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Zhao L, Wang Y, Cui R, Cui Y, Lu X, Chen X, Wang J, Wang D, Yin Z, Wang S, Peng F, Guo L, Chen C, Ye W. Analysis of the histidine kinase gene family and the role of GhHK8 in response to drought tolerance in cotton. PHYSIOLOGIA PLANTARUM 2023; 175:e14022. [PMID: 37882310 DOI: 10.1111/ppl.14022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/27/2023] [Accepted: 08/29/2023] [Indexed: 10/27/2023]
Abstract
As an important member of the two-component system (TCS), histidine kinases (HKs) play important roles in various plant developmental processes and signal transduction in response to a wide range of biotic and abiotic stresses. So far, the HK gene family has not been investigated in Gossypium. In this study, a total of 177 HK gene family members were identified in cotton. They were further divided into seven groups, and the protein characteristics, genetic relationship, gene structure, chromosome location, collinearity, and cis-elements identification were comprehensively analyzed. Whole genome duplication (WGD) / segmental duplication may be the reason why the number of HK genes doubled in tetraploid Gossypium species. Expression analysis revealed that most cotton HK genes were mainly expressed in the reproductive organs and the fiber at initial stage. Gene expression analysis revealed that HK family genes are involved in cotton abiotic stress, especially drought stress and salt stress. In addition, gene interaction networks showed that HKs were involved in the regulation of cotton abiotic stress, especially drought stress. VIGS experiments have shown that GhHK8 is a negative regulatory factor in response to drought stress. Our systematic analysis provided insights into the characteristics of the HK genes in cotton and laid a foundation for further exploring their potential in drought stress resistance in cotton.
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Affiliation(s)
- Lanjie Zhao
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization/National Engineering Research Center of Cotton Biology Breeding and Industrial Technology, Anyang, Henan, China
| | - Yongbo Wang
- Hunan Institute of Cotton Science, Changde, China
| | - Ruifeng Cui
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization/National Engineering Research Center of Cotton Biology Breeding and Industrial Technology, Anyang, Henan, China
| | - Yupeng Cui
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization/National Engineering Research Center of Cotton Biology Breeding and Industrial Technology, Anyang, Henan, China
| | - Xuke Lu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization/National Engineering Research Center of Cotton Biology Breeding and Industrial Technology, Anyang, Henan, China
| | - Xiugui Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization/National Engineering Research Center of Cotton Biology Breeding and Industrial Technology, Anyang, Henan, China
| | - Junjuan Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization/National Engineering Research Center of Cotton Biology Breeding and Industrial Technology, Anyang, Henan, China
| | - Delong Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization/National Engineering Research Center of Cotton Biology Breeding and Industrial Technology, Anyang, Henan, China
| | - Zujun Yin
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization/National Engineering Research Center of Cotton Biology Breeding and Industrial Technology, Anyang, Henan, China
| | - Shuai Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization/National Engineering Research Center of Cotton Biology Breeding and Industrial Technology, Anyang, Henan, China
| | - Fanjia Peng
- Hunan Institute of Cotton Science, Changde, China
| | - Lixue Guo
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization/National Engineering Research Center of Cotton Biology Breeding and Industrial Technology, Anyang, Henan, China
| | - Chao Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization/National Engineering Research Center of Cotton Biology Breeding and Industrial Technology, Anyang, Henan, China
| | - Wuwei Ye
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization/National Engineering Research Center of Cotton Biology Breeding and Industrial Technology, Anyang, Henan, China
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Qiang Y, He X, Li Z, Li S, Zhang J, Liu T, Tursunniyaz M, Wang X, Liu Z, Fang L. Genome-wide identification and expression analysis of the response regulator gene family in alfalfa ( Medicago sativa L.) reveals their multifarious roles in stress response. FRONTIERS IN PLANT SCIENCE 2023; 14:1149880. [PMID: 36998691 PMCID: PMC10043395 DOI: 10.3389/fpls.2023.1149880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 02/23/2023] [Indexed: 06/19/2023]
Abstract
As important components of the two-component regulatory system, response regulatory proteins (RRPs) play a crucial role in histidine phosphorylation-mediated signal transduction in response to environmental fluctuations. Accumulating evidence has revealed that RRPs play important roles in plant growth and stress response. However, the specific functions of RR genes (RRs) in cultivated alfalfa remain ambiguous. Therefore, in this study, we identified and characterized the RR family genes in the alfalfa genome using bioinformatics methods. Our analysis revealed 37 RRs in the alfalfa genome of Zhongmu No.1 that were unevenly distributed on the chromosomes. Cis-elements analysis revealed the involvement of RRs in responses to light, stress, and various plant hormones. Expression analysis of RRs in different tissues revealed their distinct tissue expression patterns. These findings provide preliminary insights into the roles of RRs in plant responses to abiotic stress, which can be used to improve the stress tolerance of autotetraploid-cultivated alfalfa plants via genetic engineering.
