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Singh SK, Richmond MD, Pearce RC, Bailey WA, Hou X, Pattanaik S, Yuan L. Maleic hydrazide elicits global transcriptomic changes in chemically topped tobacco to influence shoot bud development. PLANTA 2020; 252:64. [PMID: 32968874 DOI: 10.1007/s00425-020-03460-9] [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: 06/24/2020] [Accepted: 09/12/2020] [Indexed: 06/11/2023]
Abstract
MAIN CONCLUSION Transcriptomic analysis revealed maleic hydrazide suppresses apical and axillary bud development by altering the expression of genes related to meristem development, cell division, DNA replication, DNA damage and recombination, and phytohormone signaling. Topping (removal of apical buds) is a common agricultural practice for some crop plants including cotton, cannabis, and tobacco. Maleic hydrazide (MH) is a systemic suckercide, a chemical that inhibits shoot bud growth, used to control the growth of apical (ApB) and axillary buds (AxB) following topping. However, the influence of MH on gene expression and the underlying molecular mechanism of controlling meristem development are not well studied. Our RNA sequencing analysis showed that MH significantly influences the transcriptomic landscape in ApB and AxB of chemically topped tobacco. Gene ontology (GO) enrichment analysis revealed that upregulated genes in ApB were enriched for phosphorelay signal transduction, and the regulation of transition timing from vegetative to reproductive phase, whereas downregulated genes were largely associated with meristem maintenance, cytokinin metabolism, cell wall synthesis, photosynthesis, and DNA metabolism. In MH-treated AxB, GO terms related to defense response and oxylipin metabolism were overrepresented in upregulated genes. GO terms associated with cell cycle, DNA metabolism, and cytokinin metabolism were enriched in downregulated genes. Expression of KNOX and MADS transcription factor (TF) family genes, known to be involved in meristem development, were affected in ApB and AxB by MH treatment. The promoters of MH-responsive genes are enriched for several known cis-acting elements, suggesting the involvement of a subset of TF families. Our findings suggest that MH affects shoot bud development in chemically topped tobacco by altering the expression of genes related to meristem development, DNA repair and recombination, cell division, and phytohormone signaling.
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Affiliation(s)
- Sanjay K Singh
- Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA
| | - Mitchell D Richmond
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546, USA
- Canadian Tobacco Research Foundation, Tillsonburg, ON, N4G 4H5, Canada
| | - Robert C Pearce
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546, USA
| | - William A Bailey
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546, USA
| | - Xin Hou
- Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA
- Department of Tobacco, College of Plant Protection, Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai`an, 271018, China
| | - Sitakanta Pattanaik
- Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA.
| | - Ling Yuan
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546, USA.
- Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA.
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2
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Jin J, Xu Y, Lu P, Chen Q, Liu P, Wang J, Zhang J, Li Z, Yang A, Li F, Cao P. Degradome, small RNAs and transcriptome sequencing of a high-nicotine cultivated tobacco uncovers miRNA's function in nicotine biosynthesis. Sci Rep 2020; 10:11751. [PMID: 32678207 PMCID: PMC7366715 DOI: 10.1038/s41598-020-68691-y] [Citation(s) in RCA: 7] [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: 02/28/2020] [Accepted: 06/25/2020] [Indexed: 11/26/2022] Open
Abstract
Tobacco (Nicotiana tabacum) is considered as the model plant for alkaloid research, of which nicotine accounts for 90%. Many nicotine biosynthetic genes have been identified and were known to be regulated by jasmonate-responsive transcription factors. As an important regulator in plant physiological processes, whether small RNAs are involved in nicotine biosynthesis is largely unknown. Here, we combine transcriptome, small RNAs and degradome analysis of two native tobacco germplasms YJ1 and ZY100 to investigate small RNA's function. YJ1 leaves accumulate twofold higher nicotine than ZY100. Transcriptome analysis revealed 3,865 genes which were differently expressed in leaf and root of two germplasms, including some known nicotine and jasmonate pathway genes. By small RNA sequencing, 193 miRNAs were identified to be differentially expressed between YJ1 and ZY100. Using in silico and degradome sequencing approaches, six nicotine biosynthetic genes and seven jasmonate pathway genes were predicted to be targeted by 77 miRNA loci. Three pairs among them were validated by transient expression in vivo. Combined analysis of degradome and transcriptome datasets revealed 51 novel miRNA-mRNA interactions that may regulate nicotine biosynthesis. The comprehensive analysis of our study may provide new insights into the regulatory network of nicotine biosynthesis.
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Affiliation(s)
- Jingjing Jin
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Yalong Xu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Peng Lu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Qiansi Chen
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Pingping Liu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Jinbang Wang
- China Tobacco Science and Technology Information Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Jianfeng Zhang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Zefeng Li
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Aiguo Yang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Fengxia Li
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China.
