Dallas, TX 75252, USA
| | - Qingxi J Shen
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA
| | - Paul J Rushton
- Texas A&M AgriLife Research & Extension Center Dallas, TX 75252, USA
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15
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Rabara RC, Tripathi P, Choudhary MK, Timko MP, Shen QJ, Rushton PJ. Transcriptome profiling of tobacco under water deficit conditions. Genom Data 2015; 5:61-3. [PMID: 26484226 PMCID: PMC4583635 DOI: 10.1016/j.gdata.2015.05.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 05/24/2015] [Indexed: 11/17/2022]
Abstract
Drought is one of the limiting environmental factors that affect crop production. Understanding the molecular basis of how plants respond to this water deficit stress is key to developing drought tolerant crops. In this study we generated time course-based transcriptome profiles of tobacco plants under water deficit conditions using microarray technology. In this paper, we describe in detail the experimental procedures and analyses performed in our study. The data set we generated (available in the NCBI/GEO database under GSE67434) has been analysed to identify genes that are involved in the regulation of tobacco's responses to drought.
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Affiliation(s)
- Roel C Rabara
- Texas A&M AgriLife Research and Extension Center, Dallas, TX 75252, United States
| | - Prateek Tripathi
- Molecular and Computational Biology Section, Dana & David Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90089, United States
| | - Mani Kant Choudhary
- Texas A&M AgriLife Research and Extension Center, Dallas, TX 75252, United States
| | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, VA 22904, United States
| | - Qingxi J Shen
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, United States
| | - Paul J Rushton
- Texas A&M AgriLife Research and Extension Center, Dallas, TX 75252, United States
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16
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Rinerson CI, Rabara RC, Tripathi P, Shen QJ, Rushton PJ. The evolution of WRKY transcription factors. BMC Plant Biol 2015; 15:66. [PMID: 25849216 PMCID: PMC4350883 DOI: 10.1186/s12870-015-0456-y] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 02/13/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND The availability of increasing numbers of sequenced genomes has necessitated a re-evaluation of the evolution of the WRKY transcription factor family. Modern day plants descended from a charophyte green alga that colonized the land between 430 and 470 million years ago. The first charophyte genome sequence from Klebsormidium flaccidum filled a gap in the available genome sequences in the plant kingdom between unicellular green algae that typically have 1-3 WRKY genes and mosses that contain 30-40. WRKY genes have been previously found in non-plant species but their occurrence has been difficult to explain. RESULTS Only two WRKY genes are present in the Klebsormidium flaccidum genome and the presence of a Group IIb gene was unexpected because it had previously been thought that Group IIb WRKY genes first appeared in mosses. We found WRKY transcription factor genes outside of the plant lineage in some diplomonads, social amoebae, fungi incertae sedis, and amoebozoa. This patchy distribution suggests that lateral gene transfer is responsible. These lateral gene transfer events appear to pre-date the formation of the WRKY groups in flowering plants. Flowering plants contain proteins with domains typical for both resistance (R) proteins and WRKY transcription factors. R protein-WRKY genes have evolved numerous times in flowering plants, each type being restricted to specific flowering plant lineages. These chimeric proteins contain not only novel combinations of protein domains but also novel combinations and numbers of WRKY domains. Once formed, R protein WRKY genes may combine different components of signalling pathways that may either create new diversity in signalling or accelerate signalling by short circuiting signalling pathways. CONCLUSIONS We propose that the evolution of WRKY transcription factors includes early lateral gene transfers to non-plant organisms and the occurrence of algal WRKY genes that have no counterparts in flowering plants. We propose two alternative hypotheses of WRKY gene evolution: The "Group I Hypothesis" sees all WRKY genes evolving from Group I C-terminal WRKY domains. The alternative "IIa + b Separate Hypothesis" sees Groups IIa and IIb evolving directly from a single domain algal gene separate from the Group I-derived lineage.
