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Wu S, Gao Y, Zhang Q, Liu F, Hu W. Application of Multi-Omics Technologies to the Study of Phytochromes in Plants. Antioxidants (Basel) 2024; 13:99. [PMID: 38247523 PMCID: PMC10812741 DOI: 10.3390/antiox13010099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
Phytochromes (phy) are distributed in various plant organs, and their physiological effects influence plant germination, flowering, fruiting, and senescence, as well as regulate morphogenesis throughout the plant life cycle. Reactive oxygen species (ROS) are a key regulatory factor in plant systemic responses to environmental stimuli, with an attractive regulatory relationship with phytochromes. With the development of high-throughput sequencing technology, omics techniques have become powerful tools, and researchers have used omics techniques to facilitate the big data revolution. For an in-depth analysis of phytochrome-mediated signaling pathways, integrated multi-omics (transcriptomics, proteomics, and metabolomics) approaches may provide the answer from a global perspective. This article comprehensively elaborates on applying multi-omics techniques in studying phytochromes. We describe the current research status and future directions on transcriptome-, proteome-, and metabolome-related network components mediated by phytochromes when cells are subjected to various stimulation. We emphasize the importance of multi-omics technologies in exploring the effects of phytochromes on cells and their molecular mechanisms. Additionally, we provide methods and ideas for future crop improvement.
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Affiliation(s)
- Shumei Wu
- Basic Medical Experiment Center, School of Traditional Chinese Medicine, Jiangxi University of Chinese Medicine, Nanchang 330004, China; (S.W.); (Y.G.); (Q.Z.)
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang 332000, China
| | - Yue Gao
- Basic Medical Experiment Center, School of Traditional Chinese Medicine, Jiangxi University of Chinese Medicine, Nanchang 330004, China; (S.W.); (Y.G.); (Q.Z.)
| | - Qi Zhang
- Basic Medical Experiment Center, School of Traditional Chinese Medicine, Jiangxi University of Chinese Medicine, Nanchang 330004, China; (S.W.); (Y.G.); (Q.Z.)
| | - Fen Liu
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang 332000, China
| | - Weiming Hu
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang 332000, China
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2
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Kaeser G, Krauß N, Roughan C, Sauthof L, Scheerer P, Lamparter T. Phytochrome-Interacting Proteins. Biomolecules 2023; 14:9. [PMID: 38275750 PMCID: PMC10813442 DOI: 10.3390/biom14010009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
Phytochromes are photoreceptors of plants, fungi, slime molds bacteria and heterokonts. These biliproteins sense red and far-red light and undergo light-induced changes between the two spectral forms, Pr and Pfr. Photoconversion triggered by light induces conformational changes in the bilin chromophore around the ring C-D-connecting methine bridge and is followed by conformational changes in the protein. For plant phytochromes, multiple phytochrome interacting proteins that mediate signal transduction, nuclear translocation or protein degradation have been identified. Few interacting proteins are known as bacterial or fungal phytochromes. Here, we describe how the interacting partners were identified, what is known about the different interactions and in which context of signal transduction these interactions are to be seen. The three-dimensional arrangement of these interacting partners is not known. Using an artificial intelligence system-based modeling software, a few predicted and modulated examples of interactions of bacterial phytochromes with their interaction partners are interpreted.
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Affiliation(s)
- Gero Kaeser
- Karlsruhe Institute of Technology (KIT), Joseph Gottlieb Kölreuter Institut für Pflanzenwissenschaften (JKIP), Fritz-Haber-Weg 4, D-76131 Karlsruhe, Germany; (G.K.); (N.K.); (C.R.)
| | - Norbert Krauß
- Karlsruhe Institute of Technology (KIT), Joseph Gottlieb Kölreuter Institut für Pflanzenwissenschaften (JKIP), Fritz-Haber-Weg 4, D-76131 Karlsruhe, Germany; (G.K.); (N.K.); (C.R.)
| | - Clare Roughan
- Karlsruhe Institute of Technology (KIT), Joseph Gottlieb Kölreuter Institut für Pflanzenwissenschaften (JKIP), Fritz-Haber-Weg 4, D-76131 Karlsruhe, Germany; (G.K.); (N.K.); (C.R.)
| | - Luisa Sauthof
- Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Group Structural Biology of Cellular Signaling, Charitéplatz 1, D-10117 Berlin, Germany; (L.S.); (P.S.)
| | - Patrick Scheerer
- Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Group Structural Biology of Cellular Signaling, Charitéplatz 1, D-10117 Berlin, Germany; (L.S.); (P.S.)
| | - Tilman Lamparter
- Karlsruhe Institute of Technology (KIT), Joseph Gottlieb Kölreuter Institut für Pflanzenwissenschaften (JKIP), Fritz-Haber-Weg 4, D-76131 Karlsruhe, Germany; (G.K.); (N.K.); (C.R.)
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Sineshchekov VA. Two Distinct Molecular Types of Phytochrome A in Plants: Evidence of Existence and Implications for Functioning. Int J Mol Sci 2023; 24:ijms24098139. [PMID: 37175844 PMCID: PMC10179679 DOI: 10.3390/ijms24098139] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Phytochrome (phy) system in plants comprising a small number of phytochromes with phyA and phyB as major ones is responsible for acquiring light information in the red-far-red region of the solar spectrum. It provides optimal strategy for plant development under changing light conditions throughout all its life cycle beginning from seed germination and seedling establishment to fruiting and plant senescence. The phyA was shown to participate in the regulation of this cycle which is especially evident at its early stages. It mediates three modes of reactions-the very low and low fluence responses (VLFR and LFR) and the high irradiance responses (HIR). The phyA is the sole light receptor in the far-red spectral region responsible for plant's survival under a dense plant canopy where light is enriched with the far-red component. Its appearance is believed to be one of the main factors of plants' successful evolution. So far, it is widely accepted that one molecular phyA species is responsible for its complex functional manifestations. In this review, the evidence of the existence of two distinct phyA types-major, light-labile and soluble phyA' and minor, relatively light-stable and amphiphilic phyA″-is presented as what may account for the diverse modes of phyA action.
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Sineshchekov VA. Two Distinct Molecular Types of Phytochrome A in Plants: Evidence of Existence and Implications for Functioning. Int J Mol Sci 2023; 24:8139. [DOI: https:/doi.org/10.3390/ijms24098139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Abstract
Phytochrome (phy) system in plants comprising a small number of phytochromes with phyA and phyB as major ones is responsible for acquiring light information in the red—far-red region of the solar spectrum. It provides optimal strategy for plant development under changing light conditions throughout all its life cycle beginning from seed germination and seedling establishment to fruiting and plant senescence. The phyA was shown to participate in the regulation of this cycle which is especially evident at its early stages. It mediates three modes of reactions—the very low and low fluence responses (VLFR and LFR) and the high irradiance responses (HIR). The phyA is the sole light receptor in the far-red spectral region responsible for plant’s survival under a dense plant canopy where light is enriched with the far-red component. Its appearance is believed to be one of the main factors of plants′ successful evolution. So far, it is widely accepted that one molecular phyA species is responsible for its complex functional manifestations. In this review, the evidence of the existence of two distinct phyA types—major, light-labile and soluble phyA′ and minor, relatively light-stable and amphiphilic phyA″—is presented as what may account for the diverse modes of phyA action.