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3
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Weng ST, Kuo YW, King YC, Lin HH, Tu PY, Tung KS, Jeng ST. Regulation of micoRNA2111 and its target IbFBK in sweet potato on wounding. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 292:110391. [PMID: 32005396 DOI: 10.1016/j.plantsci.2019.110391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/25/2019] [Accepted: 12/24/2019] [Indexed: 05/14/2023]
Abstract
Plant microRNAs (miRNAs) are non-coding RNAs, which are composed of 20-24 nucleotides. MiRNAs play important roles in plant growth and responses to biotic and abiotic stresses. Wounding is one of the most serious stresses for plants; however, the regulation of miRNAs in plants upon wounding is not well studied. In this study, miR2111, a wound-repressed miRNA, identified previously in sweet potato (Ipomoea batatas cv Tainung 57) by small RNA deep sequencing was chosen for further analysis. Based on sweet potato transcriptome database, F-box/kelch repeat protein (IbFBK), a target gene of miR2111, was identified. IbFBK is a wound-inducible gene, and the miR2111-induced cleavage site in IbFBK mRNA is between the 10th and 11th nucleotides of miR2111. IbFBK is a component of the E3 ligase SCF (SKP1-Cullin-F-box) complex participating in protein ubiquitination and degradation. The results of yeast two-hybrid and bimolecular fluorescence complementation assays demonstrate that IbFBK was conjugated with IbSKP1 through the F-box domain in IbFBK N-terminus to form SCF complex, and interacted with IbCNR8 through the kelch-repeat domain in IbFBK C-terminus. The interaction of IbFBK and IbCNR8 may lead to the ubiquitination and degradation of IbCNR8. In conclusion, the suppression of miR2111 resulted in the increase of IbFBK, and may regulate protein degradation of IbCNR8 in sweet potato responding to wounding.
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Affiliation(s)
- Shiau-Ting Weng
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei 10617, Taiwan.
| | - Yun-Wei Kuo
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei 10617, Taiwan; Academy of Agricultural Sciences, Sanming 365000, Fujian, China.
| | - Yu-Chi King
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei 10617, Taiwan.
| | - Hsin-Hung Lin
- Department of Horticulture and Biotechnology, Chinese Culture University, Taipei 11114, Taiwan.
| | - Pin-Yang Tu
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei 10617, Taiwan.
| | - Kuei-Shu Tung
- Institute of Molecular and Cellular Biology and Department of Life Science, National Taiwan University, Taipei 10617, Taiwan.
| | - Shih-Tong Jeng
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei 10617, Taiwan.
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Chen X, Sun S, Liu F, Shen E, Liu L, Ye C, Xiao B, Timko MP, Zhu QH, Fan L, Cao P. A transcriptomic profile of topping responsive non-coding RNAs in tobacco roots (Nicotiana tabacum). BMC Genomics 2019; 20:856. [PMID: 31726968 PMCID: PMC6854694 DOI: 10.1186/s12864-019-6236-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 10/28/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long ncRNAs (lncRNAs) and circular RNAs (circRNAs), accomplish remarkable variety of biological functions. However, the composition of ncRNAs and their interactions with coding RNAs in modulating and controlling of cellular process in plants is largely unknown. Using a diverse group of high-throughput sequencing strategies, the mRNA, miRNA, lncRNA and circRNA compositions of tobacco (Nicotiana tabacum) roots determined and their alteration and potential biological functions in response to topping treatment analyzed. RESULTS A total of 688 miRNAs, 7423 non-redundant lncRNAs and 12,414 circRNAs were identified, among which, some selected differentially expressed RNAs were verified by quantitative real-time PCR. Using the differentially expressed RNAs, a co-expression network was established that included all four types of RNAs. The number of circRNAs identified were higher than that of miRNAs and lncRNAs, but only two circRNAs were present in the co-expression network. LncRNAs appear to be the most active ncRNAs based on their numbers presented in the co-expression network, but none of them seems to be an eTM (endogenous Target Mimicry) of miRNAs. Integrated with analyses of sequence interaction, several mRNA-circRNA-miRNA interaction networks with a potential role in the regulation of nicotine biosynthesis were uncovered, including a QS-circQS-miR6024 interaction network. In this network miR6024 was significantly down-regulated, while the expression levels of its two targets, circQS and its host gene QS, were sharply increased following the topping treatment. CONCLUSIONS These results illustrated the transcriptomic profiles of tobacco roots, the organ responsible for nicotine biosynthesis. mRNAs always play the most important roles, while ncRNAs are also expressed extensively for topping treatment response, especially circRNAs are the most activated in the ncRNA pool. These studies also provided insights on the coordinated regulation module of coding and non-coding RNAs in a single plant biological sample. The findings reported here indicate that ncRNAs appear to form interaction complex for the regulation of stress response forming regulation networks with transcripts involved in nicotine biosynthesis in tobacco.
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Affiliation(s)
- Xi Chen
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058 China
- Research Center for Air Pollution and Health, Zhejiang University, Hangzhou, 310058 China
| | - Shuo Sun
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058 China
| | - Fangjie Liu
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058 China
- Research Center for Air Pollution and Health, Zhejiang University, Hangzhou, 310058 China
| | - Enhui Shen
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058 China
| | - Lu Liu
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058 China
| | - Chuyu Ye
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058 China
| | - Bingguang Xiao
- Key Laboratory of Tobacco Biotechnological Breeding, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021 China
| | - Michael P. Timko
- Department of Biology, University of Virginia, Charlottesville, VA 22904 USA
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2601 Australia
| | - Longjiang Fan
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058 China
- Research Center for Air Pollution and Health, Zhejiang University, Hangzhou, 310058 China
| | - Peijian Cao
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001 China
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5
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Yan S, Niu Z, Yan H, Zhang A, Liu G. Transcriptome sequencing reveals the effect of biochar improvement on the development of tobacco plants before and after topping. PLoS One 2019; 14:e0224556. [PMID: 31671156 PMCID: PMC6822942 DOI: 10.1371/journal.pone.0224556] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 10/16/2019] [Indexed: 11/19/2022] Open
Abstract
The application of biochar is one of the most useful methods for improving soil quality, which is of the utmost significance for the continuous production of crops. As there are no conclusive studies on the specific effects of biochar application on tobacco quality, this study aimed to improve the yield and quality of tobacco as a model crop for economic and genetic research in southern China, by such application. We used transcriptome sequencing to reveal the effects of applied biochar on tobacco development before and after topping. Our results showed that topping affected carbon and nitrogen metabolism, photosynthesis and secondary metabolism in the tobacco plants, while straw biochar-application to the soil resulted in amino acid and lipid synthesis; additionally, it affected secondary metabolism of the tobacco plants through carbon restoration and hormonal action, before and after topping. In addition to the new insights into the impact of biochar on crops, our findings provide a basis for biochar application measures in tobacco and other crops.