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Affiliation(s)
- Yuqin Qiang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiaojuan He
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Zhen Li
- National Engineering Laboratory for Volatile Organic Compounds Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Siqi Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Jia Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Tao Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Mamateliy Tursunniyaz
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xinyu Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Zhipeng Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Longfa Fang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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Bhaskar A, Paul LK, Sharma E, Jha S, Jain M, Khurana JP. OsRR6, a type-A response regulator in rice, mediates cytokinin, light and stress responses when over-expressed in Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 161:98-112. [PMID: 33581623 DOI: 10.1016/j.plaphy.2021.01.047] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/28/2021] [Indexed: 05/27/2023]
Abstract
Plants have evolved a complex network of components that sense and respond to diverse signals. In the present study, we have characterized OsRR6, a type-A response regulator, which is part of the two-component sensor-regulator machinery in rice. The expression of OsRR6 is induced by exogenous cytokinin and various abiotic stress treatments, including drought, cold and salinity stress. Organ-specific expression analysis revealed that its expression is high in anther and low in shoot apical meristem. The Arabidopsis plants constitutively expressing OsRR6 (OsRR6OX) exhibited reduced cytokinin sensitivity, adventitious root formation and enhanced anthocyanin accumulation in seeds. OsRR6OX plants were more tolerant to drought and salinity conditions when compared to wild-type. The hypocotyl growth in OsRR6OX seedlings was significantly inhibited under red, far-red and blue-light conditions and also a decline in transcript levels of OsRR6 was observed in rice under the above monochromatic as well as white light treatments. Transcriptome profiling revealed that the genes associated with defense responses and anthocyanin metabolism are up-regulated in OsRR6OX seedlings. Comparative transcriptome analysis showed that the genes associated with phenylpropanoid and triterpenoid biosynthesis are enriched among differentially expressed genes in OsRR6OX seedlings of Arabidopsis, which is in conformity with reanalysis of the transcriptome data performed in rice transgenics for OsRR6. Further, genes like DREB1A/CBF3, COR15A, KIN1, ERD10 and RD29A are significantly upregulated in OsRR6OX seedlings when subjected to ABA and abiotic stress treatments. Thus, a negative regulator of cytokinin signaling, OsRR6, plays a positive role in imparting abiotic stress tolerance.
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Affiliation(s)
- Avantika Bhaskar
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Laju K Paul
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Eshan Sharma
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Sampoornananda Jha
- Central Department of Biotechnology, Institute of Science and Technology, Tribhuvan University, Kathmandu, Nepal
| | - Mukesh Jain
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India; School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Jitendra P Khurana
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.
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Liu Z, Hua Y, Wang S, Liu X, Zou L, Chen C, Zhao H, Yan Y. Analysis of the Prunellae Spica transcriptome under salt stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 156:314-322. [PMID: 32998098 DOI: 10.1016/j.plaphy.2020.09.023] [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: 03/23/2020] [Accepted: 09/17/2020] [Indexed: 06/11/2023]
Abstract
Prunella vulgaris L. is a moderately salt tolerant plant commonly found in China and Europe, whose spica (Prunellae Spica) has been used as a traditional medicine. The scant transcriptomic and genomic resources of Prunellae Spica have greatly hindered further exploration of the underlying salt tolerance mechanism of this species. To clarify the genetic basis of its salt tolerance, high-throughput sequencing of mRNAs was employed for de novo transcriptome assembly differential expression analysis of Prunellae Spica under salt stress. 118,664 unigenes were obtained by assembling pooled reads from all libraries with 68,119 sequences annotated. A total of 3857 unigenes were differentially expressed under low, medium and high salt stress, including 2456 up-regulated and 1401 down-regulated DEGs, respectively. Gene ontology analysis revealed that salt stress-related categories involving 'catalytic activity', 'binding', 'metabolic process' and 'cellular process' were highly enriched. KEGG pathway annotation showed that the DEGs from different salt stress treatment groups were mainly enriched in the pathways of translation, signal transduction, carbohydrate metabolism, energy metabolism, lipid metabolism and amino acid metabolism, accounting for over 60% of all DEGs. Finally, it showed that the results of quantitative real-time polymerase chain reaction (qRT-PCR) analysis for 10 unigenes that randomly selected were significantly consistent with RNA-seq data, which further assisted in the selection of salt stress-responsive candidate genes in Prunellae Spica. This study represents a significant step forward in understanding the salt tolerance mechanism of Prunellae Spica, and also provides a significant transcriptomic resource for future work.