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Xue P, El Kurdi A, Kohler A, Ma H, Kaeser G, Ali A, Fischer R, Krauß N, Lamparter T. Evidence for weak interaction between phytochromes Agp1 and Agp2 from Agrobacterium fabrum. FEBS Lett 2019; 593:926-941. [PMID: 30941759 DOI: 10.1002/1873-3468.13376] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/25/2019] [Accepted: 03/28/2019] [Indexed: 11/09/2022]
Abstract
During bacterial conjugation, plasmid DNA is transferred from cell to cell. In Agrobacterium fabrum, conjugation is regulated by the phytochrome photoreceptors Agp1 and Agp2. Both contribute equally to this regulation. Agp1 and Agp2 are histidine kinases, but, for Agp2, we found no autophosphorylation activity. A clear autophosphorylation signal, however, was obtained with mutants in which the phosphoaccepting Asp of the C-terminal response regulator domain is replaced. Thus, the Agp2 histidine kinase differs from the classical transphosphorylation pattern. We performed size exclusion, photoconversion, dark reversion, autophosphorylation, chromophore assembly kinetics and fluorescence resonance energy transfer measurements on mixed Agp1/Agp2 samples. These assays pointed to an interaction between both proteins. This could partially explain the coaction of both phytochromes in the cell.
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Affiliation(s)
- Peng Xue
- Botanical Institute, Karlsruhe Institute of Technology, Germany
| | - Afaf El Kurdi
- Botanical Institute, Karlsruhe Institute of Technology, Germany
| | - Anja Kohler
- Botanical Institute, Karlsruhe Institute of Technology, Germany
| | - Hongju Ma
- Botanical Institute, Karlsruhe Institute of Technology, Germany
| | - Gero Kaeser
- Botanical Institute, Karlsruhe Institute of Technology, Germany
| | - Arin Ali
- Institute for Applied Biosciences, Karlsruhe Institute of Technology, Germany
| | - Reinhard Fischer
- Institute for Applied Biosciences, Karlsruhe Institute of Technology, Germany
| | - Norbert Krauß
- Botanical Institute, Karlsruhe Institute of Technology, Germany
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Zhang J, Movahedi A, Sang M, Wei Z, Xu J, Wang X, Wu X, Wang M, Yin T, Zhuge Q. Functional analyses of NDPK2 in Populus trichocarpa and overexpression of PtNDPK2 enhances growth and tolerance to abiotic stresses in transgenic poplar. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 117:61-74. [PMID: 28587994 DOI: 10.1016/j.plaphy.2017.05.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 05/27/2017] [Accepted: 05/29/2017] [Indexed: 05/04/2023]
Abstract
Nucleoside diphosphate kinases (NDPKs) are multifunctional proteins that regulate a variety of eukaryotic cellular activities, including cell proliferation, development, and differentiation. NDPK2 regulates the expression of antioxidant genes in plants. In a previous study, the Arabidopsis thaliana NDPK2 gene (AtNDPK2) was found to be associated with H2O2-mediated mitogen-activated protein kinase signaling in Arabidopsis thaliana. Proteins from transgenic plants overexpressing AtNDPK2 showed higher levels of autophosphorylation and NDPK activity and lower levels of reactive oxygen species (ROS) than those of wild-type (WT) plants. Therefore, constitutive overexpression of AtNDPK2 in Arabidopsis plants conferred enhanced tolerance to multiple environmental stresses that elicit ROS accumulation in situ. In this study, we cloned the Populus trichocarpa NDPK2 gene and analyzed its molecular structure and function. We generated and evaluated transgenic poplar plants expressing the PtNDPK2 gene under the control of the 35S promoter to achieve enhanced tolerance to various abiotic stresses. Transgenic poplar plants showed enhanced tolerance to salt and drought stress at the whole-plant level. The transgenic poplar plants showed significantly greater tolerance to 200 mM NaCl and drought stresses than WT poplar plants. In addition, the transgenic plants exhibited better growth due to increased expression of auxin-related indole acetic acid genes under normal growth conditions compared with WT plants. Our results suggest that induction of PtNDPK2 overexpression in poplars will be useful for increasing biomass production in the presence of various abiotic stresses.
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Affiliation(s)
- Jiaxin Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Ali Movahedi
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Ming Sang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Zhiheng Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Junjie Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Xiaoli Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Xiaolong Wu
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Mengyang Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Tongming Yin
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Qiang Zhuge
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China.
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Hetmann A, Wujak M, Kowalczyk S. Protein Transphosphorylation During the Mutual Interaction between Phytochrome A and a Nuclear Isoform of Nucleoside Diphosphate Kinase Is Regulated by Red Light. BIOCHEMISTRY (MOSCOW) 2017; 81:1153-1162. [PMID: 27908239 DOI: 10.1134/s0006297916100126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The nuclear isoform of nucleoside diphosphate kinase isoenzyme NDPK-In undergoes strong catalytic activation upon its interaction with the active form of phytochrome A (Pfr) in red light. The autophosphorylation or intermolecular transphosphorylation of NDPK-In leads to the formation of phosphoester bonds stable in acidic solution. The phosphate residue of the phosphamide bond in the active center of NDPK-In can also be transferred to serine and threonine residues localized in other proteins, including phytochrome A. Phytochrome A, similarly to NDPK-In, undergoes autophosphorylation on serine and threonine residues and can phosphorylate some potential substrate proteins. The physical interaction between phytochrome A in the Pfr form and NDPK-In results in a significant increase in the kinase activity of NDPK-In. The results presented in this work indicate that NDPK-In may function as a protein kinase regulated by light.
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Affiliation(s)
- A Hetmann
- Nicolaus Copernicus University, Faculty of Biology and Environment Protection, Department of Biochemistry, Toruń 87-100, Poland.
