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Zhao K, Lan Y, Shi Y, Duan C, Yu K. Metabolite and transcriptome analyses reveal the effects of salinity stress on the biosynthesis of proanthocyanidins and anthocyanins in grape suspension cells. FRONTIERS IN PLANT SCIENCE 2024; 15:1351008. [PMID: 38576780 PMCID: PMC10993317 DOI: 10.3389/fpls.2024.1351008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/07/2024] [Indexed: 04/06/2024]
Abstract
Proanthocyanidins (PAs) and anthocyanins are flavonoids that contribute to the quality and health benefits of grapes and wine. Salinity affects their biosynthesis, but the underlying mechanism is still unclear. We studied the effects of NaCl stress on PA and anthocyanin biosynthesis in grape suspension cells derived from berry skins of Vitis vinifera L. Cabernet Sauvignon using metabolite profiling and transcriptome analysis. We treated the cells with low (75 mM NaCl) and high (150 mM NaCl) salinity for 4 and 7 days. High salinity inhibited cell growth and enhanced PA and anthocyanin accumulation more than low salinity. The salinity-induced PAs and anthocyanins lacked C5'-hydroxylation modification, suggesting the biological significance of delphinidin- and epigallocatechin-derivatives in coping with stress. The genes up-regulated by salinity stress indicated that the anthocyanin pathway was more sensitive to salt concentration than the PA pathway, and WGCNA analysis revealed the coordination between flavonoid biosynthesis and cell wall metabolism under salinity stress. We identified transcription factors potentially involved in regulating NaCl dose- and time-dependent PA and anthocyanin accumulation, showing the dynamic remodeling of flavonoid regulation network under different salinity levels and durations. Our study provides new insights into regulator candidates for tailoring flavonoid composition and molecular indicators of salt stress in grape cells.
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Affiliation(s)
- Kainan Zhao
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Yibin Lan
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Ying Shi
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Changqing Duan
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Keji Yu
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
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2
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Soliman ERS. Preserving the adaptive salt stress response activity of a tissue-specific promoter with modulating activity. J Genet Eng Biotechnol 2024; 22:100354. [PMID: 38494266 PMCID: PMC10941203 DOI: 10.1016/j.jgeb.2024.100354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/17/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND The Arabidopsis "Redox Responsive Transcription Factor1" (RRTF1) promoter is transiently activated by salt stress in roots over 6 h period, followed by an adaptation phase during which its activity returns to baseline levels, even if the salt stress is prolonged. This enables the short-term production of genes that, while initially advantageous to the plant, will have long-term detrimental effects if expressed at high levels indefinitely. RESULTS In this paper, we demonstrate that the RRTF1 promoter salt adaption response is a dominant feature of the promoter, that cannot be overwritten by a strong enhancer. While maintaining the transient activation profile of the RRTF1 promoter, linking it to the 35S enhancer results in a significant boost of salt stress induction in roots. CONCLUSION The RRTF1 promoter's enhanced and still adaptable activity could become a useful tool in plant biotechnology.
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Affiliation(s)
- Elham R S Soliman
- Cytogenetics and Molecular Genetics Unit, Botany and Microbiology Department, Faculty of Science, Helwan University, Helwan, Egypt.
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3
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Namgial T, Singh AK, Singh NP, Francis A, Chattopadhyay D, Voloudakis A, Chakraborty S. Differential expression of genes during recovery of Nicotiana tabacum from tomato leaf curl Gujarat virus infection. PLANTA 2023; 258:37. [PMID: 37405593 PMCID: PMC10322791 DOI: 10.1007/s00425-023-04182-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/10/2023] [Indexed: 07/06/2023]
Abstract
MAIN CONCLUSION Nicotiana tabacum exhibits recovery response towards tomato leaf curl Gujarat virus. Transcriptome analysis revealed the differential expression of defense-related genes. Genes encoding for cysteine protease inhibitor, hormonal- and stress-related to DNA repair mechanism are found to be involved in the recovery process. Elucidating the role of host factors in response to viral infection is crucial in understanding the plant host-virus interaction. Begomovirus, a genus in the family Geminiviridae, is reported throughout the globe and is known to cause serious crop diseases. Tomato leaf curl Gujarat virus (ToLCGV) infection in Nicotiana tabacum resulted in initial symptom expression followed by a quick recovery in the systemic leaves. Transcriptome analysis using next-generation sequencing (NGS) revealed a large number of differentially expressed genes both in symptomatic as well as recovered leaves when compared to mock-inoculated plants. The virus infected N. tabacum results in alteration of various metabolic pathways, phytohormone signaling pathway, defense related protein, protease inhibitor, and DNA repair pathway. RT-qPCR results indicated that Germin-like protein subfamily T member 2 (NtGLPST), Cysteine protease inhibitor 1-like (NtCPI), Thaumatin-like protein (NtTLP), Kirola-like (NtKL), and Ethylene-responsive transcription factor ERF109-like (NtERTFL) were down-regulated in symptomatic leaves when compared to recovered leaves of ToLCGV-infected plants. In contrast, the Auxin-responsive protein SAUR71-like (NtARPSL) was found to be differentially down-regulated in recovered leaves when compared to symptomatic leaves and the mock-inoculated plants. Lastly, Histone 2X protein like (NtHH2L) gene was found to be down-regulated, whereas Uncharacterized (NtUNCD) was up-regulated in both symptomatic as well as recovered leaves compared to the mock-inoculated plants. Taken together, the present study suggests potential roles of the differentially expressed genes that might govern tobacco's susceptibility and/or recovery response towards ToLCGV infection.