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Affiliation(s)
- Zixiu Liu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China; National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing, China; Department of Pharmacy, Air Force Hospital of Eastern Theater Command, Nanjing, China
| | - Yujiao Hua
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China; National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing, China
| | - Shengnan Wang
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China; National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing, China
| | - Xunhong Liu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China; National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing, China.
| | - Lisi Zou
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China; National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing, China
| | - Cuihua Chen
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China; National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing, China
| | - Hui Zhao
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China; National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing, China
| | - Ying Yan
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China; National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing, China
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Chefdor F, Héricourt F, Koudounas K, Carqueijeiro I, Courdavault V, Mascagni F, Bertheau L, Larcher M, Depierreux C, Lamblin F, Racchi ML, Carpin S. Highlighting type A RRs as potential regulators of the dkHK1 multi-step phosphorelay pathway in Populus. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 277:68-78. [PMID: 30466602 DOI: 10.1016/j.plantsci.2018.09.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/10/2018] [Accepted: 09/14/2018] [Indexed: 06/09/2023]
Abstract
In previous studies, we highlighted a multistep phosphorelay (MSP) system in poplars composed of two hybrid-type Histidine aspartate Kinases, dkHK1a and dkHK1b, which interact with three Histidine Phosphotransfer proteins, dkHPt2, 7, and 9, which in turn interact with six type B Response Regulators. These interactions correspond to the dkHK1a-b/dkHPts/dkRRBs MSP. This MSP is putatively involved in an osmosensing pathway, as dkHK1a-b are orthologous to the Arabidopsis osmosensor AHK1, and able to complement a mutant yeast deleted for its osmosensors. Since type A RRs have been characterized as negative regulators in cytokinin MSP signaling due to their interaction with HPt proteins, we decided in this study to characterize poplar type A RRs and their implication in the MSP. For a global view of this MSP, we isolated 10 poplar type A RR cDNAs, and determined their subcellular localization to check the in silico prediction experimentally. For most of them, the in planta subcellular localization was as predicted, except for three RRAs, for which this experimental approach gave a more precise localization. Interaction studies using yeast two-hybrid and in planta BiFC assays, together with transcript expression analysis in poplar organs led to eight dkRRAs being singled out as partners which could interfere the dkHK1a-b/dkHPts/dkRRBs MSP identified in previous studies. Consequently, the results obtained in this study now provide an exhaustive view of dkHK1a-b partners belonging to a poplar MSP.
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Affiliation(s)
- F Chefdor
- LBLGC, Université d'Orléans, INRA, USC1328, 45067, Orléans Cedex 2, France
| | - F Héricourt
- LBLGC, Université d'Orléans, INRA, USC1328, 45067, Orléans Cedex 2, France
| | - K Koudounas
- Biomolécules et Biotechnologies Végétales (BBV), EA 2106, Université François Rabelais de Tours, 31 avenue Monge, 37200 Tours, France
| | - I Carqueijeiro
- Biomolécules et Biotechnologies Végétales (BBV), EA 2106, Université François Rabelais de Tours, 31 avenue Monge, 37200 Tours, France
| | - V Courdavault
- Biomolécules et Biotechnologies Végétales (BBV), EA 2106, Université François Rabelais de Tours, 31 avenue Monge, 37200 Tours, France
| | - F Mascagni
- Università di Pisa, Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, Via del Borghetto 80, 56124 Pisa, Italy
| | - L Bertheau
- LBLGC, Université d'Orléans, INRA, USC1328, 45067, Orléans Cedex 2, France
| | - M Larcher
- LBLGC, Université d'Orléans, INRA, USC1328, 45067, Orléans Cedex 2, France
| | - C Depierreux
- LBLGC, Université d'Orléans, INRA, USC1328, 45067, Orléans Cedex 2, France
| | - F Lamblin
- LBLGC, Université d'Orléans, INRA, USC1328, 45067, Orléans Cedex 2, France
| | - M L Racchi
- Scienze delle Produzioni Agroalimentari e dell'Ambiente, sezione di Genetica agraria, via Maragliano, 75 50144 Firenze, Italy
| | - S Carpin
- LBLGC, Université d'Orléans, INRA, USC1328, 45067, Orléans Cedex 2, France.