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Vargas-Cortez T, Morones-Ramirez JR, Balderas-Renteria I, Zarate X. Expression and purification of recombinant proteins in Escherichia coli tagged with a small metal-binding protein from Nitrosomonas europaea. Protein Expr Purif 2016; 118:49-54. [DOI: 10.1016/j.pep.2015.10.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 10/13/2015] [Accepted: 10/14/2015] [Indexed: 11/26/2022]
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Ye W, Hu S, Wu L, Ge C, Cui Y, Chen P, Wang X, Xu J, Ren D, Dong G, Qian Q, Guo L. White stripe leaf 12 ( WSL12), encoding a nucleoside diphosphate kinase 2 (OsNDPK2), regulates chloroplast development and abiotic stress response in rice ( Oryza sativa L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2016; 36:57. [PMID: 27212889 PMCID: PMC4851688 DOI: 10.1007/s11032-016-0479-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/18/2016] [Indexed: 05/02/2023]
Abstract
Chloroplast is a crucial organelle for plant photosynthesis and maintaining normal life activities in higher plants. Although some genes related to chloroplast development and pigment synthesis have been identified or cloned in rice, little is known about the relationship between these genes and abiotic stress response. In this study, we identified a novel mutant white stripe leaf 12 (wsl12) affecting pigment synthesis, chloroplast development and abiotic stress response in rice. The mutant phenotype was obvious at seeding and tillering stages and in response to the temperature change. Genetic analysis of reciprocal crosses between wsl12 and wild-type plants showed that wsl12 was a recessive mutant in a single nuclear locus. Map-based cloning revealed that the WSL12 locus encoded OsNDPK2, one of the three nucleoside diphosphate kinases (OsNDPKs). WSL12 expressed in all tested tissues, while it highly expressed in leaves and young tissues. The WSL12 protein localized to the chloroplast. The wsl12 mutant showed higher superoxide anion level and enhanced sensitivity to abscisic acid (ABA) and salinity. The transcription pattern of many genes involved in chlorophyll biosynthesis, ABA synthesis, light signaling pathway, reactive oxygen species-scavenging pathway and the other two OsNDPKs was altered in the wsl12 mutant. These results indicate that the OsNDPK2 encoded by WSL12 plays an important role in chloroplast development and chlorophyll biosynthesis by regulating the expression levels of related genes. In addition, WSL12 also affects the response to abiotic stress, such as ABA and salinity in rice, and is beneficial to molecular breeding of stress tolerance.
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Affiliation(s)
- Weijun Ye
- />State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Tiyuchang Road 359, Hangzhou, 310006 China
- />College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Shikai Hu
- />State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Tiyuchang Road 359, Hangzhou, 310006 China
- />Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
| | - Liwen Wu
- />State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Tiyuchang Road 359, Hangzhou, 310006 China
| | - Changwei Ge
- />State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Tiyuchang Road 359, Hangzhou, 310006 China
| | - Yongtao Cui
- />State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Tiyuchang Road 359, Hangzhou, 310006 China
| | - Ping Chen
- />State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Tiyuchang Road 359, Hangzhou, 310006 China
| | - Xiaoqi Wang
- />State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Tiyuchang Road 359, Hangzhou, 310006 China
| | - Jie Xu
- />State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Tiyuchang Road 359, Hangzhou, 310006 China
| | - Deyong Ren
- />State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Tiyuchang Road 359, Hangzhou, 310006 China
| | - Guojun Dong
- />State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Tiyuchang Road 359, Hangzhou, 310006 China
| | - Qian Qian
- />State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Tiyuchang Road 359, Hangzhou, 310006 China
- />Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
| | - Longbiao Guo
- />State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Tiyuchang Road 359, Hangzhou, 310006 China
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Dubovskaya LV, Bakakina YS, Volotovski ID. Cyclic guanosine monophosphate as a mediator in processes of stress-signal transduction in higher plants. Biophysics (Nagoya-shi) 2015. [DOI: 10.1134/s0006350915040089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Kopylov M, Bass HW, Stroupe ME. The Maize (Zea mays L.) Nucleoside Diphosphate Kinase1 (ZmNDPK1) Gene Encodes a Human NM23-H2 Homologue That Binds and Stabilizes G-Quadruplex DNA. Biochemistry 2015; 54:1743-57. [DOI: 10.1021/bi501284g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Mykhailo Kopylov
- Department of Biological Science and ‡Institute of
Molecular Biophysics, Florida State University, 91 Chieftan Way, Tallahassee, Florida 32306-4380, United States
| | - Hank W. Bass
- Department of Biological Science and ‡Institute of
Molecular Biophysics, Florida State University, 91 Chieftan Way, Tallahassee, Florida 32306-4380, United States
| | - M. Elizabeth Stroupe
- Department of Biological Science and ‡Institute of
Molecular Biophysics, Florida State University, 91 Chieftan Way, Tallahassee, Florida 32306-4380, United States
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Wang Z, Li H, Ke Q, Jeong JC, Lee HS, Xu B, Deng XP, Lim YP, Kwak SS. Transgenic alfalfa plants expressing AtNDPK2 exhibit increased growth and tolerance to abiotic stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 84:67-77. [PMID: 25240265 DOI: 10.1016/j.plaphy.2014.08.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 08/29/2014] [Indexed: 05/18/2023]
Abstract
In this study, we generated and evaluated transgenic alfalfa plants (Medicago sativa L. cv. Xinjiang Daye) expressing the Arabidopsis nucleoside diphosphate kinase 2 (AtNDPK2) gene under the control of the oxidative stress-inducible SWPA2 promoter (referred to as SN plants) to develop plants with enhanced tolerance to various abiotic stresses. We selected two SN plants (SN4 and SN7) according to the expression levels of AtNDPK2 and the enzyme activity of NDPK in response to methyl viologen (MV)-mediated oxidative stress treatment using leaf discs for further characterization. SN plants showed enhanced tolerance to high temperature, NaCl, and drought stress on the whole-plant level. When the plants were subjected to high temperature treatment (42 °C for 24 h), the non-transgenic (NT) plants were severely wilted, whereas the SN plants were not affected because they maintained high relative water and chlorophyll contents. The SN plants also showed significantly higher tolerance to 250 mM NaCl and water stress treatment than the NT plants. In addition, the SN plants exhibited better plant growth through increased expression of auxin-related indole acetic acid (IAA) genes (MsIAA3, MsIAA5, MsIAA6, MsIAA7, and MsIAA16) under normal growth conditions compared to NT plants. The results suggest that induced overexpression of AtNDPK2 in alfalfa will be useful for increasing biomass production under various abiotic stress conditions.
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Affiliation(s)
- Zhi Wang
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea; Department of Horticulture, Chungnam National University, Daejeon, Republic of Korea
| | - Hongbing Li
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea; State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Science and Ministry of Water Resources, Northwest A & F University, Yangling, Shaanxi 712100, PR China
| | - Qingbo Ke
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea; Department of Green Chemistry and Environmental Biotechnology, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Jae Cheol Jeong
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea; Department of Green Chemistry and Environmental Biotechnology, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Haeng-Soon Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea; Department of Green Chemistry and Environmental Biotechnology, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Bingcheng Xu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Science and Ministry of Water Resources, Northwest A & F University, Yangling, Shaanxi 712100, PR China
| | - Xi-Ping Deng
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Science and Ministry of Water Resources, Northwest A & F University, Yangling, Shaanxi 712100, PR China
| | - Yong Pyo Lim
- Department of Horticulture, Chungnam National University, Daejeon, Republic of Korea
| | - Sang-Soo Kwak
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea; Department of Green Chemistry and Environmental Biotechnology, Korea University of Science and Technology, Daejeon, Republic of Korea.