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Affiliation(s)
- Charles I Rinerson
- />Texas A&M AgriLife Research and Extension Center, Dallas, Texas 75252 USA
| | - Roel C Rabara
- />Texas A&M AgriLife Research and Extension Center, Dallas, Texas 75252 USA
| | - Prateek Tripathi
- />Molecular and Computational Biology Section, Dana & David Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA USA
| | - Qingxi J Shen
- />School of Life Sciences, University of Nevada, Las Vegas, 89154 USA
| | - Paul J Rushton
- />Texas A&M AgriLife Research and Extension Center, Dallas, Texas 75252 USA
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17
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Tripathi P, Rabara RC, Choudhary MK, Miller MA, Huang YS, Shen QJ, Blachon S, Rushton PJ. The interactome of soybean GmWRKY53 using yeast 2-hybrid library screening to saturation. Plant Signal Behav 2015; 10:e1028705. [PMID: 26102586 PMCID: PMC4623026 DOI: 10.1080/15592324.2015.1028705] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 03/03/2015] [Accepted: 03/06/2015] [Indexed: 05/10/2023]
Abstract
Soybean GmWRKY53 functions in both biotic and abiotic stress signaling. Using GmWRKY53 as a bait yeast 2-hybrid library screening to saturation isolated multiple independent fragments for many interacting proteins, enabling delineation of minimal interacting domains and computation of a confidence score. Multiple independent clones coding for the LATE ELONGATED HYPOCOTYL clock protein GmLCL2 (MYB114) were isolated and the binding site for GmWRKY53 was mapped to 90 amino acids separate from the MYB domain. This suggests a direct input from the clock on GmWRKY53 activity. The GmWRKY53-interacting proteins also included 3 water stress-inducible AP2/ERF transcription factors. One of these (Glyma03g26310) is one of the most strongly water stress induced genes in soybean roots, suggesting that GmWRKY53/ERF complexes regulate water stress responses.
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Affiliation(s)
- Prateek Tripathi
- Molecular and Computational Biology Section; University of Southern California; Los Angeles, CA USA
- These authors contributed equally to this article
| | - Roel C Rabara
- Texas A&M AgriLife Research and Extension Center; Dallas, TX USA
- These authors contributed equally to this article
| | | | - Marissa A Miller
- Texas A&M AgriLife Research and Extension Center; Dallas, TX USA
| | - Ying-Sheng Huang
- Texas A&M AgriLife Research and Extension Center; Dallas, TX USA
| | - Qingxi J Shen
- School of Life Sciences; University of Nevada Las Vegas; Las Vegas; NV USA
| | | | - Paul J Rushton
- Texas A&M AgriLife Research and Extension Center; Dallas, TX USA
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18
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Cheng JX, Anastasi J, Watanabe K, Kleinbrink EL, Grimley E, Knibbs R, Shen QJ, Vardiman JW. Genome-wide profiling reveals epigenetic inactivation of the PU.1 pathway by histone H3 lysine 27 trimethylation in cytogenetically normal myelodysplastic syndrome. Leukemia 2013; 27:1291-300. [DOI: 10.1038/leu.2013.45] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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19
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Rushton DL, Tripathi P, Rabara RC, Lin J, Ringler P, Boken AK, Langum TJ, Smidt L, Boomsma DD, Emme NJ, Chen X, Finer JJ, Shen QJ, Rushton PJ. WRKY transcription factors: key components in abscisic acid signalling. Plant Biotechnol J 2012; 10:2-11. [PMID: 21696534 DOI: 10.1111/j.1467-7652.2011.00634.x] [Citation(s) in RCA: 338] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
WRKY transcription factors (TFs) are key regulators of many plant processes, including the responses to biotic and abiotic stresses, senescence, seed dormancy and seed germination. For over 15 years, limited evidence has been available suggesting that WRKY TFs may play roles in regulating plant responses to the phytohormone abscisic acid (ABA), notably some WRKY TFs are ABA-inducible repressors of seed germination. However, the roles of WRKY TFs in other aspects of ABA signalling, and the mechanisms involved, have remained unclear. Recent significant progress in ABA research has now placed specific WRKY TFs firmly in ABA-responsive signalling pathways, where they act at multiple levels. In Arabidopsis, WRKY TFs appear to act downstream of at least two ABA receptors: the cytoplasmic PYR/PYL/RCAR-protein phosphatase 2C-ABA complex and the chloroplast envelope-located ABAR-ABA complex. In vivo and in vitro promoter-binding studies show that the target genes for WRKY TFs that are involved in ABA signalling include well-known ABA-responsive genes such as ABF2, ABF4, ABI4, ABI5, MYB2, DREB1a, DREB2a and RAB18. Additional well-characterized stress-inducible genes such as RD29A and COR47 are also found in signalling pathways downstream of WRKY TFs. These new insights also reveal that some WRKY TFs are positive regulators of ABA-mediated stomatal closure and hence drought responses. Conversely, many WRKY TFs are negative regulators of seed germination, and controlling seed germination appears a common function of a subset of WRKY TFs in flowering plants. Taken together, these new data demonstrate that WRKY TFs are key nodes in ABA-responsive signalling networks.