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Affiliation(s)
- T Namgial
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Athens, 11855, Greece
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - A K Singh
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - N P Singh
- Laboratory of Plant Molecular Biology, National Institute of Plant Genome Research, New Delhi, 110067, India
| | - A Francis
- Laboratory of Plant Molecular Biology, National Institute of Plant Genome Research, New Delhi, 110067, India
| | - D Chattopadhyay
- Laboratory of Plant Molecular Biology, National Institute of Plant Genome Research, New Delhi, 110067, India
| | - A Voloudakis
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Athens, 11855, Greece.
| | - S Chakraborty
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
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Qiu D, Zhu C, Fan R, Mao G, Wu P, Zeng J. Arsenic inhibits citric acid accumulation via downregulating vacuolar proton pump gene expression in citrus fruits. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 246:114153. [PMID: 36252515 DOI: 10.1016/j.ecoenv.2022.114153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Citric acid content is a critical quality determinant in citrus (Citrus spp.) fruits. Although arsenic (As) can effectively reduce citric acid content to improve citrus fruit quality, it can have adverse environmental effects. The discovery of nontoxic substitutes is hampered by the incomplete elucidation of the underlying mechanisms of As action in citrus fruits. Metabolic, transcriptomic, and physiological analyses were employed to investigate As action on citric acid accumulation to discover the mechanisms of As action in citrus. The enzyme activity related to citrate biosynthesis was not inhibited and the content of the involved metabolites was not reduced in As-treated fruits. However, the proton pump genes CitPH5 and CitPH1 control the vacuolar citric acid accumulation and transcription factor genes CitTT8 and CitMYB5, which regulate CitPH5 and CitPH1, were downregulated. The oxidative stress-response genes were upregulated in As-treated fruits. The reactive oxygen species (ROS) treatment also downregulated CitTT8 and CitMYB5 in juice cells. The mitochondrial ROS production rate increased in As-treated fruits. AsIII was more potent in stimulating isolated mitochondria to overproduce ROS compared to AsV. Our results indicate that the As inhibition of citric acid accumulation may be primarily due to the transcriptional downregulation of CitPH5, CitPH1, CitTT8, and CitMYB5. As-induced oxidative stress signaling may operate upstream to downregulate these acid regulator genes. Mitochondrial thiol proteins may be the principal targets of As action in citrus fruits.
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Affiliation(s)
- Diyang Qiu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MARA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China.
| | - Congyi Zhu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MARA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China.
| | - Ruiyi Fan
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MARA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China.
| | - Genlin Mao
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MARA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China.
| | - Pingzhi Wu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MARA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China.
| | - Jiwu Zeng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MARA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China.
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Barczak-Brzyżek A, Brzyżek G, Koter M, Siedlecka E, Gawroński P, Filipecki M. Plastid retrograde regulation of miRNA expression in response to light stress. BMC PLANT BIOLOGY 2022; 22:150. [PMID: 35346032 PMCID: PMC8962581 DOI: 10.1186/s12870-022-03525-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 03/10/2022] [Indexed: 05/03/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are a class of endogenous noncoding RNAs that play a pivotal role in the regulation of plant development and responses to the surrounding environment. Despite the efforts made to elucidate their function in the adaptation of plants to many abiotic and biotic stresses, their role in high light (HL) stress is still vague. HL stress often arises upon plant exposure to full sunlight. Subsequent changes in nuclear gene expression are triggered by chloroplast-derived retrograde signals. RESULTS In this study, we show that HL is involved in miRNA-dependent regulation in Arabidopsis thaliana rosettes. Microtranscriptomic screening revealed a limited number of miRNAs reacting to HL. To explain the miRNA regulation mechanisms at the different biogenesis stages, chemical and genetic approaches were applied. First, we tested the possible role of plastoquinone (PQ) redox changes using photosynthetic electron transport chain inhibitors. The results suggest that increased primary transcript abundance (pri-miRNAs) of HL-regulated miRNAs is dependent on signals upstream of PQ. This indicates that such signals may originate from photosystem II, which is the main singlet oxygen (1O2) source. Nevertheless, no changes in pri-miRNA expression upon a dark-light shift in the conditional fluorescent (flu) mutant producing 1O2 were observed when compared to wild-type plants. Thus, we explored the 1O2 signaling pathway, which is initiated independently in HL and is related to β-carotene oxidation and production of volatile derivatives, such as β-cyclocitral (β-CC). Pri-miRNA induction by β-CC, which is a component of this 1O2 pathway, as well as an altered response in the methylene blue sensitivity 1 (mbs1) mutant support the role of 1O2 signaling in miRNA regulation. CONCLUSIONS We show that light stress triggers changes in miRNA expression. This stress response may be regulated by reactive oxygen species (ROS)-related signaling. In conclusion, our results link ROS action to miRNA biogenesis, suggesting its contribution to inconsistent pri- and mature miRNA dynamics.