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Affiliation(s)
- Shen Yan
- Department of Tobacco cultivation, College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan Province, China
- Henan Biochar Engineering Technology Research Center, Zhengzhou, Henan Province, China
- Henan Biochar Technology Engineering Laboratory, Zhengzhou, Henan Province, China
- Department of Microbiology, College of Agriculture and Life Science, Cornell University, Ithaca, NY, United States of America
| | - Zhengyang Niu
- Department of Tobacco cultivation, College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan Province, China
- Henan Biochar Engineering Technology Research Center, Zhengzhou, Henan Province, China
- Henan Biochar Technology Engineering Laboratory, Zhengzhou, Henan Province, China
| | - Haitao Yan
- Department of Tobacco cultivation, College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan Province, China
- Henan Biochar Engineering Technology Research Center, Zhengzhou, Henan Province, China
- Henan Biochar Technology Engineering Laboratory, Zhengzhou, Henan Province, China
| | - Aigai Zhang
- Department of Tobacco cultivation, College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan Province, China
- Henan Biochar Engineering Technology Research Center, Zhengzhou, Henan Province, China
- Henan Biochar Technology Engineering Laboratory, Zhengzhou, Henan Province, China
| | - Guoshun Liu
- Department of Tobacco cultivation, College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan Province, China
- Henan Biochar Engineering Technology Research Center, Zhengzhou, Henan Province, China
- Henan Biochar Technology Engineering Laboratory, Zhengzhou, Henan Province, China
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6
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Liu J, Gao Y, Tang Y, Wang D, Chen X, Yao Y, Guo Y. Genome-Wide Identification, Comprehensive Gene Feature, Evolution, and Expression Analysis of Plant Metal Tolerance Proteins in Tobacco Under Heavy Metal Toxicity. Front Genet 2019; 10:345. [PMID: 31105736 PMCID: PMC6491887 DOI: 10.3389/fgene.2019.00345] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/29/2019] [Indexed: 11/13/2022] Open
Abstract
Plant metal tolerance proteins (MTPs) comprise a family of membrane divalent cation transporters that play essential roles in plant mineral nutrition maintenance and heavy metal stresses resistance. However, the evolutionary relationships and biological functions of MTP family in tobacco remain unclear. In the present study, 26, 13, and 12 MTPs in three main Nicotiana species (N. tabacum, N. sylvestris, and N. tomentosiformis) were identified and designated, respectively. The phylogenetic relationships, gene structures, chromosome distributions, conserved motifs, and domains of NtMTPs were systematic analyzed. According to the phylogenetic features, 26 NtMTPs were classified into three major substrate-specific groups that were Zn-cation diffusion facilitators (CDFs), Zn/Fe-CDFs, and Mn-CDFs, and seven primary groups (1, 5, 6, 7, 8, 9, and 12). All of the NtMTPs contained a modified signature sequence and the cation_efflux domain, whereas some of them also harbored the ZT_dimer. Evolutionary analysis showed that NtMTP family of N. tabacum originated from its parental genome of N. sylvestris and N. tomentosiformis, and further underwent gene loss and expanded via one segmental duplication event. Moreover, the prediction of cis-acting elements (CREs) and the microRNA target sites of NtMTP genes suggested the diverse and complex regulatory mechanisms that control NtMTPs gene expression. Expression profile analysis derived from transcriptome data and quantitative real-time reverse transcription-PCR (qRT-PCR) analysis showed that the tissue expression patterns of NtMTPs in the same group were similar but varied among groups. Besides, under heavy metal toxicity, NtMTP genes exhibited various responses in either tobacco leaves or roots. 19 and 15 NtMTPs were found to response to at least one metal ion treatment in leaves and roots, respectively. In addition, NtMTP8.1, NtMTP8.4, and NtMTP11.1 exhibited Mn transport abilities in yeast cells. These results provided a perspective on the evolution of MTP genes in tobacco and were helpful for further functional characterization of NtMTP genes.