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Affiliation(s)
- Deena L Rushton
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
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Rushton PJ, Somssich IE, Ringler P, Shen QJ. WRKY transcription factors. Trends Plant Sci 2010; 15:247-58. [PMID: 20304701 DOI: 10.1016/j.tplants.2010.02.006] [Citation(s) in RCA: 1437] [Impact Index Per Article: 102.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Revised: 02/16/2010] [Accepted: 02/17/2010] [Indexed: 05/17/2023]
Abstract
WRKY transcription factors are one of the largest families of transcriptional regulators in plants and form integral parts of signalling webs that modulate many plant processes. Here, we review recent significant progress in WRKY transcription factor research. New findings illustrate that WRKY proteins often act as repressors as well as activators, and that members of the family play roles in both the repression and de-repression of important plant processes. Furthermore, it is becoming clear that a single WRKY transcription factor might be involved in regulating several seemingly disparate processes. Mechanisms of signalling and transcriptional regulation are being dissected, uncovering WRKY protein functions via interactions with a diverse array of protein partners, including MAP kinases, MAP kinase kinases, 14-3-3 proteins, calmodulin, histone deacetylases, resistance proteins and other WRKY transcription factors. WRKY genes exhibit extensive autoregulation and cross-regulation that facilitates transcriptional reprogramming in a dynamic web with built-in redundancy.
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Affiliation(s)
- Paul J Rushton
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA
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21
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Rushton PJ, Somssich IE, Ringler P, Shen QJ. WRKY transcription factors. Trends Plant Sci 2010; 15:247-258. [PMID: 20304701 DOI: 10.1016/j.tplants.2010.02] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Revised: 02/16/2010] [Accepted: 02/17/2010] [Indexed: 05/24/2023]
Abstract
WRKY transcription factors are one of the largest families of transcriptional regulators in plants and form integral parts of signalling webs that modulate many plant processes. Here, we review recent significant progress in WRKY transcription factor research. New findings illustrate that WRKY proteins often act as repressors as well as activators, and that members of the family play roles in both the repression and de-repression of important plant processes. Furthermore, it is becoming clear that a single WRKY transcription factor might be involved in regulating several seemingly disparate processes. Mechanisms of signalling and transcriptional regulation are being dissected, uncovering WRKY protein functions via interactions with a diverse array of protein partners, including MAP kinases, MAP kinase kinases, 14-3-3 proteins, calmodulin, histone deacetylases, resistance proteins and other WRKY transcription factors. WRKY genes exhibit extensive autoregulation and cross-regulation that facilitates transcriptional reprogramming in a dynamic web with built-in redundancy.
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Affiliation(s)
- Paul J Rushton
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA
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22
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Zhang ZL, Shin M, Zou X, Huang J, Ho THD, Shen QJ. A negative regulator encoded by a rice WRKY gene represses both abscisic acid and gibberellins signaling in aleurone cells. Plant Mol Biol 2009; 70:139-51. [PMID: 19199048 DOI: 10.1007/s11103-009-9463-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2008] [Accepted: 01/19/2009] [Indexed: 05/05/2023]
Abstract
Abscisic acid (ABA) and gibberellins (GAs) control several developmental processes including seed maturation, dormancy, and germination. The antagonism of these two hormones is well-documented. However, recent data from transcription profiling studies indicate that they can function as agonists in regulating the expression of many genes although the underlying mechanism is unclear. Here we report a rice WRKY gene, OsWRKY24, which encodes a protein that functions as a negative regulator of both GA and ABA signaling. Overexpression of OsWRKY24 via particle bombardment-mediated transient expression in aleurone cells represses the expression of two reporter constructs: the beta-glucuronidase gene driven by the GA-inducible Amy32b alpha-amylase promoter (Amy32b-GUS) and the ABA-inducible HVA22 promoter (HVA22-GUS). OsWRKY24 is unlikely a general repressor because it has little effect on the expression of the luciferase reporter gene driven by a constitutive ubiquitin promoter (UBI-Luciferase). As to the GA signaling, OsWRKY24 differs from OsWRKY51 and -71, two negative regulators specifically function in the GA signaling pathway, in several ways. First, OsWRKY24 contains two WRKY domains while OsWRKY51 and -71 have only one; both WRKY domains are essential for the full repressing activity of OsWRKY24. Second, binding of OsWRKY24 to the Amy32b promoter appears to involve sequences in addition to the TGAC cores of the W-boxes. Third, unlike OsWRKY71, OsWRKY24 is stable upon GA treatment. Together, these data demonstrate that OsWRKY24 is a novel type of transcriptional repressor that inhibits both GA and ABA signaling.