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Yamburenko MV, Kieber JJ, Schaller GE. Dynamic patterns of expression for genes regulating cytokinin metabolism and signaling during rice inflorescence development. PLoS One 2017; 12:e0176060. [PMID: 28419168 PMCID: PMC5395194 DOI: 10.1371/journal.pone.0176060] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Accepted: 04/04/2017] [Indexed: 11/18/2022] Open
Abstract
Inflorescence development in cereals, including such important crops as rice, maize, and wheat, directly affects grain number and size and is a key determinant of yield. Cytokinin regulates meristem size and activity and, as a result, has profound effects on inflorescence development and architecture. To clarify the role of cytokinin action in inflorescence development, we used the NanoString nCounter system to analyze gene expression in the early stages of rice panicle development, focusing on 67 genes involved in cytokinin biosynthesis, degradation, and signaling. Results point toward key members of these gene families involved in panicle development and indicate that the expression of many genes involved in cytokinin action differs between the panicle and vegetative tissues. Dynamic patterns of gene expression suggest that subnetworks mediate cytokinin action during different stages of panicle development. The variation of expression during panicle development is greater among genes encoding proteins involved in cytokinin metabolism and negative regulators of the pathway than for the genes in the primary response pathway. These results provide insight into the expression patterns of genes involved in cytokinin action during inflorescence development in a crop of agricultural importance, with relevance to similar processes in other monocots. The identification of subnetworks of genes expressed at different stages of early panicle development suggests that manipulation of their expression could have substantial effects on inflorescence architecture.
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Affiliation(s)
- Maria V. Yamburenko
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Joseph J. Kieber
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - G. Eric Schaller
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, United States of America
- * E-mail:
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He Y, Liu X, Zou T, Pan C, Qin L, Chen L, Lu G. Genome-Wide Identification of Two-Component System Genes in Cucurbitaceae Crops and Expression Profiling Analyses in Cucumber. FRONTIERS IN PLANT SCIENCE 2016; 7:899. [PMID: 27446129 PMCID: PMC4916222 DOI: 10.3389/fpls.2016.00899] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/07/2016] [Indexed: 05/30/2023]
Abstract
Cucumber and watermelon, which belong to Cucurbitaceae family, are economically important cultivated crops worldwide. However, these crops are vulnerable to various adverse environments. Two-component system (TCS), consisting of histidine kinases (HKs), phosphotransfers (HPs), and response regulator proteins (RRs), plays important roles in various plant developmental processes and signaling transduction in responses to a wide range of biotic and abiotic stresses. No systematic investigation has been conducted on TCS genes in Cucurbitaceae species. Based on the completion of the cucumber and watermelon genome draft, we identified 46 and 49 TCS genes in cucumber and watermelon, respectively. The cucumber TCS members included 18 HK(L)s, 7 HPs, and 21 RRs, whereas the watermelon TCS system consisted of 19 HK(L)s, 6 HPs, and 24 RRs. The sequences and domains of TCS members from these two species were highly conserved. Gene duplication events occurred rarely, which might have resulted from the absence of recent whole-genome duplication event in these two Cucurbitaceae crops. Numerous stress- and hormone-responsive cis-elements were detected in the putative promoter regions of the cucumber TCS genes. Meanwhile, quantitative real-time PCR indicated that most of the TCS genes in cucumber were specifically or preferentially expressed in certain tissues or organs, especially in the early developing fruit. Some TCS genes exhibited diverse patterns of gene expression in response to abiotic stresses as well as exogenous trans-zeatin (ZT) and abscisic acid (ABA) treatment, suggesting that TCS genes might play significant roles in responses to various abiotic stresses and hormones in Cucurbitaceae crops.