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Affiliation(s)
- Jikai Liu
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, China.,State Defense Key Laboratory of the Nuclear Waste and Environmental Security, Southwest University of Science and Technology, Mianyang, China
| | - Yongfeng Gao
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Yunlai Tang
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, China.,State Defense Key Laboratory of the Nuclear Waste and Environmental Security, Southwest University of Science and Technology, Mianyang, China
| | - Dan Wang
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, China.,State Defense Key Laboratory of the Nuclear Waste and Environmental Security, Southwest University of Science and Technology, Mianyang, China
| | - XiaoMing Chen
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, China.,State Defense Key Laboratory of the Nuclear Waste and Environmental Security, Southwest University of Science and Technology, Mianyang, China
| | - Yinan Yao
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Yaoling Guo
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, China
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Chen Y, Dong J, Bennetzen JL, Zhong M, Yang J, Zhang J, Li S, Hao X, Zhang Z, Wang X. Integrating transcriptome and microRNA analysis identifies genes and microRNAs for AHO-induced systemic acquired resistance in N. tabacum. Sci Rep 2017; 7:12504. [PMID: 28970509 PMCID: PMC5624873 DOI: 10.1038/s41598-017-12249-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 09/04/2017] [Indexed: 11/09/2022] Open
Abstract
3-Acetonyl-3-hydroxyoxindole (AHO) induces systemic acquired resistance (SAR) in Nicotiana. However, the underlying molecular mechanism is not well understood. To understand the molecular regulation during SAR induction, we examined mRNA levels, microRNA (miRNA) expression, and their regulatory mechanisms in control and AHO-treated tobacco leaves. Using RNA-seq analysis, we identified 1,445 significantly differentially expressed genes (DEGs) at least 2 folds with AHO treatment. The DEGs significantly enriched in six metabolism pathways including phenylpropanoid biosynthesis, sesquiterpenoid and triterpenoid biosynthesis for protective cuticle and wax. Key DEGs including PALs and PR-10 in salicylic acid pathway involved in SAR were significantly regulated. In addition, we identified 403 miRNAs belonging to 200 miRNA families by miRNA sequencing. In total, AHO treatment led to 17 up- and 6 down-regulated at least 2 folds (Wald test, P < 0.05) miRNAs (DEMs), respectively. Targeting analysis implicated four DEMs regulating three DEGs involved in disease resistance, including miR156, miR172f, miR172g, miR408a, SPL6 and AP2. We concluded that both mRNA and miRNA regulation enhances AHO-induced SAR. These data regarding DEGs, miRNAs, and their regulatory mechanisms provide molecular evidence for the mechanisms involved in tobacco SAR, which are likely to be present in other plants.
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Affiliation(s)
- Yongdui Chen
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences; Yunnan Provincial Key Laboratory of Agricultural Biotechnology; Key Lab of Southwestern Crop Gene Resource and Germplasm Innovation, Ministry of Agriculture, Kunming, 650223, P. R. China
| | - Jiahong Dong
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences; Yunnan Provincial Key Laboratory of Agricultural Biotechnology; Key Lab of Southwestern Crop Gene Resource and Germplasm Innovation, Ministry of Agriculture, Kunming, 650223, P. R. China
| | - Jeffrey L Bennetzen
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, P. R. China
- Department of Genetics, University of Georgia, Athens, USA
| | - Micai Zhong
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, P. R. China
| | - Jun Yang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, P. R. China
| | - Jie Zhang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences; Yunnan Provincial Key Laboratory of Agricultural Biotechnology; Key Lab of Southwestern Crop Gene Resource and Germplasm Innovation, Ministry of Agriculture, Kunming, 650223, P. R. China
| | - Shunlin Li
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, P. R. China
| | - Xiaojiang Hao
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, P. R. China
| | - Zhongkai Zhang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences; Yunnan Provincial Key Laboratory of Agricultural Biotechnology; Key Lab of Southwestern Crop Gene Resource and Germplasm Innovation, Ministry of Agriculture, Kunming, 650223, P. R. China.
| | - Xuewen Wang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, P. R. China.
- Department of Genetics, University of Georgia, Athens, USA.
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Djami-Tchatchou AT, Sanan-Mishra N, Ntushelo K, Dubery IA. Functional Roles of microRNAs in Agronomically Important Plants-Potential as Targets for Crop Improvement and Protection. FRONTIERS IN PLANT SCIENCE 2017; 8:378. [PMID: 28382044 PMCID: PMC5360763 DOI: 10.3389/fpls.2017.00378] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/06/2017] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs that have recently emerged as important regulators of gene expression, mainly through cleavage and/or translation inhibition of the target mRNAs during or after transcription. miRNAs play important roles by regulating a multitude of biological processes in plants which include maintenance of genome integrity, development, metabolism, and adaptive responses toward environmental stresses. The increasing population of the world and their food demands requires focused efforts for the improvement of crop plants to ensure sustainable food production. Manipulation of mRNA transcript abundance via miRNA control provides a unique strategy for modulating differential plant gene expression and miRNAs are thus emerging as the next generation targets for genetic engineering for improvement of the agronomic properties of crops. However, a deeper understanding of its potential and the mechanisms involved will facilitate the design of suitable strategies to obtain the desirable traits with minimum trade-offs in the modified crops. In this regard, this review highlights the diverse roles of conserved and newly identified miRNAs in various food and industrial crops and recent advances made in the uses of miRNAs to improve plants of agronomically importance so as to significantly enhance crop yields and increase tolerance to various environmental stress agents of biotic-or abiotic origin.