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Affiliation(s)
- Zhong-Lin Zhang
- School of Life Sciences, University of Nevada, M/S 4004, 4505 Maryland Parkway, Las Vegas, NV 89154, USA
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Jiang Y, Cukic B, Adjeroh DA, Skinner HD, Lin J, Shen QJ, Jiang BH. An algorithm for identifying novel targets of transcription factor families: application to hypoxia-inducible factor 1 targets. Cancer Inform 2009; 7:75-89. [PMID: 19352460 PMCID: PMC2664698 DOI: 10.4137/cin.s1054] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Efficient and effective analysis of the growing genomic databases requires the development of adequate computational tools. We introduce a fast method based on the suffix tree data structure for predicting novel targets of hypoxia-inducible factor 1 (HIF-1) from huge genome databases. The suffix tree data structure has two powerful applications here: one is to extract unknown patterns from multiple strings/sequences in linear time; the other is to search multiple strings/sequences using multiple patterns in linear time. Using 15 known HIF-1 target gene sequences as a training set, we extracted 105 common patterns that all occur in the 15 training genes using suffix trees. Using these 105 common patterns along with known subsequences surrounding HIF-1 binding sites from the literature, the algorithm searches a genome database that contains 2,078,786 DNA sequences. It reported 258 potentially novel HIF-1 targets including 25 known HIF-1 targets. Based on microarray studies from the literature, 17 putative genes were confirmed to be upregulated by HIF-1 or hypoxia inside these 258 genes. We further studied one of the potential targets, COX-2, in the biological lab; and showed that it was a biologically relevant HIF-1 target. These results demonstrate that our methodology is an effective computational approach for identifying novel HIF-1 targets.
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Affiliation(s)
- Yue Jiang
- Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV 26506, USA.
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Zou X, Neuman D, Shen QJ. Interactions of two transcriptional repressors and two transcriptional activators in modulating gibberellin signaling in aleurone cells. Plant Physiol 2008; 148:176-86. [PMID: 18621977 PMCID: PMC2528090 DOI: 10.1104/pp.108.123653] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2008] [Accepted: 06/18/2008] [Indexed: 05/19/2023]
Abstract
Gibberellins (GAs) regulate many aspects of plant development, such as germination, growth, and flowering. The barley (Hordeum vulgare) Amy32b alpha-amylase promoter contains at least five cis-acting elements that govern its GA-induced expression. Our previous studies indicate that a barley WRKY gene, HvWRKY38, and its rice (Oryza sativa) ortholog, OsWRKY71, block GA-induced expression of Amy32b-GUS. In this work, we investigated the functional and physical interactions of HvWRKY38 with another repressor and two activators in barley. HvWRKY38 blocks the inductive activities of SAD (a DOF protein) and HvGAMYB (a R2R3 MYB protein) when either of these proteins is present individually. However, SAD and HvGAMYB together overcome the inhibitory effect of HvWRKY38. Yet, the combination of HvWRKY38 and BPBF (another DOF protein) almost diminishes the synergistic effect of SAD and HvGAMYB transcriptional activators. Electrophoretic mobility shift assays indicate that HvWRKY38 blocks the GA-induced expression of Amy32b by interfering with the binding of HvGAMYB to the cis-acting elements in the alpha-amylase promoter. The physical interaction of HvWRKY38 and BPBF repressors is demonstrated via bimolecular fluorescence complementation assays. These data suggest that the expression of Amy32b is modulated by protein complexes that contain either activators (e.g. HvGAMYB and SAD) or repressors (e.g. HvWRKY38 and BPBF). The relative amounts of the repressor or activator complexes binding to the Amy32b promoter regulate its expression level in barley aleurone cells.