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Shin AY, Han YJ, Song PS, Kim JI. Expression of recombinant full-length plant phytochromes assembled with phytochromobilin in Pichia pastoris. FEBS Lett 2014; 588:2964-70. [PMID: 24911206 DOI: 10.1016/j.febslet.2014.05.050] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 05/26/2014] [Accepted: 05/26/2014] [Indexed: 11/17/2022]
Abstract
We have successfully developed a system to produce full-length plant phytochrome assembled with phytochromobilin in Pichia pastoris by co-expressing apophytochromes and chromophore biosynthetic genes, heme oxygenase (HY1) and phytochromobilin synthase (HY2) from Arabidopsis. Affinity-purified phytochrome proteins from Pichia cells displayed zinc fluorescence indicating chromophore attachment. Spectroscopic analyses showed absorbance maximum peaks identical to in vitro reconstituted phytochromobilin-assembled phytochromes, suggesting that the co-expression system is effective to generate holo-phytochromes. Moreover, mitochondria localization of the phytochromobilin biosynthetic genes increased the efficiency of holophytochrome biosynthesis. Therefore, this system provides an excellent source of holophytochromes, including oat phytochrome A and Arabidopsis phytochrome B.
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Affiliation(s)
- Ah-Young Shin
- Department of Biotechnology and Kumho Life Science Laboratory, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Yun-Jeong Han
- Department of Biotechnology and Kumho Life Science Laboratory, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Pill-Soon Song
- Faculty of Biotechnology and Subtropical Horticulture Research Institute, Jeju National University, Jeju 690-756, Republic of Korea
| | - Jeong-Il Kim
- Department of Biotechnology and Kumho Life Science Laboratory, Chonnam National University, Gwangju 500-757, Republic of Korea.
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14
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Berenschot AS, Quecini V. A reverse genetics approach identifies novel mutants in light responses and anthocyanin metabolism in petunia. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2014; 20:1-13. [PMID: 24554834 PMCID: PMC3925473 DOI: 10.1007/s12298-013-0212-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 09/22/2013] [Accepted: 10/18/2013] [Indexed: 05/03/2023]
Abstract
Flower color and plant architecture are important commercially valuable features for ornamental petunias (Petunia x hybrida Vilm.). Photoperception and light signaling are the major environmental factors controlling anthocyanin and chlorophyll biosynthesis and shade-avoidance responses in higher plants. The genetic regulators of these processes were investigated in petunia by in silico analyses and the sequence information was used to devise a reverse genetics approach to probe mutant populations. Petunia orthologs of photoreceptor, light-signaling components and anthocyanin metabolism genes were identified and investigated for functional conservation by phylogenetic and protein motif analyses. The expression profiles of photoreceptor gene families and of transcription factors regulating anthocyanin biosynthesis were obtained by bioinformatic tools. Two mutant populations, generated by an alkalyting agent and by gamma irradiation, were screened using a phenotype-independent, sequence-based method by high-throughput PCR-based assay. The strategy allowed the identification of novel mutant alleles for anthocyanin biosynthesis (CHALCONE SYNTHASE) and regulation (PH4), and for light signaling (CONSTANS) genes.
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Affiliation(s)
- Amanda S. Berenschot
- />Centro de Pesquisa e Desenvolvimento de Recursos Genéticos, Instituto Agronômico, Caixa Postal 28, 13001-970 Campinas, SP Brazil
| | - Vera Quecini
- />Embrapa Uva e Vinho, Rua Livramento, 515, 95700-000 Bento Gonçalves, RS Brazil
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15
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Dubovskaya LV, Bakakina YS, Kolesneva EV, Sodel DL, McAinsh MR, Hetherington AM, Volotovski ID. cGMP-dependent ABA-induced stomatal closure in the ABA-insensitive Arabidopsis mutant abi1-1. THE NEW PHYTOLOGIST 2011; 191:57-69. [PMID: 21371039 DOI: 10.1111/j.1469-8137.2011.03661.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
• The drought hormone abscisic acid (ABA) is widely known to produce reductions in stomatal aperture in guard cells. The second messenger cyclic guanosine 3', 5'-monophosphate (cGMP) is thought to form part of the signalling pathway by which ABA induces stomatal closure. • We have examined the signalling events during cGMP-dependent ABA-induced stomatal closure in wild-type Arabidopsis plants and plants of the ABA-insensitive Arabidopsis mutant abi1-1. • We show that cGMP acts downstream of hydrogen peroxide (H(2) O(2) ) and nitric oxide (NO) in the signalling pathway by which ABA induces stomatal closure. H(2) O(2) - and NO-induced increases in the cytosolic free calcium concentration ([Ca(2+) ](cyt) ) were cGMP-dependent, positioning cGMP upstream of [Ca(2+) ](cyt) , and involved the action of the type 2C protein phosphatase ABI1. Increases in cGMP were mediated through the stimulation of guanylyl cyclase by H(2) O(2) and NO. We identify nucleoside diphosphate kinase as a new cGMP target protein in Arabidopsis. • This study positions cGMP downstream of ABA-induced changes in H(2) O(2) and NO, and upstream of increases in [Ca(2+) ](cyt) in the signalling pathway leading to stomatal closure.
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Affiliation(s)
- Lyudmila V Dubovskaya
- National Academy of Sciences of Belarus, Institute of Biophysics and Cell Engineering, Minsk 220072, Academicheskaya 27, Belarus
| | - Yulia S Bakakina
- National Academy of Sciences of Belarus, Institute of Biophysics and Cell Engineering, Minsk 220072, Academicheskaya 27, Belarus
| | - Ekaterina V Kolesneva
- National Academy of Sciences of Belarus, Institute of Biophysics and Cell Engineering, Minsk 220072, Academicheskaya 27, Belarus
| | - Dmitry L Sodel
- National Academy of Sciences of Belarus, Institute of Biophysics and Cell Engineering, Minsk 220072, Academicheskaya 27, Belarus
| | - Martin R McAinsh
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | | | - Igor D Volotovski
- National Academy of Sciences of Belarus, Institute of Biophysics and Cell Engineering, Minsk 220072, Academicheskaya 27, Belarus
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16
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Kim YH, Kim MD, Choi YI, Park SC, Yun DJ, Noh EW, Lee HS, Kwak SS. Transgenic poplar expressing Arabidopsis NDPK2 enhances growth as well as oxidative stress tolerance. PLANT BIOTECHNOLOGY JOURNAL 2011; 9:334-47. [PMID: 20649941 DOI: 10.1111/j.1467-7652.2010.00551.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Nucleoside diphosphate kinase 2 (NDPK2) is known to regulate the expression of antioxidant genes in plants. Previously, we reported that overexpression of Arabidopsis NDPK2 (AtNDPK2) under the control of an oxidative stress-inducible SWPA2 promoter in transgenic potato and sweetpotato plants enhanced tolerance to various abiotic stresses. In this study, transgenic poplar (Populus alba × Poplus glandulosa) expressing the AtNDPK2 gene under the control of a SWPA2 promoter (referred to as SN) was generated to develop plants with enhanced tolerance to oxidative stress. The level of AtNDPK2 expression and NDPK activity in SN plants following methyl viologen (MV) treatment was positively correlated with the plant's tolerance to MV-mediated oxidative stress. We also observed that antioxidant enzyme activities such as ascorbate peroxidase, catalase and peroxidase were increased in MV-treated leaf discs of SN plants. The growth of SN plants was substantially increased under field conditions including increased branch number and stem diameter. SN plants exhibited higher transcript levels of the auxin-response genes IAA2 and IAA5. These results suggest that enhanced AtNDPK2 expression affects oxidative stress tolerance leading to improved plant growth in transgenic poplar.