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Affiliation(s)
- Arnaud T. Djami-Tchatchou
- Department of Agriculture and Animal Health, University of South Africa (Florida Campus)Pretoria, South Africa
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and BiotechnologyNew Delhi, India
| | - Khayalethu Ntushelo
- Department of Agriculture and Animal Health, University of South Africa (Florida Campus)Pretoria, South Africa
| | - Ian A. Dubery
- Department of Biochemistry, University of Johannesburg (Auckland Park Kingsway Campus)Johannesburg, South Africa
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9
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Chen Q, Li M, Zhang Z, Tie W, Chen X, Jin L, Zhai N, Zheng Q, Zhang J, Wang R, Xu G, Zhang H, Liu P, Zhou H. Integrated mRNA and microRNA analysis identifies genes and small miRNA molecules associated with transcriptional and post-transcriptional-level responses to both drought stress and re-watering treatment in tobacco. BMC Genomics 2017; 18:62. [PMID: 28068898 PMCID: PMC5223433 DOI: 10.1186/s12864-016-3372-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 12/02/2016] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Drought stress is one of the most severe problem limited agricultural productivity worldwide. It has been reported that plants response to drought-stress by sophisticated mechanisms at both transcriptional and post-transcriptional levels. However, the precise molecular mechanisms governing the responses of tobacco leaves to drought stress and water status are not well understood. To identify genes and miRNAs involved in drought-stress responses in tobacco, we performed both mRNA and small RNA sequencing on tobacco leaf samples from the following three treatments: untreated-control (CL), drought stress (DL), and re-watering (WL). RESULTS In total, we identified 798 differentially expressed genes (DEGs) between the DL and CL (DL vs. CL) treatments and identified 571 DEGs between the WL and DL (WL vs. DL) treatments. Further analysis revealed 443 overlapping DEGs between the DL vs. CL and WL vs. DL comparisons, and, strikingly, all of these genes exhibited opposing expression trends between these two comparisons, strongly suggesting that these overlapping DEGs are somehow involved in the responses of tobacco leaves to drought stress. Functional annotation analysis showed significant up-regulation of genes annotated to be involved in responses to stimulus and stress, (e.g., late embryogenesis abundant proteins and heat-shock proteins) antioxidant defense (e.g., peroxidases and glutathione S-transferases), down regulation of genes related to the cell cycle pathway, and photosynthesis processes. We also found 69 and 56 transcription factors (TFs) among the DEGs in, respectively, the DL vs. CL and the WL vs. DL comparisons. In addition, small RNA sequencing revealed 63 known microRNAs (miRNA) from 32 families and 368 novel miRNA candidates in tobacco. We also found that five known miRNA families (miR398, miR390, miR162, miR166, and miR168) showed differential regulation under drought conditions. Analysis to identify negative correlations between the differentially expressed miRNAs (DEMs) and DEGs revealed 92 mRNA-miRNA interactions between CL and DL plants, and 32 mRNA-miRNA interactions between DL and WL plants. CONCLUSIONS This study provides a global view of the transcriptional and the post-transcriptional responses of tobacco under drought stress and re-watering conditions. Our results establish an empirical foundation that should prove valuable for further investigations into the molecular mechanisms through which tobacco, and plants more generally, respond to drought stress at multiple molecular genetic levels.
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Affiliation(s)
- Qiansi Chen
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Meng Li
- Key Laboratory of Cultivation and Protection for Non-wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, 410000, China
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, 410000, China
| | - Zhongchun Zhang
- School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Weiwei Tie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Xia Chen
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Lifeng Jin
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Niu Zhai
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Qingxia Zheng
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Jianfeng Zhang
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Ran Wang
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Guoyun Xu
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Hui Zhang
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Pingping Liu
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China.
| | - Huina Zhou
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China.
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10
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He X, Zheng W, Cao F, Wu F. Identification and comparative analysis of the microRNA transcriptome in roots of two contrasting tobacco genotypes in response to cadmium stress. Sci Rep 2016; 6:32805. [PMID: 27667199 PMCID: PMC5036098 DOI: 10.1038/srep32805] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 08/15/2016] [Indexed: 01/07/2023] Open
Abstract
Tobacco (Nicotiana tabacum L.) is more acclimated to cadmium (Cd) uptake and preferentially enriches Cd in leaves than other crops. MicroRNAs (miRNAs) play crucial roles in regulating expression of various stress response genes in plants. However, genome-wide expression of miRNAs and their target genes in response to Cd stress in tobacco are still unknown. Here, miRNA high-throughput sequencing technology was performed using two contrasting tobacco genotypes Guiyan 1 and Yunyan 2 of Cd-sensitive and tolerance. Comprehensive analysis of miRNA expression profiles in control and Cd treated plants identified 72 known (27 families) and 14 novel differentially expressed miRNAs in the two genotypes. Among them, 28 known (14 families) and 5 novel miRNAs were considered as Cd tolerance associated miRNAs, which mainly involved in cell growth, ion homeostasis, stress defense, antioxidant and hormone signaling. Finally, a hypothetical model of Cd tolerance mechanism in Yunyan 2 was presented. Our findings suggest that some miRNAs and their target genes and pathways may play critical roles in Cd tolerance.
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Affiliation(s)
- Xiaoyan He
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, P.R. China
| | - Weite Zheng
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, P.R. China
| | - Fangbin Cao
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, P.R. China
| | - Feibo Wu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, P.R. China
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11
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Xie J, Fan L. Nicotine biosynthesis is regulated by two more layers: Small and long non-protein-coding RNAs. PLANT SIGNALING & BEHAVIOR 2016; 11:e1184811. [PMID: 27172239 PMCID: PMC4973799 DOI: 10.1080/15592324.2016.1184811] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 04/23/2016] [Accepted: 04/26/2016] [Indexed: 05/08/2023]
Abstract
In recent years, many small RNAs and long non-protein-coding RNAs (lncRNAs) have been identified and characterized. They have been proved to play essential regulatory roles in gene expression in both primary and secondary metabolisms. In nature, many plants produce alkaloids. However, there are only few reports on the involvement of non-coding RNAs in alkaloid biosynthesis. Nicotine is major alkaloid in tobacco plants. Its biosynthesis and regulation in tobacco (Nicotiana tabacum) have been well studied; and major structural genes involved in the nicotine biosynthesis and transcriptional regulators related to its biosynthesis have been identified and characterized. In our recent studies, we identified a microRNA (nta-miRX27) and also a lncRNA (nta-eTMX27) as an endogenous target mimicry (eTM) in tobacco targeting the nicotine biosynthesis key gene QPT2 encoding quinolinate phosphoribosyltransferase (QPT) and thereby regulating the nicotine content. Their regulatory pattern leads us to conclude that nicotine biosynthesis is regulated by 2 more layers besides previously known mechanisms. Future study on the relationship between the non-coding RNAs and transcription factors in nicotine biosynthesis was discussed in this article.