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Affiliation(s)
- Xiaolu Zou
- School of Life Sciences, University of Nevada, Las Vegas, Nevada 89154, USA
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25
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Xie Z, Zhang ZL, Hanzlik S, Cook E, Shen QJ. Salicylic acid inhibits gibberellin-induced alpha-amylase expression and seed germination via a pathway involving an abscisic-acid-inducible WRKY gene. Plant Mol Biol 2007; 64:293-303. [PMID: 17390108 DOI: 10.1007/s11103-007-9152-0] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2006] [Accepted: 02/12/2007] [Indexed: 05/14/2023]
Abstract
It is well known that abscisic acid (ABA) antagonizes gibberellin (GA)-promoted seed germination. Recent circumstantial evidence suggests that salicylic acid (SA) also inhibits seed germination in maize and Arabidopsis. Our study shows that SA blocks barley seed germination in a dosage dependent manner. As an initial effort to addressing the mechanism controlling the crosstalk of SA, GA and ABA signaling in barley, we studied the regulation of alpha-amylases by SA and a WRKY gene whose expression is modulated by these hormones. Assays of alpha-amylase activity reveal that GA-induced alpha-amylase production in aleurone cells is inhibited by bioactive SA, but not its analogs, 3-hydroxybenzoic acid and 4-hydroxybenzoic acid. This inhibitory effect is unlikely due to repressing alpha-amylase secretion or inhibiting alpha-amylase enzyme activities. Northern blot analyses indicate that SA suppresses GA-induced expression of a barley low pI alpha-amylase gene (Amy32b). Because our previous data indicate that ABA-inducible and GA-suppressible WRKY genes inhibit the expression of alpha-amylase genes in rice, we studied the steady state mRNA levels of a barley WRKY gene, HvWRKY38. The expression of HvWRKY38 in barley aleurone cells is down-regulated by GA, but up-regulated by SA and ABA. However, the regulation of HvWRKY38 by SA appears to be different from that of ABA in term of the kinetics and levels of induction. Over-expression of HvWRKY38 in aleurone cells by particle bombardment blocks GA induction of the Amy32b promoter reporter construct (Amy32b-GUS). Therefore, HvWRKY38 might serve as a converging node of SA and ABA signal pathways involved in suppressing GA-induced seed germination.
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Affiliation(s)
- Zhen Xie
- Department of Biological Sciences, University of Nevada, M/S 4004, 4505 Maryland Parkway, Las Vegas, NV 89154, USA
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26
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Ross C, Shen QJ. Computational prediction and experimental verification of HVA1-like abscisic acid responsive promoters in rice (Oryza sativa). Plant Mol Biol 2006; 62:233-46. [PMID: 16845480 DOI: 10.1007/s11103-006-9017-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2006] [Accepted: 05/09/2006] [Indexed: 05/10/2023]
Abstract
Abscisic acid (ABA) is one of the central plant hormones, responsible for controlling both maturation and germination in seeds, as well as mediating adaptive responses to desiccation, injury, and pathogen infection in vegetative tissues. Thorough analyses of two barley genes, HVA1 and HVA22, indicate that their response to ABA relies on the interaction of two cis-acting elements in their promoters, an ABA response element (ABRE) and a coupling element (CE). Together, they form an ABA response promoter complex (ABRC). Comparison of promoters of barley HVA1 and it rice orthologue indicates that the structures and sequences of their ABRCs are highly similar. Prediction of ABA responsive genes in the rice genome is then tractable to a bioinformatics approach based on the structures of the well-defined barley ABRCs. Here we describe a model developed based on the consensus, inter-element spacing and orientations of experimentally determined ABREs and CEs. Our search of the rice promoter database for promoters that fit the model has generated a partial list of genes in rice that have a high likelihood of being involved in the ABA signaling network. The ABA inducibility of some of the rice genes identified was validated with quantitative reverse transcription PCR (QPCR). By limiting our input data to known enhancer modules and experimentally derived rules, we have generated a high confidence subset of ABA-regulated genes. The results suggest that the pathways by which cereals respond to biotic and abiotic stresses overlap significantly, and that regulation is not confined to the level transcription. The large fraction of putative regulatory genes carrying HVA1-like enhancer modules in their promoters suggests the ABA signal enters at multiple points into a complex regulatory network that remains largely unmapped.