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Affiliation(s)
- Anna Barczak-Brzyżek
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences-SGGW, 02-776, Warsaw, Poland
| | - Grzegorz Brzyżek
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106, Warsaw, Poland
| | - Marek Koter
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences-SGGW, 02-776, Warsaw, Poland
| | - Ewa Siedlecka
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences-SGGW, 02-776, Warsaw, Poland
| | - Piotr Gawroński
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences-SGGW, 02-776, Warsaw, Poland
| | - Marcin Filipecki
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences-SGGW, 02-776, Warsaw, Poland.
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Pogány M, Dankó T, Hegyi-Kaló J, Kámán-Tóth E, Szám DR, Hamow KÁ, Kalapos B, Kiss L, Fodor J, Gullner G, Váczy KZ, Barna B. Redox and Hormonal Changes in the Transcriptome of Grape (Vitis vinifera) Berries during Natural Noble Rot Development. PLANTS 2022; 11:plants11070864. [PMID: 35406844 PMCID: PMC9003472 DOI: 10.3390/plants11070864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/10/2022] [Accepted: 03/17/2022] [Indexed: 01/18/2023]
Abstract
Noble rot is a favorable form of the interaction between grape (Vitis spp.) berries and the phytopathogenic fungus Botrytis cinerea. The transcriptome pattern of grapevine cells subject to natural noble rot development in the historic Hungarian Tokaj wine region has not been previously published. Furmint, a traditional white Tokaj variety suited to develop great quality noble rot was used in the experiments. Exploring a subset of the Furmint transcriptome redox and hormonal changes distinguishing between noble rot and bunch rot was revealed. Noble rot is defined by an early spike in abscisic acid (ABA) accumulation and a pronounced remodeling of ABA-related gene expression. Transcription of glutathione S-transferase isoforms is uniquely upregulated, whereas gene expression of some sectors of the antioxidative apparatus (e.g., catalases, carotenoid biosynthesis) is downregulated. These mRNA responses are lacking in berries exposed to bunch rot. Our results help to explain molecular details behind the fine and dynamic balance between noble rot and bunch rot development.
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Affiliation(s)
- Miklós Pogány
- Centre for Agricultural Research, 2462 Martonvásár, Hungary; (T.D.); (E.K.-T.); (K.Á.H.); (B.K.); or (L.K.); (J.F.); (G.G.); (B.B.)
- Correspondence:
| | - Tamás Dankó
- Centre for Agricultural Research, 2462 Martonvásár, Hungary; (T.D.); (E.K.-T.); (K.Á.H.); (B.K.); or (L.K.); (J.F.); (G.G.); (B.B.)
| | - Júlia Hegyi-Kaló
- Food and Wine Research Institute, Eszterházy Károly Catholic University, 3300 Eger, Hungary; (J.H.-K.); (K.Z.V.)
| | - Evelin Kámán-Tóth
- Centre for Agricultural Research, 2462 Martonvásár, Hungary; (T.D.); (E.K.-T.); (K.Á.H.); (B.K.); or (L.K.); (J.F.); (G.G.); (B.B.)
| | - Dorottya Réka Szám
- Georgikon Campus, Hungarian University of Agriculture and Life Sciences, 8360 Keszthely, Hungary;
| | - Kamirán Áron Hamow
- Centre for Agricultural Research, 2462 Martonvásár, Hungary; (T.D.); (E.K.-T.); (K.Á.H.); (B.K.); or (L.K.); (J.F.); (G.G.); (B.B.)
| | - Balázs Kalapos
- Centre for Agricultural Research, 2462 Martonvásár, Hungary; (T.D.); (E.K.-T.); (K.Á.H.); (B.K.); or (L.K.); (J.F.); (G.G.); (B.B.)
| | - Levente Kiss
- Centre for Agricultural Research, 2462 Martonvásár, Hungary; (T.D.); (E.K.-T.); (K.Á.H.); (B.K.); or (L.K.); (J.F.); (G.G.); (B.B.)