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Affiliation(s)
- Jiahua Xie
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute & Technology Enterprise, North Carolina Central University, Durham, NC, USA
| | - Longjiang Fan
- Research Center for Air Pollution and Health, Zhejiang University, Hangzhou, China
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12
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Li F, Zhang H, Wang S, Xiao W, Ding C, Liu W, Guo H. Identification of Topping Responsive Proteins in Tobacco Roots. FRONTIERS IN PLANT SCIENCE 2016; 7:582. [PMID: 27200055 PMCID: PMC4848317 DOI: 10.3389/fpls.2016.00582] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 04/14/2016] [Indexed: 05/27/2023]
Abstract
The process of topping elicits many responses in the tobacco plant, including an increase in nicotine biosynthesis, and the secondary growth of roots. Some topping responsive miRNAs and genes have been identified in our previous study, but the mechanism of the tobacco response to topping has not yet been fully elucidated. In this study, topping responsive proteins isolated from tobacco roots were screened using two-dimensional electrophoresis. Of the proteins identified, calreticulin and auxin-responsive protein indole acetic acid (IAA9) were involved in the secondary growth of roots; leucine-rich repeat disease resistance, heat shock protein 70, and farnesyl pyrophosphate synthase 1 were involved in the wounding stress response; and F-box protein played an important role in promoting the ability of nicotine synthesis after topping. In addition, we identified five tobacco bHLH proteins (NtbHLH, NtMYC1a, NtMYC1b, NtMYC2a, and NtMYC2b) related to nicotine biosynthesis. NtMYC2 was suggested to be the main positive transcription factor, with NtbHLH protein being a negative regulator in the jasmonic acid (JA)-mediated activation of nicotine biosynthesis after topping. Tobacco topping activates a comprehensive range of biological processes involving the IAA and JA signaling pathways, and the identification of proteins involved in these processes will improve our understanding of the topping response.
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Affiliation(s)
- Fei Li
- College of Life Sciences, Henan Agricultural UniversityZhengzhou, China
| | - Huizhen Zhang
- College of Public Health, Zhengzhou UniversityZhengzhou, China
| | - Shaoxin Wang
- College of Life Sciences, Henan Agricultural UniversityZhengzhou, China
| | - Wanfu Xiao
- College of Life Sciences, Henan Agricultural UniversityZhengzhou, China
| | - Chao Ding
- College of Life Sciences, Henan Agricultural UniversityZhengzhou, China
| | - Weiqun Liu
- College of Life Sciences, Henan Agricultural UniversityZhengzhou, China
| | - Hongxiang Guo
- College of Life Sciences, Henan Agricultural UniversityZhengzhou, China
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13
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Singh SK, Wu Y, Ghosh JS, Pattanaik S, Fisher C, Wang Y, Lawson D, Yuan L. RNA-sequencing Reveals Global Transcriptomic Changes in Nicotiana tabacum Responding to Topping and Treatment of Axillary-shoot Control Chemicals. Sci Rep 2015; 5:18148. [PMID: 26670135 PMCID: PMC4680964 DOI: 10.1038/srep18148] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/12/2015] [Indexed: 11/30/2022] Open
Abstract
Removal of terminal buds (topping) and control of the formation of axillary shoots (suckers) are common agronomic practices that significantly impact the yield and quality of various crop plants. Application of chemicals (suckercides) to plants following topping is an effective method for sucker control. However, our current knowledge of the influence of topping, and subsequent suckercide applications, to gene expression is limited. We analyzed the differential gene expression using RNA-sequencing in tobacco (Nicotiana tabacum) that are topped, or treated after topping by two different suckercides, the contact-localized-systemic, Flupro(®) (FP), and contact, Off-Shoot-T(®). Among the differentially expressed genes (DEGs), 179 were identified as common to all three conditions. DEGs, largely related to wounding, phytohormone metabolism and secondary metabolite biosynthesis, exhibited significant upregulation following topping, and downregulation after suckercide treatments. DEGs related to photosynthetic processes were repressed following topping and suckercide treatments. Moreover, topping and FP-treatment affect the expression of auxin and cytokinin signaling pathway genes that are possibly involved in axillary shoot formation. Our results provide insights into the global change of plant gene expression in response to topping and suckercide treatments. The regulatory elements of topping-inducible genes are potentially useful for the development of a chemical-free sucker control system.
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Affiliation(s)
- Sanjay K. Singh
- Kentucky Tobacco Research and Development Center , University of Kentucky, Lexington, KY 40546, U.S.A
| | - Yongmei Wu
- Kentucky Tobacco Research and Development Center , University of Kentucky, Lexington, KY 40546, U.S.A
| | - Jayadri S. Ghosh
- Kentucky Tobacco Research and Development Center , University of Kentucky, Lexington, KY 40546, U.S.A
| | - Sitakanta Pattanaik
- Kentucky Tobacco Research and Development Center , University of Kentucky, Lexington, KY 40546, U.S.A
| | - Colin Fisher
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, U.S.A.
| | - Ying Wang
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Darlene Lawson
- R J Reynolds, Inc. 950 Reynolds Blvd, Winston-Salem, NC 27102, U.S.A.
| | - Ling Yuan
- Kentucky Tobacco Research and Development Center , University of Kentucky, Lexington, KY 40546, U.S.A
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, U.S.A.