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Affiliation(s)
- Christian Ross
- Bioinformatics Core, Department of Biological Sciences, University of Nevada, Las Vegas, NV 89154, USA
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27
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Xie Z, Zhang ZL, Zou X, Yang G, Komatsu S, Shen QJ. Interactions of two abscisic-acid induced WRKY genes in repressing gibberellin signaling in aleurone cells. Plant J 2006; 46:231-42. [PMID: 16623886 DOI: 10.1111/j.1365-313x.2006.02694.x] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Gibberellins (GA) promote while abscisic acid (ABA) inhibits seed germination and post-germination growth. To address the cross-talk of GA and ABA signaling, we studied two rice WRKY genes (OsWRKY51 and OsWRKY71) that are ABA-inducible and GA-repressible in embryos and aleurone cells. Over-expression of these two genes in aleurone cells specifically and synergistically represses induction of the ABA-repressible and GA-inducible Amy32b alpha-amylase promoter reporter construct (Amy32b-GUS) by GA or the GA-inducible transcriptional activator, GAMYB. The physical interactions of OsWRKY71 proteins themselves and that of OsWRKY71 and OsWRKY51 are revealed in the nuclei of aleurone cells using bimolecular fluorescence complementation (BiFC) assays. Although OsWRKY51 itself does not bind to the Amy32b promoter in vitro, it interacts with OsWRKY71 and enhances the binding affinity of OsWRKY71 to W boxes in the Amy32b promoter. The binding activity of OsWRKY71 is abolished by deleting the C-terminus containing the WRKY domain or substituting the key amino acids in the WRKY motif and the zinc finger region. However, two of these non-DNA-binding mutants are still able to repress GA induction by enhancing the binding affinity of the wild-type DNA-binding OsWRKY71 repressors. In contrast, the third non-DNA-binding mutant enhances GA induction of Amy32b-GUS, by interfering with the binding of the wild-type OsWRKY71 or the OsWRKY71/OsWRKY51 repressing complex. These data demonstrate the synergistic interaction of ABA-inducible WRKY genes in regulating GAMYB-mediated GA signaling in aleurone cells, thereby establishing a novel mechanism for ABA and GA signaling cross-talk.
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Affiliation(s)
- Zhen Xie
- Department of Biological Sciences, University of Nevada, Las Vegas, NV 89154, USA
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28
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Abstract
Structurally similar to retinoic acid (RA), the phytohormone abscisic acid (ABA) controls many developmental and physiological processes via complicated signaling networks that are composed of receptors, secondary messengers, protein kinase/phosphatase cascades, transcription factors, and chromatin-remodeling factors. In addition, ABA signaling is further modulated by mRNA maturation and stability, microRNA (miRNA) levels, nuclear speckling, and protein degradation. This chapter highlights the identified regulators of ABA signaling and reports their homologues in dicotyledonous and monocotyledonous plants.
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Affiliation(s)
- Zhen Xie
- Department of Biological Sciences, University of Nevada, Las Vegas, Nevada 89154, USA
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29
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Xie Z, Zhang ZL, Zou X, Huang J, Ruas P, Thompson D, Shen QJ. Annotations and functional analyses of the rice WRKY gene superfamily reveal positive and negative regulators of abscisic acid signaling in aleurone cells. Plant Physiol 2005; 137:176-89. [PMID: 15618416 PMCID: PMC548849 DOI: 10.1104/pp.104.054312] [Citation(s) in RCA: 298] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2004] [Revised: 11/11/2004] [Accepted: 11/15/2004] [Indexed: 05/18/2023]
Abstract
The WRKY proteins are a superfamily of regulators that control diverse developmental and physiological processes. This family was believed to be plant specific until the recent identification of WRKY genes in nonphotosynthetic eukaryotes. We have undertaken a comprehensive computational analysis of the rice (Oryza sativa) genomic sequences and predicted the structures of 81 OsWRKY genes, 48 of which are supported by full-length cDNA sequences. Eleven OsWRKY proteins contain two conserved WRKY domains, while the rest have only one. Phylogenetic analyses of the WRKY domain sequences provide support for the hypothesis that gene duplication of single- and two-domain WRKY genes, and loss of the WRKY domain, occurred in the evolutionary history of this gene family in rice. The phylogeny deduced from the WRKY domain peptide sequences is further supported by the position and phase of the intron in the regions encoding the WRKY domains. Analyses for chromosomal distributions reveal that 26% of the predicted OsWRKY genes are located on chromosome 1. Among the dozen genes tested, OsWRKY24, -51, -71, and -72 are induced by abscisic acid (ABA) in aleurone cells. Using a transient expression system, we have demonstrated that OsWRKY24 and -45 repress ABA induction of the HVA22 promoter-beta-glucuronidase construct, while OsWRKY72 and -77 synergistically interact with ABA to activate this reporter construct. This study provides a solid base for functional genomics studies of this important superfamily of regulatory genes in monocotyledonous plants and reveals a novel function for WRKY genes, i.e. mediating plant responses to ABA.