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD 4350, Australia
| | - József Fodor
- Centre for Agricultural Research, 2462 Martonvásár, Hungary; (T.D.); (E.K.-T.); (K.Á.H.); (B.K.); or (L.K.); (J.F.); (G.G.); (B.B.)
| | - Gábor Gullner
- Centre for Agricultural Research, 2462 Martonvásár, Hungary; (T.D.); (E.K.-T.); (K.Á.H.); (B.K.); or (L.K.); (J.F.); (G.G.); (B.B.)
| | - Kálmán Zoltán Váczy
- Food and Wine Research Institute, Eszterházy Károly Catholic University, 3300 Eger, Hungary; (J.H.-K.); (K.Z.V.)
| | - Balázs Barna
- Centre for Agricultural Research, 2462 Martonvásár, Hungary; (T.D.); (E.K.-T.); (K.Á.H.); (B.K.); or (L.K.); (J.F.); (G.G.); (B.B.)
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Yang CL, Huang YT, Schmidt W, Klein P, Chan MT, Pan IC. Ethylene Response Factor109 Attunes Immunity, Photosynthesis, and Iron Homeostasis in Arabidopsis Leaves. FRONTIERS IN PLANT SCIENCE 2022; 13:841366. [PMID: 35310669 PMCID: PMC8924546 DOI: 10.3389/fpls.2022.841366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/09/2022] [Indexed: 06/09/2023]
Abstract
Iron (Fe) is an essential micronutrient element for all organisms including plants. Chlorosis of young leaves is a common symptom of Fe deficiency, reducing the efficiency of photosynthesis, and, ultimately, crop yield. Previous research revealed strong responsiveness of the putative key transcription factor ERF109 to the Fe regime. To elucidate the possible role of ERF109 in leaf Fe homeostasis and photosynthesis, we subjected Arabidopsis thaliana erf109 knockout lines and Col-0 wild-type plants to transcriptome profiling via RNA-seq. The transcriptome profile of Fe-sufficient erf109 leaves showed a 71% overlap with Fe-deficient Col-0 plants. On the other hand, genes that were differentially expressed between Fe-deficient and Fe-sufficient Col-0 plants remained unchanged in erf109 plants under conditions of Fe deficiency. Mutations in ERF109 increased the expression of the clade Ib bHLH proteins bHLH38, bHLH39, bHLH101, the nicotianamine synthase NAS4, and the Fe storage gene FER1. Moreover, mutations in ERF109 led to significant down-regulation of defense genes, including CML37, WRKY40, ERF13, and EXO70B2. Leaves of erf109 exhibited increased Fe levels under both Fe-sufficient and Fe-deficient conditions. Reduced Fv/Fm and Soil Plant Analysis Development (SPAD) values in erf109 lines under Fe deficiency indicate curtailed ability of photosynthesis relative to the wild-type. Our findings suggest that ERF109 is a negative regulator of the leaf response to Fe deficiency. It further appears that the function of ERF109 in the Fe response is critical for regulating pathogen defense and photosynthetic efficiency. Taken together, our study reveals a novel function of ERF109 and provides a systematic perspective on the intertwining of the immunity regulatory network and cellular Fe homeostasis.
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Affiliation(s)
- Chiu-Ling Yang
- Department of Horticulture, National Chung-Hsing University, Taichung City, Taiwan
| | - Yu-Ting Huang
- Department of Horticulture, National Chung-Hsing University, Taichung City, Taiwan
| | - Wolfgang Schmidt
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Patricia Klein
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| | - Ming-Tsair Chan
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - I-Chun Pan
- Department of Horticulture, National Chung-Hsing University, Taichung City, Taiwan
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Yoo H, Shrivastava S, Lynch JH, Huang XQ, Widhalm JR, Guo L, Carter BC, Qian Y, Maeda HA, Ogas JP, Morgan JA, Marshall-Colón A, Dudareva N. Overexpression of arogenate dehydratase reveals an upstream point of metabolic control in phenylalanine biosynthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:737-751. [PMID: 34403557 DOI: 10.1111/tpj.15467] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/12/2021] [Indexed: 06/13/2023]
Abstract
Out of the three aromatic amino acids, the highest flux in plants is directed towards phenylalanine, which is utilized to synthesize proteins and thousands of phenolic metabolites contributing to plant fitness. Phenylalanine is produced predominantly in plastids via the shikimate pathway and subsequent arogenate pathway, both of which are subject to complex transcriptional and post-transcriptional regulation. Previously, it was shown that allosteric feedback inhibition of arogenate dehydratase (ADT), which catalyzes the final step of the arogenate pathway, restricts flux through phenylalanine biosynthesis. Here, we show that in petunia (Petunia hybrida) flowers, which typically produce high phenylalanine levels, ADT regulation is relaxed, but not eliminated. Moderate expression of a feedback-insensitive ADT increased flux towards phenylalanine, while high overexpression paradoxically reduced phenylalanine formation. This reduction could be partially, but not fully, recovered by bypassing other known metabolic flux control points in the aromatic amino acid network. Using comparative transcriptomics, reverse genetics, and metabolic flux analysis, we discovered that transcriptional regulation of the d-ribulose-5-phosphate 3-epimerase gene in the pentose phosphate pathway controls flux into the shikimate pathway. Taken together, our findings reveal that regulation within and upstream of the shikimate pathway shares control over phenylalanine biosynthesis in the plant cell.