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Affiliation(s)
- Yanjun He
- Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang UniversityHangzhou, China
| | - Xue Liu
- Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang UniversityHangzhou, China
| | - Tao Zou
- Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang UniversityHangzhou, China
| | - Changtian Pan
- Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang UniversityHangzhou, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative BiologyHangzhou, China
| | - Li Qin
- Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang UniversityHangzhou, China
| | - Lifei Chen
- Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang UniversityHangzhou, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative BiologyHangzhou, China
| | - Gang Lu
- Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang UniversityHangzhou, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative BiologyHangzhou, China
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Wen F, Qin T, Wang Y, Dong W, Zhang A, Tan M, Jiang M. OsHK3 is a crucial regulator of abscisic acid signaling involved in antioxidant defense in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2015; 57:213-28. [PMID: 24912543 DOI: 10.1111/jipb.12222] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Accepted: 06/07/2014] [Indexed: 05/21/2023]
Abstract
In this study, the role of the rice (Oryza sativa L.) histidine kinase OsHK3 in abscisic acid (ABA)-induced antioxidant defense was investigated. Treatments with ABA, H2 O2 , and polyethylene glycol (PEG) induced the expression of OsHK3 in rice leaves, and H2 O2 is required for ABA-induced increase in the expression of OsHK3 under water stress. Subcellular localization analysis showed that OsHK3 is located in the cytoplasm and the plasma membrane. The transient expression analysis and the transient RNA interference test in rice protoplasts showed that OsHK3 is required for ABA-induced upregulation in the expression of antioxidant enzymes genes and the activities of antioxidant enzymes. Further analysis showed that OsHK3 functions upstream of the calcium/calmodulin-dependent protein kinase OsDMI3 and the mitogen-activated protein kinase OsMPK1 to regulate the activities of antioxidant enzymes in ABA signaling. Moreover, OsHK3 was also shown to regulate the expression of nicotinamide adenine dinucleotide phosphate oxidase genes, OsrbohB and OsrbohE, and the production of H2 O2 in ABA signaling. Our data indicate that OsHK3 play an important role in the regulation of ABA-induced antioxidant defense and in the feedback regulation of H2 O2 production in ABA signaling.
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Affiliation(s)
- Feng Wen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
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A multi-step phosphorelay two-component system impacts on tolerance against dehydration stress in common wheat. Funct Integr Genomics 2014; 14:707-16. [PMID: 25228409 DOI: 10.1007/s10142-014-0398-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 08/27/2014] [Accepted: 08/31/2014] [Indexed: 02/02/2023]
Abstract
Wheat is an important staple crop, and its productivity is severely constrained by drought stress (DS). An understanding of the molecular basis of drought tolerance is necessary for genetic improvement of wheat for tolerance to DS. The two-component system (TCS) serves as a common sensor-regulator coupling mechanism implicated in the regulation of diverse biological processes (including response to DS) not only in prokaryotes, but also in higher plants. In the latter, TCS generally consists of two signalling elements, a histidine kinase (HK) and a response regulator (RR) associated with an intermediate element called histidine phosphotransferase (HPT). Keeping in view the possible utility of TCS in developing water use efficient (WUE) wheat cultivars, we identified and characterized 62 wheat genes encoding TCS elements in a silico study; these included 7 HKs, 45 RRs along with 10 HPTs. Twelve of the 62 genes showed relatively higher alterations in the expression under drought. The quantitative RT-PCR (qRT-PCR)-based expression analysis of these 12 TCS genes was carried out in wheat seedlings of a drought sensitive (HD2967) and a tolerant (Dharwar Dry) cultivar subjected to either dehydration stress or cytokinin treatment. The expression of these 12 genes under dehydration stress differed in sensitive and tolerant genotypes, even though for individual genes, both showed either up-regulation or down-regulation. In response to the treatment of cytokinin, the expression of type-A RR genes was higher in the tolerant genotype, relative to that in the sensitive genotype, the situation being reverse for the type-B RRs. These results have been discussed in the context of the role of TCS elements in drought tolerance in wheat.
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Thu NBA, Hoang XLT, Doan H, Nguyen TH, Bui D, Thao NP, Tran LSP. Differential expression analysis of a subset of GmNAC genes in shoots of two contrasting drought-responsive soybean cultivars DT51 and MTD720 under normal and drought conditions. Mol Biol Rep 2014. [PMID: 24985975 DOI: 10.1007/s11105-014-0825-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
NAC transcription factors are known to be involved in regulation of plant responses to drought stress. In this study, the expression of 23 drought-responsive GmNAC genes was assessed in the shoot tissues of DT51 and MTD720, the two soybean varieties with contrasting drought-responsive phenotypes, by real-time quantitative PCR (RT-qPCR) under normal and drought conditions. Results indicated that expression profile of GmNAC genes was genotype-dependent, and six GmNACs (GmNAC019, 043, 062, 085, 095 and 101) had higher transcript levels in the shoots of the drought-tolerant DT51 in comparison with the drought-sensitive MTD720 under drought. Our study suggests a positive correlation between the higher drought tolerance degree of DT51 versus MTD720 and the up-regulation of at least these six drought-responsive GmNACs in the shoot tissues. Furthermore, on the basis of our analysis, three genes, GmNAC043, 085 and 101, were identified as promising candidates for development of drought-tolerant soybean cultivars by genetic engineering.