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Affiliation(s)
- Zhen Xie
- Department of Biological Sciences, University of Nevada, Las Vegas, Nevada 89154, USA
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30
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Abstract
The creosote bush (Larrea tridentata) is a xerophytic evergreen C3 shrub thriving in vast arid areas of North America. As the first step toward understanding the molecular mechanisms controlling the drought tolerance of this desert plant, we have isolated a dozen genes encoding transcription factors, including LtWRKY21 that encodes a protein of 314 amino acid residues. Transient expression studies with the GFP-LtWRKY21 fusion construct indicate that the LtWRKY21 protein is localized in the nucleus and is able to activate the promoter of an abscisic acid (ABA)-inducible gene, HVA22, in a dosage-dependent manner. The transactivating activity of LtWRKY21 relies on the C-terminal sequence containing the WRKY domain and a N-terminal motif that is essential for the repression activity of some regulators in ethylene signaling. LtWRKY21 interacts synergistically with ABA and transcriptional activators VP1 and ABI5 to control the expression of the HVA22 promoter. Co-expression of VP1, ABI5, and LtWRKY21 leads to a much higher expression of the HVA22 promoter than does the ABA treatment alone. In contrast, the Lt-WRKY21-mediated transactivation is inhibited by two known negative regulators of ABA signaling: 1-butanol, an inhibitor of phospholipase D, and abi1-1, a dominant negative mutant protein phosphatase. Interestingly, abi1-1 does not block the synergistic effect of LtWRKY21, VP1, and ABI5 co-expression, indicating that LtWRKY21, VP1, and ABI5 may form a complex that functions downstream of ABI1 to control ABA-regulated expression of genes.
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MESH Headings
- 1-Butanol/pharmacology
- Abscisic Acid/metabolism
- Amino Acid Motifs
- Amino Acid Sequence
- Blotting, Northern
- Cell Nucleus/metabolism
- DNA/metabolism
- DNA, Complementary/metabolism
- DNA-Binding Proteins/physiology
- Dose-Response Relationship, Drug
- Ethylenes/chemistry
- Gene Expression Regulation, Plant
- Gene Library
- Genes, Dominant
- Genes, Plant
- Genes, Reporter
- Green Fluorescent Proteins/chemistry
- Green Fluorescent Proteins/metabolism
- Models, Genetic
- Molecular Sequence Data
- Mutation
- Phospholipase D/antagonists & inhibitors
- Plant Proteins/physiology
- Plants/metabolism
- Promoter Regions, Genetic
- Protein Binding
- Protein Structure, Tertiary
- RNA/chemistry
- Recombinant Fusion Proteins/chemistry
- Sequence Homology, Amino Acid
- Signal Transduction
- Transcription Factors/physiology
- Transcriptional Activation
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Affiliation(s)
- Xiaolu Zou
- Department of Biological Sciences, University of Nevada-Las Vegas, 4505 Maryland Parkway, Las Vegas, NV 89154, USA
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31
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Zhang ZL, Xie Z, Zou X, Casaretto J, Ho THD, Shen QJ. A rice WRKY gene encodes a transcriptional repressor of the gibberellin signaling pathway in aleurone cells. Plant Physiol 2004; 134:1500-13. [PMID: 15047897 PMCID: PMC419826 DOI: 10.1104/pp.103.034967] [Citation(s) in RCA: 219] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2003] [Revised: 11/21/2003] [Accepted: 01/13/2004] [Indexed: 05/18/2023]
Abstract
The molecular mechanism by which GA regulates plant growth and development has been a subject of active research. Analyses of the rice (Oryza sativa) genomic sequences identified 77 WRKY genes, among which OsWRKY71 is highly expressed in aleurone cells. Transient expression of OsWRKY71 by particle bombardment specifically represses GA-induced Amy32b alpha-amylase promoter but not abscisic acid-induced HVA22 or HVA1 promoter activity in aleurone cells. Moreover, OsWRKY71 blocks the activation of the Amy32b promoter by the GA-inducible transcriptional activator OsGAMYB. Consistent with its role as a transcriptional repressor, OsWRKY71 is localized to nuclei of aleurone cells and binds specifically to functionally defined TGAC-containing W boxes of the Amy32b promoter in vitro. Mutation of the two W boxes prevents the binding of OsWRKY71 to the mutated promoter, and releases the suppression of the OsGAMYB-activated Amy32b expression by OsWRKY71, suggesting that OsWRKY71 blocks GA signaling by functionally interfering with OsGAMYB. Exogenous GA treatment decreases the steady-state mRNA level of OsWRKY71 and destabilizes the GFP:OsWRKY71 fusion protein. These findings suggest that OsWRKY71 encodes a transcriptional repressor of GA signaling in aleurone cells.