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14
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Gao J, Yin F, Liu M, Luo M, Qin C, Yang A, Yang S, Zhang Z, Shen Y, Lin H, Pan G. Identification and characterisation of tobacco microRNA transcriptome using high-throughput sequencing. PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17:591-8. [PMID: 25287651 DOI: 10.1111/plb.12275] [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: 06/28/2014] [Accepted: 09/26/2014] [Indexed: 05/09/2023]
Abstract
MicroRNAs (miRNAs) are post-transcriptional regulators that are involved in numerous biological processes in plants. In this study, we investigate miRNAs in Honghua Dajinyuan, an agronomically important species of tobacco in China. Here, we report a comprehensive analysis of miRNA expression profiles in the leaf, stem and root using a high-throughput sequencing approach. A total of 165 miRNAs, representing 55 conserved families, and 50 novel miRNAs, representing 19 families, were identified in three libraries. In addition, 12 miRNAs were randomly selected from a differentially expressed conserved miRNA family in three libraries with expression alterations and subjected to qRT-PCR validation. Of these, the expression level of nta-miR167d is highly enriched in the leaf tissue. In addition, the expression level of nta-miR319a is prominently enriched in the stem, while nta-miR160c is highly enriched in the root. Moreover, the target prediction showed that most of the targets coded for transcription factors that are involved in cellular and metabolic processes. GO analysis showed that most of the targets were involved in organelle function, served binding functions, and take part in cellular and metabolic processes. This study helps shed new light on understanding the role of miRNAs in different parts of the tobacco plant and adds a significant number of novel miRNAs to the tobacco miRNA transcriptome.
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Affiliation(s)
- J Gao
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, China
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15
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Guo H, Li F, Wang S, Li S, Xiao W, Liu W. Enhanced Protein Extraction from Tobacco Roots for Proteomic Analysis. ANAL LETT 2014. [DOI: 10.1080/00032719.2014.930871] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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16
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Yin F, Gao J, Liu M, Qin C, Zhang W, Yang A, Xia M, Zhang Z, Shen Y, Lin H, Luo C, Pan G. Genome-wide analysis of water-stress-responsive microRNA expression profile in tobacco roots. Funct Integr Genomics 2014; 14:319-32. [PMID: 24664280 DOI: 10.1007/s10142-014-0365-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 01/09/2014] [Accepted: 02/24/2014] [Indexed: 01/06/2023]
Abstract
MicroRNAs (miRNAs) play a pivotal role in post-transcriptional regulation of gene expression in plants. In this study, we investigate miRNAs in an agronomically important common tobacco in China, named Honghua Dajinyuan (a drought-tolerant cultivar). Here, we report a comprehensive analysis of miRNA expression profiles in mock-treat grown (CK) and 20 % polyethylene glycol-grown (PEG-grown) tobacco roots using a high-throughput sequencing approach. A total of 656 unique miRNAs representing 53 miRNA families were identified in the two libraries, of which 286 unique miRNAs representing 162 microRNAs were differentially expressed. In addition, nine differentially expressed microRNAs selected from different expressed miRNA family with high abundance were subjected to further analysis and validated by quantitative real-time PCR (Q-PCR). In addition, the expression pattern of these identified candidate conserved miRNA and target genes of three identified miRNA (nta-miR172b, nta-miR156i, and nta-miR160a) were also validated by Q-PCR. Gene ontology (GO) enrichment analysis suggests that the putative target genes of these differentially expressed miRNAs are involved in metabolic process and response to stimulus. In particular, 25 target genes are involved in regulating plant hormone signal transduction and metabolism, indicating that these association microRNAs may play important regulatory roles in responding to PEG resistance. Moreover, this study adds a significant number of novel miRNAs to the tobacco miRNome.
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Affiliation(s)
- Fuqiang Yin
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, China
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17
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Bao Y, Wang C, Jiang C, Pan J, Zhang G, Liu H, Zhang H. The tumor necrosis factor receptor-associated factor (TRAF)-like family protein SEVEN IN ABSENTIA 2 (SINA2) promotes drought tolerance in an ABA-dependent manner in Arabidopsis. THE NEW PHYTOLOGIST 2014; 202:174-187. [PMID: 24350984 DOI: 10.1111/nph.12644] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 11/18/2013] [Indexed: 05/18/2023]
Abstract
Tumor necrosis factor receptor-associated factor (TRAF) proteins play crucial roles in plant development and response to abiotic stress. Here, we present genetic evidence that SEVEN IN ABSENTIA 2 (SINA2), a TRAF-like family protein, is involved in abscisic acid (ABA)-related drought stress signaling in Arabidopsis. Gene expression, protein subcellular localization, protein-protein interaction, and a transient transcription dual-luciferase assay were performed. The drought tolerance of SINA2 loss-of-function mutants and SINA2-overexpressing plants was investigated. In Arabidopsis, SINA2 was significantly induced by ABA and drought treatment. The SINA2-YFP fusion protein was predominately localized in the nuclei and cytoplasm. Loss of function of SINA2 (sina2) reduced drought tolerance, whereas overexpression of SINA2 increased stomatal closure, decreased water loss, and therefore improved drought resistance in transgenic plants. Upon ABA treatment, expression of some key ABA- and stress-responsive genes decreased in the sina2 mutant, but increased in SINA2-overexpressing plants. Furthermore, SINA2 was induced in the ABA-deficient mutant by ABA, but not by drought stress. Thus, the drought response of SINA2 was ABA-dependent. ProSINA2::LUC expression in Arabidopsis protoplasts further revealed that ABA-responsive element (ABRE) binding (AREB) protein 1 (AREB1) AREB2 and ABRE-binding factor 3 (ABF3) might regulate SINA2 expression at the transcriptional level. Our results indicate that SINA2 functions as a positive molecular link between drought tolerance and ABA signaling in Arabidopsis.