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Affiliation(s)
- Nguyen Binh Anh Thu
- School of Biotechnology, International University, Vietnam National University HCMC, Block 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
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11
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Lopato S, Borisjuk N, Langridge P, Hrmova M. Endosperm transfer cell-specific genes and proteins: structure, function and applications in biotechnology. FRONTIERS IN PLANT SCIENCE 2014; 5:64. [PMID: 24578704 PMCID: PMC3936200 DOI: 10.3389/fpls.2014.00064] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 02/07/2014] [Indexed: 05/21/2023]
Abstract
Endosperm transfer cells (ETC) are one of four main types of cells in endosperm. A characteristic feature of ETC is the presence of cell wall in-growths that create an enlarged plasma membrane surface area. This specialized cell structure is important for the specific function of ETC, which is to transfer nutrients from maternal vascular tissue to endosperm. ETC-specific genes are of particular interest to plant biotechnologists, who use genetic engineering to improve grain quality and yield characteristics of important field crops. The success of molecular biology-based approaches to manipulating ETC function is dependent on a thorough understanding of the functions of ETC-specific genes and ETC-specific promoters. The aim of this review is to summarize the existing data on structure and function of ETC-specific genes and their products. Potential applications of ETC-specific genes, and in particular their promoters for biotechnology will be discussed.
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Affiliation(s)
- Sergiy Lopato
- *Correspondence: Sergiy Lopato, Australian Centre for Plant Functional Genomics, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia e-mail:
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Abstract
Soybean (Glycine max) is one of the most important crops in legume family. Soybean and soybean-based products are also considered as popular food for human and animal husbandry. With its high oil content, soybean has become a potential resource for the production of renewable fuel. However, soybean is considered one of the most drought-sensitive crops, with approximately 40% reduction of the yield in the worst years. Recent research progresses in elucidation of biochemical, morphological and physiological responses as well as molecular mechanisms of plant adaptation to drought stress in model plants have provided a solid foundation for translational genomics of soybean toward drought tolerance. In this review, we will summarize the recent advances in development of drought-tolerant soybean cultivars by gene transfer.
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Affiliation(s)
- Nguyen Phuong Thao
- International University, Vietnam National University-HCMC, St block 6, Linh Trung ward, Thu Duc district, HCM city, Vietnam
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13
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Tsai YC, Weir NR, Hill K, Zhang W, Kim HJ, Shiu SH, Schaller GE, Kieber JJ. Characterization of genes involved in cytokinin signaling and metabolism from rice. PLANT PHYSIOLOGY 2012; 158:1666-84. [PMID: 22383541 PMCID: PMC3320177 DOI: 10.1104/pp.111.192765] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 02/23/2012] [Indexed: 05/18/2023]
Abstract
Two-component signaling elements play important roles in plants, including a central role in cytokinin signaling. We characterized two-component elements from the monocot rice (Oryza sativa) using several complementary approaches. Phylogenetic analysis reveals relatively simple orthologous relationships among the histidine kinases in rice and Arabidopsis (Arabidopsis thaliana). In contrast, the histidine-containing phosphotransfer proteins (OsHPs) and response regulators (OsRRs) display a higher degree of lineage-specific expansion. The intracellular localizations of several OsHPs and OsRRs were examined in rice and generally found to correspond to the localizations of their dicot counterparts. The functionality of rice type-B OsRRs was tested in Arabidopsis; one from a clade composed of both monocot and dicot type-B OsRRs complemented an Arabidopsis type-B response regulator mutant, but a type-B OsRR from a monocot-specific subfamily generally did not. The expression of genes encoding two-component elements and proteins involved in cytokinin biosynthesis and degradation was analyzed in rice roots and shoots and in response to phytohormones. Nearly all type-A OsRRs and OsHK4 were up-regulated in response to cytokinin, but other cytokinin signaling elements were not appreciably affected. Furthermore, multiple cytokinin oxidase (OsCKX) genes were up-regulated by cytokinin. Abscisic acid treatment decreased the expression of several genes involved in cytokinin biosynthesis and degradation. Auxin affected the expression of a few genes; brassinosteroid and gibberellin had only modest effects. Our results support a shared role for two-component elements in mediating cytokinin signaling in monocots and dicots and reveal how phytohormones can impact cytokinin function through modulating gene expression.