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Affiliation(s)
- Heejin Yoo
- Department of Horticulture and Landscape Architecture, Purdue University, 625 Agriculture Mall Dr, West Lafayette, IN, 47907-2010, USA
- Department of Biochemistry, Purdue University, 175 South University St., West Lafayette, IN, 47907-2063, USA
| | - Stuti Shrivastava
- Department of Plant Biology, University of Illinois Urbana-Champaign, 265 Morrill Hall, MC-116, Urbana, IL, 61801, USA
| | - Joseph H Lynch
- Department of Biochemistry, Purdue University, 175 South University St., West Lafayette, IN, 47907-2063, USA
| | - Xing-Qi Huang
- Department of Biochemistry, Purdue University, 175 South University St., West Lafayette, IN, 47907-2063, USA
| | - Joshua R Widhalm
- Department of Horticulture and Landscape Architecture, Purdue University, 625 Agriculture Mall Dr, West Lafayette, IN, 47907-2010, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - Longyun Guo
- Department of Biochemistry, Purdue University, 175 South University St., West Lafayette, IN, 47907-2063, USA
| | - Benjamin C Carter
- Department of Biochemistry, Purdue University, 175 South University St., West Lafayette, IN, 47907-2063, USA
| | - Yichun Qian
- Department of Horticulture and Landscape Architecture, Purdue University, 625 Agriculture Mall Dr, West Lafayette, IN, 47907-2010, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Dr., Madison, WI, 53706, USA
| | - Joseph P Ogas
- Department of Biochemistry, Purdue University, 175 South University St., West Lafayette, IN, 47907-2063, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - John A Morgan
- Department of Biochemistry, Purdue University, 175 South University St., West Lafayette, IN, 47907-2063, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
- Davidson School of Chemical Engineering, Purdue University, 480 Stadium Mall Dr., West Lafayette, IN, 47907-2100, USA
| | - Amy Marshall-Colón
- Department of Plant Biology, University of Illinois Urbana-Champaign, 265 Morrill Hall, MC-116, Urbana, IL, 61801, USA
| | - Natalia Dudareva
- Department of Horticulture and Landscape Architecture, Purdue University, 625 Agriculture Mall Dr, West Lafayette, IN, 47907-2010, USA
- Department of Biochemistry, Purdue University, 175 South University St., West Lafayette, IN, 47907-2063, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
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9
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Berkowitz O, Xu Y, Liew LC, Wang Y, Zhu Y, Hurgobin B, Lewsey MG, Whelan J. RNA-seq analysis of laser microdissected Arabidopsis thaliana leaf epidermis, mesophyll and vasculature defines tissue-specific transcriptional responses to multiple stress treatments. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:938-955. [PMID: 33974297 DOI: 10.1111/tpj.15314] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/28/2021] [Accepted: 05/05/2021] [Indexed: 06/12/2023]
Abstract
Acclimation of plants to adverse conditions requires the coordination of gene expression and signalling pathways between tissues and cell types. As the energy and carbon capturing organs, leaves are significantly affected by abiotic and biotic stresses. However, tissue- or cell type-specific analyses of stress responses have focussed on the Arabidopsis root. Here, we comparatively explore the transcriptomes of three leaf tissues (epidermis, mesophyll, vasculature) after induction of diverse stress pathways by chemical stimuli (antimycin A, 3-amino-1,2,4-triazole, methyl viologen, salicylic acid) and ultraviolet light in Arabidopsis using laser capture microdissection followed by RNA sequencing. Stimulation of stress pathways caused an overall reduction in the number of genes expressed in a tissue-specific manner, though a small subset gained or changed their tissue specificity. We find no evidence of a common stress response, with only a few genes consistently responsive to two or more treatments in the analysed tissues. However, differentially expressed genes overlap between tissues for individual treatments. A focussed analysis provided evidence for an interaction of auxin and ethylene that mediates retrograde signalling during mitochondrial dysfunction specifically in the epidermis, and a gene regulatory network defined the hierarchy of interactions. Taken together, we have generated an extensive reference dataset that will be valuable for future experiments analysing transcriptional responses on a tissue or single-cell level. Our results will enable the tailoring of the tissue-specific engineering of stress-tolerant plants.