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Affiliation(s)
- Yan Bao
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Cuiting Wang
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Chunmei Jiang
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Jing Pan
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Guobin Zhang
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Hua Liu
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Hongxia Zhang
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
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18
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Conserved miRNAs and their response to salt stress in wild eggplant Solanum linnaeanum roots. Int J Mol Sci 2014; 15:839-49. [PMID: 24413753 PMCID: PMC3907842 DOI: 10.3390/ijms15010839] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 11/19/2013] [Accepted: 12/30/2013] [Indexed: 11/17/2022] Open
Abstract
The Solanaceae family includes some important vegetable crops, and they often suffer from salinity stress. Some miRNAs have been identified to regulate gene expression in plant response to salt stress; however, little is known about the involvement of miRNAs in Solanaceae species. To identify salt-responsive miRNAs, high-throughput sequencing was used to sequence libraries constructed from roots of the salt tolerant species, Solanum linnaeanum, treated with and without NaCl. The sequencing identified 98 conserved miRNAs corresponding to 37 families, and some of these miRNAs and their expression were verified by quantitative real-time PCR. Under the salt stress, 11 of the miRNAs were down-regulated, and 3 of the miRNAs were up-regulated. Potential targets of the salt-responsive miRNAs were predicted to be involved in diverse cellular processes in plants. This investigation provides valuable information for functional characterization of miRNAs in S. linnaeanum, and would be useful for developing strategies for the genetic improvement of the Solanaceae crops.
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19
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Fu Y, Guo H, Cheng Z, Wang R, Li G, Huo G, Liu W. NtNAC-R1, a novel NAC transcription factor gene in tobacco roots, responds to mechanical damage of shoot meristem. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2013; 69:74-81. [PMID: 23728390 DOI: 10.1016/j.plaphy.2013.05.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Accepted: 05/06/2013] [Indexed: 05/14/2023]
Abstract
Topping is the important agronomic measure for flue-cured tobacco, and results in increase of the nicotine content in top leaves. Nicotine content is one of the vitals factors for the quality of tobacco leaves. Nicotine is exclusively synthesized in tobacco roots, and then transported to the leaves through the xylem. To investigate the molecular mechanism of increase in nicotine biosynthesis ability following topping, some responses of tobacco roots to topping were analyzed, and the role of NtNAC-R1 in regulating nicotine synthesis and the development of roots was discussed. The electronic cloning technique combined with RT-PCR was successfully used to clone NtNAC-R1 from tobacco roots. The number of lateral root and nicotine contents in tobacco roots increased following topping. Although spraying MeJA on leaves had no effects on the root phenotype, the nicotine contents and the expression of PMT increased markedly. The miR164 was down-regulated, and NtNAC-R1 was up-regulated in tobacco roots after topping. PMT and ODC were down-regulated in transgenic tobacco with antisense NtNAC-R1, and PMT was up-regulated in transgenic tobacco with over-expressed NtNAC-R1. In conclusion, topping can induce the decrease of miR164 and the increase of IAA content in roots, which up-regulate the expression of NtNAC-R1, resulting in the increase of lateral roots and nicotine contents. Meanwhile, topping is a mechanical wounding which can induce JA signal, and JA can enhance nicotine biosynthesis in tobacco roots. So the increase of nicotine biosynthesis ability would be related to cross-talking of JA and auxin signaling pathway after topping.
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Affiliation(s)
- Yunpeng Fu
- Key Laboratory of National Tobacco Cultivation, Henan Agricultural University, Zhengzhou 450002, China
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20
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Guo Y, Liu H, Yang Z, Chen J, Sun Y, Ren X. Identification and characterization of miRNAome in tobacco (Nicotiana tabacum) by deep sequencing combined with microarray. Gene 2012; 501:24-32. [PMID: 22575711 DOI: 10.1016/j.gene.2012.04.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Revised: 03/30/2012] [Accepted: 04/02/2012] [Indexed: 11/30/2022]
Abstract
Tobacco is one of the most important economic and agricultural crops worldwide. miRNAs have been increasingly acknowledged for their important roles in different biological processes of tobacco. However, few miRNAs have been identified so far in tobacco impeding the development of new tobacco strains with better properties. In this study, high-throughput sequencing technology was employed to identify novel tobacco miRNAs. A total of 84 potential miRNAs were obtained in tobacco, including 33 conserved and 51 novel miRNAs. Tissue-specific and topping-related miRNAs were identified. A tobacco miRNA microarray was also constructed to investigate miRNA expression patterns in different tissues, and their expression patterns were further validated by qRT-PCR and Northern Blot. Finally, the potential targets of these miRNAs were predicted based on a sequence homology search. Thus, in the current study, we have performed the comprehensive analysis of tobacco miRNAs, including their identification, expression pattern and target prediction. Our study opens a new avenue for further elucidation for their roles underlying the regulation of diversity of physiological processes.
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Affiliation(s)
- Yushuang Guo
- Guizhou Institute of Tobacco Science, Yuntanbei Road, Jinyang District, Guiyang City, Guizhou Province, 550081, PR China
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