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Le DT, Nishiyama R, Watanabe Y, Mochida K, Yamaguchi-Shinozaki K, Shinozaki K, Tran LSP. Genome-wide expression profiling of soybean two-component system genes in soybean root and shoot tissues under dehydration stress. DNA Res 2011; 18:17-29. [PMID: 21208938 PMCID: PMC3041507 DOI: 10.1093/dnares/dsq032] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Accepted: 11/29/2010] [Indexed: 11/13/2022] Open
Abstract
Two-component systems (TCSs) play vital functions in the adaptation of plants to environmental stresses. To identify soybean TCS genes involved in the regulation of drought stress response, we performed tissue-specific expression profiling of all 83 putative TCS genes in plants subjected to dehydration. Under well-watered conditions, the majority of soybean TCS genes were expressed higher in the root tissues. Additionally, a high variability in transcript abundance was observed for the TCS genes in both roots and shoots. Under dehydration, TCS genes were more responsive in shoots than in roots. Further analysis indicated that 50% more TCS genes were repressed by dehydration than induced. Specifically, 18 genes were induced by 2-fold or more, whereas 33 genes were down-regulated at least 2-fold by dehydration. TCS genes putatively involved in cytokinin and ethylene signallings strongly responded to dehydration, suggesting that crosstalk exists between different hormonal and stress pathways. Our study provides the first glance into the complex regulatory roles of soybean TCSs underlying their functions in response to dehydration. Additionally, these systematic expression analyses identified excellent dehydration-responsive candidate genes to further clarify soybean TCS functions in drought response and to enable the development of improved drought tolerance in transgenic soybeans.
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Affiliation(s)
- Dung Tien Le
- Signaling Pathway Research Unit, Plant Science Center, RIKEN Yokohama Institute, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- Agricultural Genetics Institute, Vietnamese Academy of Agricultural Science, Pham-Van-Dong Str., Hanoi, Vietnam
| | - Rie Nishiyama
- Signaling Pathway Research Unit, Plant Science Center, RIKEN Yokohama Institute, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Yasuko Watanabe
- Signaling Pathway Research Unit, Plant Science Center, RIKEN Yokohama Institute, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Keiichi Mochida
- Gene Discovery Research Group, Plant Science Center, RIKEN Yokohama Institute, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | | | - Kazuo Shinozaki
- Gene Discovery Research Group, Plant Science Center, RIKEN Yokohama Institute, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Lam-Son Phan Tran
- Signaling Pathway Research Unit, Plant Science Center, RIKEN Yokohama Institute, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
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15
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Hellmann E, Gruhn N, Heyl A. The more, the merrier: cytokinin signaling beyond Arabidopsis. PLANT SIGNALING & BEHAVIOR 2010; 5:1384-90. [PMID: 21045560 PMCID: PMC3115238 DOI: 10.4161/psb.5.11.13157] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The phytohormone cytokinin is a key player in many developmental processes and in the response of plants to biotic and abiotic stress. The cytokinin signal is perceived and transduced via a multistep variant of the bacterial two-component signaling system. Most of the research on cytokinin signaling has been done in the model plant Arabidopsis thaliana. Research on cytokinin signaling has expanded to a much broader range of plants species in recent years. This is due to the natural limitation of Arabidopsis as a model species for the investigation of processes like nodulation or wood formation. The rapidly increasing number of sequenced plant genomes also facilitates the use of other species in this line of research. This review summarizes what is known about the cytokinin signaling in the different organisms and highlights differences to Arabidopsis.