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Affiliation(s)
- Oliver Berkowitz
- Australian Research Council Centre of Excellence in Plant Energy Biology, AgriBio Building La Trobe University, Bundoora, Victoria, 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Yue Xu
- Australian Research Council Centre of Excellence in Plant Energy Biology, AgriBio Building La Trobe University, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Lim Chee Liew
- Australian Research Council Centre of Excellence in Plant Energy Biology, AgriBio Building La Trobe University, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Yan Wang
- Australian Research Council Centre of Excellence in Plant Energy Biology, AgriBio Building La Trobe University, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Yanqiao Zhu
- Australian Research Council Centre of Excellence in Plant Energy Biology, AgriBio Building La Trobe University, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Bhavna Hurgobin
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Mathew G Lewsey
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - James Whelan
- Australian Research Council Centre of Excellence in Plant Energy Biology, AgriBio Building La Trobe University, Bundoora, Victoria, 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
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10
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Sadeghi M, Balke J, Schneider C, Nagano S, Stellmacher J, Lochnit G, Lang C, Weise C, Hughes J, Alexiev U. Transient Deprotonation of the Chromophore Affects Protein Dynamics Proximal and Distal to the Linear Tetrapyrrole Chromophore in Phytochrome Cph1. Biochemistry 2020; 59:1051-1062. [PMID: 32069394 DOI: 10.1021/acs.biochem.9b00967] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phytochromes are biological red/far-red light sensors found in many organisms. Prototypical phytochromes, including Cph1 from the cyanobacterium Synechocystis 6803, act as photochemical switches that interconvert between stable red (Pr)- and metastable far-red (Pfr)-absorbing states induced by photoisomerization of the bilin chromophore. The connection between photoconversion and the cellular output signal involves light-mediated global structural changes in the interaction between the photosensory module (PAS-GAF-PHY) and the C-terminal transmitter (output) module, usually a histidine kinase, as in the case of Cph1. The chromophore deprotonates transiently during the Pr → Pfr photoconversion in association with extensive global structural changes required for signal transmission. Here, we performed equilibrium studies in the Pr state, involving pH titration of the linear tetrapyrrole chromophore in different Cph1 constructs, and measurement of pH-dependent structural changes at various positions in the protein using picosecond time-resolved fluorescence anisotropy. The fluorescent reporter group was attached at positions 371 (PHY domain), 305 (GAF domain), and 120 (PAS domain), as well as at sites in the PAS-GAF bidomain. We show direct correlation of chromophore deprotonation with pH-dependent conformational changes in the various domains. Our results suggest that chromophore deprotonation is closely associated with a higher protein mobility (conformational space) both in proximal and in distal protein sites, implying a causal relationship that might be important for the global large protein arrangements and thus intramolecular signal transduction.
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Affiliation(s)
- Maryam Sadeghi
- Freie Universität Berlin, Institut für Experimentalphysik, D-14195 Berlin, Germany
| | - Jens Balke
- Freie Universität Berlin, Institut für Experimentalphysik, D-14195 Berlin, Germany
| | - Constantin Schneider
- Freie Universität Berlin, Institut für Experimentalphysik, D-14195 Berlin, Germany
| | - Soshichiro Nagano
- Justus-Liebig-Universität, Institut für Pflanzenphysiologie, D-35390 Giessen, Germany
| | - Johannes Stellmacher
- Freie Universität Berlin, Institut für Experimentalphysik, D-14195 Berlin, Germany
| | - Günter Lochnit
- Justus-Liebig-Universität, Institut für Medizinische Biochemie, D-35390 Giessen, Germany
| | - Christina Lang
- Justus-Liebig-Universität, Institut für Pflanzenphysiologie, D-35390 Giessen, Germany
| | - Chris Weise
- Freie Universität Berlin, Institut für Chemie und Biochemie, D-14195 Berlin, Germany
| | - Jon Hughes
- Justus-Liebig-Universität, Institut für Pflanzenphysiologie, D-35390 Giessen, Germany
| | - Ulrike Alexiev
- Freie Universität Berlin, Institut für Experimentalphysik, D-14195 Berlin, Germany
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11
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Zhao X, Huang J, Chory J. Unraveling the Linkage between Retrograde Signaling and RNA Metabolism in Plants. TRENDS IN PLANT SCIENCE 2020; 25:141-147. [PMID: 31791654 DOI: 10.1016/j.tplants.2019.10.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/09/2019] [Accepted: 10/23/2019] [Indexed: 05/25/2023]
Abstract
Retrograde signals are signals that originate in organelles to regulate nuclear gene expression. In plant cells, retrograde signaling from both chloroplasts and mitochondria is essential for plant development and growth. Over the past few years, substantial progress has been made in unraveling the linkages between chloroplast retrograde signaling and nuclear RNA metabolism processes or plastidial RNA editing. These findings add to the complexity of the regulation of organelle-to-nucleus communication. Chloroplast development and function rely on the coordinated regulation of chloroplast and nuclear gene expression, especially under stress conditions. A better understanding of retrograde signaling and RNA metabolism, as well as their connection, is essential for breeding stress-tolerant plants to cope with the dynamic and rapidly changing environment.