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Affiliation(s)
- Zhong-Lin Zhang
- Department of Biological Sciences, University of Nevada, 4505 Maryland Parkway, Las Vegas, Nevada 89154, USA
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32
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Fu J, Ikegami H, Kawaguchi Y, Fujisawa T, Kawabata Y, Hamada Y, Ueda H, Shintani M, Nojima K, Babaya N, Shen QJ, Uchigata Y, Urakami T, Omori Y, Shima K, Ogihara T. Association of distal chromosome 2q with IDDM in Japanese subjects. Diabetologia 1998; 41:228-32. [PMID: 9498658 DOI: 10.1007/s001250050894] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
An insulin-dependent diabetes mellitus (IDDM)-susceptibility gene (IDDM13) has recently been mapped to a region of distal chromosome 2q, which is syntenic to the region of mouse chromosome 1 containing a murine susceptibility gene for IDDM, Idd5. To determine the contribution of this region to IDDM disease susceptibility further and to narrow the region for positional cloning of susceptibility genes, we have studied the association of distal chromosome 2q with IDDM in the genetically distinct Japanese population. A 137 mobility unit (mu) allele at D2S137 locus was significantly associated with IDDM (odds ratio 1.92, p = 0.0016). Other markers, D2S301 and D2S143, located in the same region were not associated with IDDM, indicating that IDDM13 is in linkage disequilibrium with D2S137, but not with D2S301 or D2S143. The association of D2S137 with IDDM was observed in patients lacking one of two high risk HLA alleles, DQBI*0303 and DQBI*0401, but not in patients with either of these alleles. The frequency of high risk HLA alleles was significantly lower in patients with the susceptible allele at D2S137, suggesting that IDDMI3 contributes to IDDM susceptibility in subjects without high risk genotypes at IDDM1. Demonstration of allelic association of D2S137 with IDDM localizes IDDM13 in the close vicinity (<2 centiMorgans) of D2S137, greatly facilitating fine structure mapping and positional cloning of IDDM13.
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Affiliation(s)
- J Fu
- Department of Geriatric Medicine, Osaka University Medical School, Suita, Japan
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33
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Shen QJ. [Affective disorder: clinical and basic study]. Zhonghua Yi Xue Za Zhi 1994; 74:587-8. [PMID: 7842330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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34
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Zheng YP, Xu LY, Shen QJ. Styles of verbal expression of emotional and physical experiences: a study of depressed patients and normal controls in China. Cult Med Psychiatry 1986; 10:231-43. [PMID: 3757540 DOI: 10.1007/bf00114698] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Sixty depressed patients and 52 normal controls completed three selfreport inventories: the Symptom Checklist-90 (SCL-90), the Beck Depression Inventory (BDI) and a new Verbal Style Investigation Schedule (VESIS) developed by the first author. The VESIS uses 16 key emotional and physical terms from Western inventories and identified the words and phrases most commonly used by Chinese patients to express these feeling states. Chinese subjects commonly used the key term itself for only 3 or the 16 key terms; they usually preferred to use other words or phrases to express the feeling state. We categorized these Chinese expressions into four styles of verbal expression: Psychological, Somatic, Neutral (i.e., a mixture of psychological and somatic) and Deficient (i.e., lack of expression because of denial or suppression). Three of the 12 key emotional terms of the VESIS (depressed, fearful, and anxiousness) were more commonly expressed in a somatic or neutral mode than the other key emotional terms. The key terms "suicidal interest" and "being punished" were more commonly expressed in a deficient style than other key emotional terms. The somatic factor score of the SCL-90 was not correlated with increased somatic expression of emotional states; thus patients who have multiple somatic complaints are not more likely to express emotions somatically. The hypothesis of somatization is discussed in light of this study.
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35
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Shen QJ. [Re-analysis of the diagnostic significance of the dexamethasone suppression test in depression]. Zhonghua Shen Jing Jing Shen Ke Za Zhi 1985; 18:279-83. [PMID: 3833512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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36
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Shen QJ. [A clinical analysis of 34 cases of misdiagnosed manic-depressive psychosis]. Zhonghua Shen Jing Jing Shen Ke Za Zhi 1984; 17:231-5. [PMID: 6536456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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37
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Shen QJ. [Clinical diagnosis of affective psychosis]. Zhonghua Shen Jing Jing Shen Ke Za Zhi 1983; 16:378-81. [PMID: 6678219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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38
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Shen QJ. [Quantitative analysis of gamma-aminobutyric acid and glutamic acid in the cerebrospinal fluid of schizophrenics]. Zhonghua Shen Jing Jing Shen Ke Za Zhi 1982; 15:98-103. [PMID: 6127192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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