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Affiliation(s)
- Yun-Hee Kim
- Environmental Biotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
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17
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Shin DH, Cho MH, Kim TL, Yoo J, Kim JI, Han YJ, Song PS, Jeon JS, Bhoo SH, Hahn TR. A small GTPase activator protein interacts with cytoplasmic phytochromes in regulating root development. J Biol Chem 2010; 285:32151-9. [PMID: 20551316 PMCID: PMC2952216 DOI: 10.1074/jbc.m110.133710] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 06/14/2010] [Indexed: 11/06/2022] Open
Abstract
Phytochromes enable plants to sense light information and regulate developmental responses. Phytochromes interact with partner proteins to transmit light signals to downstream components for plant development. PIRF1 (phytochrome-interacting ROP guanine-nucleotide exchange factor (RopGEF 1)) functions as a light-signaling switch regulating root development through the activation of ROPs (Rho-like GTPase of plant) in the cytoplasm. In vitro pulldown and yeast two-hybrid assays confirmed the interaction between PIRF1 and phytochromes. PIRF1 interacted with the N-terminal domain of phytochromes through its conserved PRONE (plant-specific ROP nucleotide exchanger) region. PIRF1 also interacted with ROPs and activated them in a phytochrome-dependent manner. The Pr form of phytochrome A enhanced the RopGEF activity of PIRF1, whereas the Pfr form inhibited it. A bimolecular fluorescence complementation analysis demonstrated that PIRF1 was localized in the cytoplasm and bound to the phytochromes in darkness but not in light. PIRF1 loss of function mutants (pirf1) of Arabidopsis thaliana showed a longer root phenotype in the dark. In addition, both PIRF1 overexpression mutants (PIRF1-OX) and phytochrome-null mutants (phyA-211 and phyB-9) showed retarded root elongation and irregular root hair formation, suggesting that PIRF1 is a negative regulator of phytochrome-mediated primary root development. We propose that phytochrome and ROP signaling are interconnected through PIRF1 in regulating the root growth and development in Arabidopsis.
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Affiliation(s)
- Dong Ho Shin
- From the Graduate School of Biotechnology and Plant Metabolism Research Center, Kyung Hee University, Yongin 446-701
| | - Man-Ho Cho
- From the Graduate School of Biotechnology and Plant Metabolism Research Center, Kyung Hee University, Yongin 446-701
| | - Tae-Lim Kim
- From the Graduate School of Biotechnology and Plant Metabolism Research Center, Kyung Hee University, Yongin 446-701
| | - Jihye Yoo
- From the Graduate School of Biotechnology and Plant Metabolism Research Center, Kyung Hee University, Yongin 446-701
| | - Jeong-Il Kim
- the Department of Biotechnology and Kumho Life Science Laboratory, Chonnam National University, Gwangju 500-757, and
| | - Yun-Jeong Han
- the Department of Biotechnology and Kumho Life Science Laboratory, Chonnam National University, Gwangju 500-757, and
| | - Pill-Soon Song
- the Faculty of Biotechnology, Jeju National University, Jeju 690-756, Korea
| | - Jong-Seong Jeon
- From the Graduate School of Biotechnology and Plant Metabolism Research Center, Kyung Hee University, Yongin 446-701
| | - Seong Hee Bhoo
- From the Graduate School of Biotechnology and Plant Metabolism Research Center, Kyung Hee University, Yongin 446-701
| | - Tae-Ryong Hahn
- From the Graduate School of Biotechnology and Plant Metabolism Research Center, Kyung Hee University, Yongin 446-701
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18
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Haque ME, Yoshida Y, Hasunuma K. ROS resistance in Pisum sativum cv. Alaska: the involvement of nucleoside diphosphate kinase in oxidative stress responses via the regulation of antioxidants. PLANTA 2010; 232:367-82. [PMID: 20458498 DOI: 10.1007/s00425-010-1173-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2010] [Accepted: 04/11/2010] [Indexed: 05/29/2023]
Abstract
This study investigated the reactive oxygen species (ROS) tolerance mechanism of a paraquat-resistant Pisum sativum line (R3-1) compared with the wild type (WT). Physiological and biochemical analyses showed significant differences in the phenotypes, such as delayed leaf and floral development, superior branching, and greater biomass and yields in the R3-1 line, as well as an increased level of antioxidant pigments and a lower rate of cellular lipid peroxidation in the resistant R3-1. Additionally, the phosphorylation of crude proteins showed distinguishable differences in band mobility and intensity between the R3-1 and WT plants. cDNA cloning and sequence analysis of NDPKs, which were candidate phosphorylated proteins, revealed that two of the deduced amino acids in NDPK2 (IL12L and Glu205Lys) and one in NDPK3 (P45S) were mutated in R3-1. Using glutathione S-transferase-NDPK fusion constructs, we found that the precursor recombinant R3-1 NDPK2 showed an increased level of activity and autophosphorylation in R3-1 plants compared to WT plants. Native PAGE analysis of the crude proteins revealed that NDPK and catalase (CAT) activity co-existed in the same area of the gel. In a yeast two-hybrid assay, the N-terminal region of NDPK2 showed an interaction with the full-length CAT1 protein. Furthermore, we found that WT showed a decreased level of CAT activity compared with R3-1 under illumination and/or on media containing ROS-releasing reagents. Taken together, these results suggest that there is a strong interaction between NDPK2 and CAT1 in R3-1 plants, which possibly plays a vital role in the antioxidant defense against ROS.
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Affiliation(s)
- Md Emdadul Haque
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, Japan.