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Affiliation(s)
- Xiaobo Zhao
- Institute of Nuclear Agricultural Sciences, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
| | - Jianyan Huang
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Joanne Chory
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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12
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Wang X, Li BB, Ma TT, Sun LY, Tai L, Hu CH, Liu WT, Li WQ, Chen KM. The NAD kinase OsNADK1 affects the intracellular redox balance and enhances the tolerance of rice to drought. BMC PLANT BIOLOGY 2020; 20:11. [PMID: 31910821 PMCID: PMC6947874 DOI: 10.1186/s12870-019-2234-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 12/30/2019] [Indexed: 05/04/2023]
Abstract
BACKGROUND NAD kinases (NADKs) are the only known enzymes that directly phosphorylate NAD(H) to generate NADP(H) in different subcellular compartments. They participate in multiple life activities, such as modulating the NADP/NAD ratio, maintaining the intracellular redox balance and responding to environmental stresses. However, the functions of individual NADK in plants are still under investigation. Here, a rice NADK, namely, OsNADK1, was identified, and its functions in plant growth regulation and stress tolerance were analysed by employing a series of transgenic plant lines. RESULTS OsNADK1 is a cytosol-localized NADK in rice. It was expressed in all rice tissues examined, and its transcriptional expression could be stimulated by a number of environmental stress treatments. Compared with wild-type (WT) rice, the mutant plant osnadk1 in which OsNADK1 was knocked out was a dwarf at the heading stage and had decreased NADP(H)/NAD(H), ascorbic acid (ASA)/dehydroascorbate (DHA) and reduced glutathione (GSH)/oxidized glutathione (GSSG) ratios, which led to increased oxidation states in the rice cells and sensitivity to drought. Moreover, certain stress-related genes showed differential expression patterns in osnadk1 under both normal growth and drought-stress conditions compared with WT. Among these genes, OsDREB1B and several WRKY family transcription factors, e.g., OsWRKY21 and OsWRKY42, showed correlated co-expression patterns with OsNADK1 in osnadk1 and the plants overexpressing or underexpressing OsNADK1, implying roles for these transcription factors in OsNADK1-mediated processes. In addition, overexpression of OsNADK1 enhanced the drought tolerance of rice plants, whereas loss of function of the gene reduced the tolerance. Furthermore, the proline content was dramatically increased in the leaves of the OsNADK1-overexpressing lines under drought conditions. CONCLUSIONS Altogether, the results suggest that an OsNADK1-mediated intracellular redox balance is involved in the tolerance of rice plants to drought.
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Affiliation(s)
- Xiang Wang
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 Hubei China
| | - Bin-Bin Li
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Tian-Tian Ma
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Liang-Yu Sun
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Li Tai
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Chun-Hong Hu
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
- College of Life Science and Agriculture, Zhoukou Normal University, Zhoukou, 466001 Henan China
| | - Wen-Ting Liu
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Wen-Qiang Li
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Kun-Ming Chen
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
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13
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Kastoori Ramamurthy R, Xiang Q, Hsieh EJ, Liu K, Zhang C, Waters BM. New aspects of iron-copper crosstalk uncovered by transcriptomic characterization of Col-0 and the copper uptake mutant spl7 in Arabidopsis thaliana. Metallomics 2019; 10:1824-1840. [PMID: 30460953 DOI: 10.1039/c8mt00287h] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Iron (Fe) and copper (Cu) are essential micronutrients for energy metabolism and reactive oxygen species (ROS) scavenging. Some Cu-containing proteins can be substituted with Fe-containing proteins, and vice versa, while several Arabidopsis genes are regulated by both metals. Few details of how plants coordinate Fe-Cu crosstalk are known. Gene expression was measured in the roots and rosettes of Fe, Cu, and simultaneously Fe and Cu deficient WT plants and a mutant of the Cu-uptake transcription factor SPL7. The spl7 mutant accumulated excess Fe under normal conditions, and lower Fe supply rescued the growth phenotype and normalized the Fe : Cu ratios. Most Fe regulated genes were expressed similarly in the WT and spl7 mutant, although at higher fold-change levels in spl7 mutants. Expression patterns indicated that both SPL7 and the FIT Fe uptake transcription factor influenced the expression of many key Fe uptake genes. Most notably, the newly discovered IMA/FEP genes and the subgroup Ib bHLH genes, which are upstream of Fe uptake responses, were repressed in the WT under Cu deficiency. Several AP2/ethylene response factor (AP2/ERF) genes and other redox homeostasis network genes were derepressed in spl7 mutants. Together, we present new information about Fe-Cu crosstalk in plants that could be applied for developing abiotic stress tolerant crops.