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Affiliation(s)
- Eva Hellmann
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Science, Freie Universität Berlin, Berlin, Germany
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Mochida K, Yoshida T, Sakurai T, Yamaguchi-Shinozaki K, Shinozaki K, Tran LSP. Genome-wide analysis of two-component systems and prediction of stress-responsive two-component system members in soybean. DNA Res 2010; 17:303-24. [PMID: 20817745 PMCID: PMC2955714 DOI: 10.1093/dnares/dsq021] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Accepted: 08/01/2010] [Indexed: 01/22/2023] Open
Abstract
In plants, the two-component systems (TCSs) play important roles in regulating diverse biological processes, including responses to environmental stress stimuli. Within the soybean genome, the TCSs consist of at least 21 histidine kinases, 13 authentic and pseudo-phosphotransfers and 18 type-A, 15 type-B, 3 type-C and 11 pseudo-response regulator proteins. Structural and phylogenetic analyses of soybean TCS members with their Arabidopsis and rice counterparts revealed similar architecture of their TCSs. We identified a large number of closely homologous soybean TCS genes, which likely resulted from genome duplication. Additionally, we analysed tissue-specific expression profiles of those TCS genes, whose data are available from public resources. To predict the putative regulatory functions of soybean TCS members, with special emphasis on stress-responsive functions, we performed comparative analyses from all the TCS members of soybean, Arabidopsis and rice and coupled these data with annotations of known abiotic stress-responsive cis-elements in the promoter region of each soybean TCS gene. Our study provides insights into the architecture and a solid foundation for further functional characterization of soybean TCS elements. In addition, we provide a new resource for studying the conservation and divergence among the TCSs within plant species and/or between plants and other organisms.
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Affiliation(s)
- Keiichi Mochida
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa230-0045, Japan
- RIKEN Biomass Engineering Program, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama230-0045, Japan
| | - Takuhiro Yoshida
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa230-0045, Japan
| | - Tetsuya Sakurai
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa230-0045, Japan
| | | | - Kazuo Shinozaki
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa230-0045, Japan
| | - Lam-Son Phan Tran
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa230-0045, Japan
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Karan R, Singla-Pareek SL, Pareek A. Histidine kinase and response regulator genes as they relate to salinity tolerance in rice. Funct Integr Genomics 2009; 9:411-7. [PMID: 19277738 DOI: 10.1007/s10142-009-0119-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Revised: 02/13/2009] [Accepted: 02/13/2009] [Indexed: 12/13/2022]
Abstract
We have previously shown that Oryza sativa L. Pokkali maintains higher levels of transcripts under non-saline conditions, which are otherwise induced under salinity in the sensitive genotype-IR64. We wanted to test this hypothesis of differential gene regulation further, within the members of a given stress responsive gene family, which share significant structural and functional similarities. For this purpose, we chose to work on the two-component system (TCS family) which plays an important role in stress perception and signal transduction under hormonal, abiotic stress, light and developmental regulation. We present data to show that all members of TCS family, including sensory histidine kinases, phosphotransfer proteins and response regulators, are having differential transcript abundance (under both non-stress and salinity stress conditions) in contrasting rice genotypes. Further, under non-stress conditions, transcript abundance for all TCS members (except RR21) was found to be higher in the salt-tolerant genotype-Pokkali. TCS transcripts are otherwise induced by salinity stress to a relatively higher level in the sensitive cultivar IR64. A few of these members were also found to be localised within important salinity-related quantitative trait loci identified earlier. Based on the above findings, we propose that the TCS members may have a significant role in salinity tolerance in rice and can serve as useful 'candidate genes' for raising salinity-tolerant crop plants.
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Affiliation(s)
- Ratna Karan
- Stress Physiology and Molecular Biology, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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Jain M, Tyagi AK, Khurana JP. Genome-wide identification, classification, evolutionary expansion and expression analyses of homeobox genes in rice. FEBS J 2008; 275:2845-61. [PMID: 18430022 DOI: 10.1111/j.1742-4658.2008.06424.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Homeobox genes play a critical role in regulating various aspects of plant growth and development. In the present study, we identified a total of 107 homeobox genes in the rice genome and grouped them into ten distinct subfamilies based upon their domain composition and phylogenetic analysis. A significantly large number of homeobox genes are located in the duplicated segments of the rice genome, which suggests that the expansion of homeobox gene family, in large part, might have occurred due to segmental duplications in rice. Furthermore, microarray analysis was performed to elucidate the expression profiles of these genes in different tissues and during various stages of vegetative and reproductive development. Several genes with predominant expression during various stages of panicle and seed development were identified. At least 37 homeobox genes were found to be differentially expressed significantly (more than two-fold; P < 0.05) under various abiotic stress conditions. The results of the study suggest a critical role of homeobox genes in reproductive development and abiotic stress signaling in rice, and will facilitate the selection of candidate genes of agronomic importance for functional validation.
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Affiliation(s)
- Mukesh Jain
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, India
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