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19
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Transduction mechanisms of photoreceptor signals in plant cells. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2009. [DOI: 10.1016/j.jphotochemrev.2009.04.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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20
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Verslues PE, Batelli G, Grillo S, Agius F, Kim YS, Zhu J, Agarwal M, Katiyar-Agarwal S, Zhu JK. Interaction of SOS2 with nucleoside diphosphate kinase 2 and catalases reveals a point of connection between salt stress and H2O2 signaling in Arabidopsis thaliana. Mol Cell Biol 2007; 27:7771-80. [PMID: 17785451 PMCID: PMC2169147 DOI: 10.1128/mcb.00429-07] [Citation(s) in RCA: 154] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
SOS2, a class 3 sucrose-nonfermenting 1-related kinase, has emerged as an important mediator of salt stress response and stress signaling through its interactions with proteins involved in membrane transport and in regulation of stress responses. We have identified additional SOS2-interacting proteins that suggest a connection between SOS2 and reactive oxygen signaling. SOS2 was found to interact with the H2O2 signaling protein nucleoside diphosphate kinase 2 (NDPK2) and to inhibit its autophosphorylation activity. A sos2-2 ndpk2 double mutant was more salt sensitive than a sos2-2 single mutant, suggesting that NDPK2 and H2O2 are involved in salt resistance. However, the double mutant did not hyperaccumulate H2O2 in response to salt stress, suggesting that it is altered signaling rather than H2O2 toxicity alone that is responsible for the increased salt sensitivity of the sos2-2 ndpk2 double mutant. SOS2 was also found to interact with catalase 2 (CAT2) and CAT3, further connecting SOS2 to H2O2 metabolism and signaling. The interaction of SOS2 with both NDPK2 and CATs reveals a point of cross talk between salt stress response and other signaling factors including H2O2.
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Affiliation(s)
- Paul E Verslues
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA
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21
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Uenaka H, Kadota A. Functional analyses of the Physcomitrella patens phytochromes in regulating chloroplast avoidance movement. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 51:1050-61. [PMID: 17662030 DOI: 10.1111/j.1365-313x.2007.03202.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Red light-induced chloroplast movement in Physcomitrella patens (Pp) is mediated by dichroic phytochrome in the cytoplasm. To analyze the molecular function of the photoreceptor in the cytoplasm, we developed a protoplast system in which chloroplast photomovement was exclusively dependent on the expression of phytochrome cDNA constructs introduced by polyethylene glycol (PEG) transformation. YFP was fused to the phytochrome constructs and their expression was detected by fluorescence. The chloroplast avoidance response was induced in the protoplasts expressing a YFP fusion of PHY1-PHY3, but not of PHY4 or YFP alone. Phy::yfp fluorescence was detected in the cytoplasm. No change in the location of phy1::yfp or phy2::yfp was revealed before and after photomovement. When phy1::yfp and phy2::yfp were targeted to the nucleus by fusing a nuclear localization signal to the constructs, red light avoidance was not induced. To determine the domains of PHY2 essential for avoidance response, various partially-deleted PHY2::YFP constructs were tested. The N-terminal extension domain (NTE) was found to be necessary but the C-terminal histidine kinase-related domain (HKRD) was dispensable. An avoidance response was not induced under expression of phytochrome N-terminal half domain [deleting both the PAS (Per, Arnt, Sim)-related domain (PRD) and HKRD]. GUS fusion of this N-terminal half domain, reported to be fully functional in Arabidopsis for several phyA- and phyB-regulated responses was not effective in chloroplast avoidance movement. Domain requirement and GUS fusion effect were also confirmed in PHY1. These results indicate that Pp phy1-Pp phy3 in the cytoplasm mediate chloroplast avoidance movement, and that NTE and PRD, but not HKRD, are required for their function.
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Affiliation(s)
- Hidetoshi Uenaka
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, Minami-Ohsawa 1-1, Hachioji, Tokyo 192-0397, Japan
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22
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Seong ES, Guo J, Kim YH, Cho JH, Lim CK, Hyun Hur J, Wang MH. Regulations of marker genes involved in biotic and abiotic stress by overexpression of the AtNDPK2 gene in rice. Biochem Biophys Res Commun 2007; 363:126-32. [PMID: 17826739 DOI: 10.1016/j.bbrc.2007.08.147] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2007] [Accepted: 08/20/2007] [Indexed: 02/02/2023]
Abstract
AtNDPK2 is involved in transcriptional regulation in response to pathogen and abiotic stresses. AtNDPK2-expressing transgenic rice plants showed regulation of the marker genes for chilling and oxidative stresses. In the present study, we produced AtNDPK2-overexpressing transgenic rice lines using the co-transformation method. Morphologically, the transgenic plants, compared with the control plants, were growth retarded. We investigated how AtNDPK2 overexpression influences the response of rice plants to marker genes related to chilling and ROS stress. The accumulation of transcripts of pBC442 and pBC601, related to chilling stress, was induced in AtNDPK2-overexpressed rice plants. On further investigation, we found that OsAPX1-, OsAPX2-, and OsSodB-scavenging free-oxygen radicals, such as superoxide (O2-) and hydrogen peroxide (H(2)O(2)), could be induced in AtNDPK2-overexpressed rice plants. In particular, transcripts encoding pathogenesis-related (PR) proteins OsPR2 and OsPR4, as well as oxidative stress response proteins, were confirmed to change the gene expression in the transgenic rice plants. Together, these results suggest that AtNDPK2 plays a regulatory role in chilling and antioxidant signaling in plants.
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Affiliation(s)
- Eun Soo Seong
- School of Biotechnology, Kangwon National University, Chuncheon, Kangwon-do 200-701, South Korea
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23
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Farkas I, Dombrádi V, Miskei M, Szabados L, Koncz C. Arabidopsis PPP family of serine/threonine phosphatases. TRENDS IN PLANT SCIENCE 2007; 12:169-76. [PMID: 17368080 DOI: 10.1016/j.tplants.2007.03.003] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2006] [Revised: 01/25/2007] [Accepted: 03/02/2007] [Indexed: 05/14/2023]
Abstract
Serine/threonine-specific phosphoprotein phosphatases (PPPs) are ubiquitous enzymes in all eukaryotes, but their regulatory functions are largely unknown in higher plants. The Arabidopsis genome encodes 26 PPP catalytic subunits related to type 1, type 2A and so-called novel phosphatases, including four plant-specific enzymes carrying large N-terminal kelch-domains, but no apparent homologue of the PP2B family. The catalytic subunits of PPPs associate with regulatory protein partners that target them to well defined cellular locations and modulate their activity. Recent studies of phosphatase partners and their interactions have directed attention again to functional dissection of plant PPP families, and highlight their intriguing roles in the regulation of metabolism, cell cycle and development, as well as their roles in light, stress and hormonal signalling.
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Affiliation(s)
- Ilona Farkas
- Department of Medical Chemistry, Research Center for Molecular Medicine, Medical and Health Science Center, University of Debrecen, Egyetem tér 1, Debrecen H-4032, Hungary
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24
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Palmieri D, Horak CE, Lee JH, Halverson DO, Steeg PS. Translational approaches using metastasis suppressor genes. J Bioenerg Biomembr 2007; 38:151-61. [PMID: 16944301 DOI: 10.1007/s10863-006-9039-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Cancer metastasis is a significant contributor to breast cancer patient morbidity and mortality. In order to develop new anti-metastatic therapies, we need to understand the biological and biochemical mechanisms of metastasis. Toward these efforts, we and others have studied metastasis suppressor genes, which halt metastasis in vivo without affecting primary tumor growth. The first metastasis suppressor gene identified was nm23, also known as NDP kinase. Nm23 represents the most widely validated metastasis suppressor gene, based on transfection and knock-out mouse strategies. The biochemical mechanism of metastasis suppression via Nm23 is unknown and likely complex. Two potential mechanisms include binding proteins and a histidine kinase activity. Elevation of Nm23 expression in micrometastatic tumor cells may constitute a translational strategy for the limitation of metastatic colonization in high risk cancer patients. To date, medroxyprogesterone acetate (MPA) has been identified as a candidate compound for clinical testing.
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Affiliation(s)
- Diane Palmieri
- Women's Cancers Section, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Building 37, Room 1122, NIH, Bethesda, MD 20892, USA
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25
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Natori C, Kim JI, Bhoo SH, Han YJ, Hanzawa H, Furuya M, Song PS. Differential interactions of phytochrome A (Pr vs. Pfr) with monoclonal antibodies probed by a surface plasmon resonance technique. Photochem Photobiol Sci 2006; 6:83-9. [PMID: 17200742 DOI: 10.1039/b611077k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Phytochromes are red- and far-red light-reversible photoreceptors for photomorphogenesis in plants. Phytochrome A is a dimeric chromopeptide that mediates very low fluence and high irradiance responses. To analyze the surface properties of phytochrome A (phyA), the epitopes of 21 anti-phyA monoclonal antibodies were determined by variously engineered recombinant phyA proteins and the dissociation constants of seven anti-phyA monoclonal antibodies with phyA were measured using a surface plasmon resonance (SPR)-based resonant mirror biosensor (IAsys). Purified oat phyA was immobilized on the sensor surface using a carboxymethyl dextran cuvette in advance, and the interactions of each chosen monoclonal antibody against phyA in either red light absorbing form (Pr) or far-red light absorbing form (Pfr) at different concentrations were monitored. The binding profiles were analyzed using the FAST Fit program of IAsys. The resultant values of dissociation constants clearly demonstrated the differential affinities between the phyA epitopes and the monoclonal antibodies dependent upon Pr vs. Pfr conformations. Monoclonal antibody mAP20 preferentially recognized the epitope at amino acids 653-731 in the Pr form, whereas mAA02, mAP21 and mAR07/mAR08 displayed preferential affinities for the Pfr's surfaces at epitopes 494-601 (the hinge region between the N- and C-terminal domains), 601-653 (hinge in PASI domain), and 772-1128 (C-terminal domain), respectively. The N-terminal extension (1-74) was not recognized by mAP09 and mAP15, suggesting that the N-terminal extreme is not exposed in the native conformation of phyA. On the other hand, the C-terminal domain becomes apparently exposed on Pr-to-Pfr phototransformation, suggesting an inter-domain cross-talk. The use of surface plasmon resonance spectroscopy offers a new approach to study the surface properties of phytochromes associated with the photoreversible structural changes, as well as for the study of protein-protein interactions of phytochromes with their interacting proteins involved in light signaling events in plants.
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Affiliation(s)
- Chihoko Natori
- Hitachi Advanced Research Laboratory, Hatoyama, Saitama 350-0395, Japan
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26
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Phee BK, Shin DH, Cho JH, Kim SH, Kim JI, Lee YH, Jeon JS, Bhoo SH, Hahn TR. Identification of phytochrome-interacting protein candidates in Arabidopsis thaliana by co-immunoprecipitation coupled with MALDI-TOF MS. Proteomics 2006; 6:3671-80. [PMID: 16705748 DOI: 10.1002/pmic.200500222] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Phytochrome-interacting proteins have been extensively studied to elucidate light-signaling pathway in plants. However, most of these proteins have been identified by yeast two-hybrid screening using the C-terminal domain of phytochromes. We used co-immunoprecipitation followed by proteomic analysis in plant cell extracts in an attempt to screen for proteins interacting either directly or indirectly with native holophytochromes including the N-terminal domain as well as C-terminal domain. A total of 16 protein candidates were identified, and were selected from 2-DE experiments. Using MALDI-TOF MS analysis, 7 of these candidates were predicted to be putative phytochrome A-interacting proteins and the remaining ones to be phytochrome B-interacting proteins. Among these putative interacting proteins, protein phosphatase type 2C (PP2C) and a 66-kDa protein were strong candidates as novel phytochrome-interacting proteins, as knockout mutants for the genes encoding these two proteins had impaired light-signaling functions. A transgenic knockout Arabidopsis study showed that a 66-kDa protein candidate regulates hypocotyl elongation in a light-specific manner, and altered cotyledon development under white light during early developmental stages. The PP2C knockout plants also displayed light-specific changes in hypocotyl elongation. These results suggest that co-immunoprecipitation, followed by proteomic analysis, is a useful method for identifying novel interacting proteins and determining real protein-protein interactions in the cell.
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Affiliation(s)
- Bong-Kwan Phee
- Graduate School of Biotechnology and Plant Metabolism Research Center, Kyung Hee University, Suwon, Korea
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27
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Dorion S, Matton DP, Rivoal J. Characterization of a cytosolic nucleoside diphosphate kinase associated with cell division and growth in potato. PLANTA 2006; 224:108-24. [PMID: 16395585 DOI: 10.1007/s00425-005-0199-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2005] [Accepted: 12/01/2005] [Indexed: 05/06/2023]
Abstract
A cDNA encoding Solanum chacoense cytosolic NDPK (NDPK1, EC 2.7.4.6) was isolated. The open reading frame encoded a 148 amino acid protein that shares homology with other cytosolic NDPKs including a conserved N-terminal domain. S. chacoense NDPK1 was expressed in Escherichia coli as a 6xHis-tagged protein and purified by affinity chromatography. The recombinant protein exhibited a pattern of abortive complex formation suggesting that the enzyme is strongly regulated by the NTP/NDP ratio. A polyclonal antibody generated against recombinant NDPK1 was specific for the cytosolic isoform in Solanum tuberosum as shown from immunoprecipitation experiments and immunoblot analysis of chloroplasts and mitochondria preparations. NDPK activity and NDPK1 protein were found at different levels in various vegetative and reproductive tissues. DEAE fractogel analyses of NDPK activity in root tips, leaves, tubers and cell cultures suggest that NDPK1 constitutes the bulk of extractable NDPK activity in all these organs. NDPK activity and NDPK1 protein levels raised during the exponential growth phase of potato cell cultures whereas no rise in activity or NDPK1 protein was observed when sucrose concentration in the culture was manipulated to limit growth. Activity measurements, immunoblot analysis as well as immunolocalization experiments performed on potato root tips and shoot apical buds demonstrated that NDPK1 was predominantly localized in the meristematic zones and provascular tissues of the apical regions. These data suggest that NDPK1 plays a specific role in the supply of UTP during early growth of plant meristematic and provascular tissues.
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Affiliation(s)
- Sonia Dorion
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke est, Montréal, PQ, Canada, H1X 2B2
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28
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Kim JI, Bhoo SH, Han YJ, Zarate X, Furuya M, Song PS. The PAS2 domain is required for dimerization of phytochrome A. J Photochem Photobiol A Chem 2006. [DOI: 10.1016/j.jphotochem.2005.10.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Peltier JB, Cai Y, Sun Q, Zabrouskov V, Giacomelli L, Rudella A, Ytterberg AJ, Rutschow H, van Wijk KJ. The oligomeric stromal proteome of Arabidopsis thaliana chloroplasts. Mol Cell Proteomics 2005; 5:114-33. [PMID: 16207701 DOI: 10.1074/mcp.m500180-mcp200] [Citation(s) in RCA: 269] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
This study presents an analysis of the stromal proteome in its oligomeric state extracted from highly purified chloroplasts of Arabidopsis thaliana. 241 proteins (88% with predicted cTP), mostly assembled in oligomeric complexes, were identified by mass spectrometry with emphasis on distinguishing between paralogues. This is critical because different paralogues in a gene family often have different subcellular localizations and/or different expression patterns and functions. The native protein masses were determined for all identified proteins. Comparison with the few well characterized stromal complexes from A. thaliana confirmed the accuracy of the native mass determination, and by extension, the usefulness of the native mass data for future in-depth protein interaction studies. Resolved protein interactions are discussed and compared with an extensive collection of native mass data of orthologues in other plants and bacteria. Relative protein expression levels were estimated from spot intensities and also provided estimates of relative concentrations of individual proteins. No such quantification has been reported so far. Surprisingly proteins dedicated to chloroplast protein synthesis, biogenesis, and fate represented nearly 10% of the total stroma protein mass. Oxidative pentose phosphate pathway, glycolysis, and Calvin cycle represented together about 75%, nitrogen assimilation represented 5-7%, and all other pathways such as biosynthesis of e.g. fatty acids, amino acids, nucleotides, tetrapyrroles, and vitamins B(1) and B(2) each represented less than 1% of total protein mass. Several proteins with diverse functions outside primary carbon metabolism, such as the isomerase ROC4, lipoxygenase 2 involved in jasmonic acid biosynthesis, and a carbonic anhydrase (CA1), were surprisingly abundant in the range of 0.75-1.5% of the total stromal mass. Native images with associated information are available via the Plastid Proteome Database.
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Affiliation(s)
- Jean-Benoit Peltier
- Department of Plant Biology, Cornell Theory Center, Cornell University, Ithaca, New York 14853, USA
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Choi G, Kim JI, Hong SW, Shin B, Choi G, Blakeslee JJ, Murphy AS, Seo YW, Kim K, Koh EJ, Song PS, Lee H. A Possible Role for NDPK2 in the Regulation of Auxin-mediated Responses for Plant Growth and Development. ACTA ACUST UNITED AC 2005; 46:1246-54. [PMID: 15927941 DOI: 10.1093/pcp/pci133] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Auxin plays many crucial roles in the course of plant growth and development, such as hook opening, leaf expansion and inhibition of mesocotyl elongation. Although its mechanism of action has not been clarified at the molecular level, recent studies have indicated that auxin triggers the induction of a number of genes known as primary auxin-responsive genes. Hence, the identification of the regulatory components in auxin-mediated cellular responses would help to elucidate the mechanism of the action of this hormone in plant growth and development. NDPK2 encodes a nucleoside diphosphate kinase 2 (NDPK2) in Arabidopsis. We aim to elucidate the possible role of NDPK2 in auxin-related cellular processes, in view of the finding that a ndpk2 mutant displays developmental defects associated with auxin. Interestingly, the ndpk2 mutant exhibits defects in cotyledon development and increased sensitivity to an inhibitor of polar auxin transport (naphthylphthalamic acid; NPA). Consistent with this phenotype, the transcript levels of specific auxin-responsive genes were reduced in the ndpk2 mutant plants treated with auxin. The amount of auxin transported from the shoot apex to the shoot/root transition zone of ndpk2 mutant plants was increased, compared with that in the wild-type plants. These results collectively suggest that NDPK2 appears to participate in auxin-regulated processes, partly through the modulation of auxin transport.
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Affiliation(s)
- Goh Choi
- Kumho Life and Environmental Science Laboratory (KLESL), 1 Oryoung-dong Buk-gu, Gwangju, 500-712 Korea
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Kim J, Shen R, Olcott MC, Rajagopal I, Mathews CK. Adenylate kinase of Escherichia coli, a component of the phage T4 dNTP synthetase complex. J Biol Chem 2005; 280:28221-9. [PMID: 15941717 DOI: 10.1074/jbc.m502201200] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Adenylate kinase, which catalyzes the reversible ATP-dependent phosphorylation of AMP to ADP and dAMP to dADP, can also catalyze the conversion of nucleoside diphosphates to the corresponding triphosphates. Lu and Inouye (Lu, Q., and Inouye, M. (1996) Proc. Natl. Acad. Sci. U. S. A. 93, 5720-5725) showed that an Escherichia coli ndk mutant, lacking nucleoside diphosphate kinase, can use adenylate kinase as an alternative source of nucleoside triphosphates. Bacteriophage T4 can reproduce in an Escherichia coli ndk mutant, implying that adenylate kinase can meet a demand for deoxyribonucleoside triphosphates that increases by up to 10-fold as a result of T4 infection. In terms of kinetic linkage and specific protein-protein associations, NDP kinase is an integral component of T4 dNTP synthetase, a multienzyme complex containing phage-coded enzymes, which facilitates the synthesis of dNTPs and their flow into DNA. Here we asked whether, by similar criteria, adenylate kinase of the host cell is also a specific component of the complex. Experiments involving protein affinity chromatography, immunoprecipitation, optical biosensor measurements, and glutathione S-transferase pulldowns demonstrated direct interactions between adenylate kinase and several phage-coded enzymes, as well as E. coli nucleoside diphosphate kinase. These results identify adenylate kinase as a specific component of the complex. The rate of DNA synthesis after infection of an ndk mutant was found to be about 40% of the rate seen in wild-type infection, implying that complementation of the missing NDP kinase function by adenylate kinase is fairly efficient, but that adenylate kinase becomes rate-limiting for DNA synthesis when it is the sole source of dNTPs.
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Affiliation(s)
- Juhyun Kim
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-7305, USA
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