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14
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Soliman ERS, Meyer P. Responsiveness and Adaptation to Salt Stress of the REDOX-RESPONSIVE TRANSCRIPTION FACTOR 1 (RRTF1) Gene are Controlled by its Promoter. Mol Biotechnol 2019; 61:254-260. [PMID: 30734200 DOI: 10.1007/s12033-019-00155-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The REDOX-RESPONSIVE TRANSCRIPTION FACTOR 1 (RRTF1) gene encodes a member of the ERF/AP2 transcription factor family involved in redox homeostasis. The RRTF1 gene shows tissue-specific responsiveness to various abiotic stress treatments including a response to salt stress in roots. An interesting feature of this response is an adaptation phase that follows its activation, when promoter levels revert to a base line level, even if salt stress is maintained. It is unclear if adaption is controlled by a switch in promoter activity or by changes in transcript levels. Here we show that the RRTF1 promoter is sufficient for the control of both activation and adaptation to salt stress. As constitutive expression of RRTF1 turned out to be detrimental to the plant, we propose that promoter-regulated adaptation evolved as a protection mechanism to balance the beneficial effects of short-term gene activation and the detrimental effects of long-term gene expression.
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Affiliation(s)
- Elham R S Soliman
- Botany and Microbiology department, Faculty of Science, Helwan University, Cairo, Egypt.
| | - Peter Meyer
- Center for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
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15
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Weise SE, Liu T, Childs KL, Preiser AL, Katulski HM, Perrin-Porzondek C, Sharkey TD. Transcriptional Regulation of the Glucose-6-Phosphate/Phosphate Translocator 2 Is Related to Carbon Exchange Across the Chloroplast Envelope. FRONTIERS IN PLANT SCIENCE 2019; 10:827. [PMID: 31316533 PMCID: PMC6609314 DOI: 10.3389/fpls.2019.00827] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/07/2019] [Indexed: 05/02/2023]
Abstract
The exchange of reduced carbon across the inner chloroplast envelope has a large impact on photosynthesis and growth. Under steady-state conditions it is thought that glucose 6-phosphate (G6P) does not cross the chloroplast membrane. However, growth at high CO2, or disruption of starch metabolism can result in the GPT2 gene for a G6P/Pi translocator to be expressed presumably allowing G6P exchange across the chloroplast envelope. We found that after an increase in light, the transcript for GPT2 transiently increases several 100-fold within 2 h in both the Col-0 and WS ecotypes of Arabidopsis thaliana. The increase in transcript for GPT2 is preceded by an increase in transcript for many transcription factors including Redox Responsive Transcription Factor 1 (RRTF1). The increase in GPT2 transcript after exposure to high light is suppressed in a mutant lacking the RRTF1 transcription factor. The GPT2 response was also suppressed in a mutant with a T-DNA insert in the gene for the triose-phosphate/Pi translocator (TPT). However, plants lacking TPT still had a robust rise in RRTF1 transcript in response to high light. From this, we conclude that both RRTF1 (and possibly other transcription factors) and high amounts of cytosolic triose phosphate are required for induction of the expression of GPT2. We hypothesize that transient GPT2 expression and subsequent translation is adaptive, allowing G6P to move into the chloroplast from the cytosol. The imported G6P can be used for starch synthesis or may flow directly into the Calvin-Benson cycle via an alternative pathway (the G6P shunt), which could be important for regulating and stabilizing photosynthetic electron transport and carbon metabolism.
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Affiliation(s)
- Sean E. Weise
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Tiffany Liu
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
| | - Kevin L. Childs
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
| | - Alyssa L. Preiser
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
| | - Hailey M. Katulski
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
| | | | - Thomas D. Sharkey
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
- Plant Resilience Institute, Michigan State University, East Lansing, MI, United States
- *Correspondence: Thomas D. Sharkey,
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16
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Bahieldin A, Atef A, Edris S, Gadalla NO, Ramadan AM, Hassan SM, Al Attas SG, Al-Kordy MA, Al-Hajar ASM, Sabir JSM, Nasr ME, Osman GH, El-Domyati FM. Multifunctional activities of ERF109 as affected by salt stress in Arabidopsis. Sci Rep 2018; 8:6403. [PMID: 29686365 PMCID: PMC5913302 DOI: 10.1038/s41598-018-24452-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 04/04/2018] [Indexed: 11/17/2022] Open
Abstract
Transcriptomic analysis was conducted in leaves of Arabidopsis T-DNA insertion ERF109-knocked out (KO) mutant or plants overexpressing (OE) the gene to detect its role in driving expression of programmed cell death- (PCD-) or growth-related genes under high salt (200 mM NaCl) stress. The analysis yielded ~22–24 million reads, of which 90% mapped to the Arabidopsis reference nuclear genome. Hierarchical cluster analysis of gene expression and principal component analysis (PCA) successfully separated transcriptomes of the two stress time points. Analysis indicated the occurrence of 65 clusters of gene expression with transcripts of four clusters differed at the genotype (e.g., WT (wild type), KOERF109 or OEERF109) level. Regulated transcripts involved DIAP1-like gene encoding a death-associated inhibitor of reactive oxygen species (ROS). Other ERF109-regulated transcripts belong to gene families encoding ROS scavenging enzymes and a large number of genes participating in three consecutive pathways, e.g., phenylalanine, tyrosine and tryptophan biosynthesis, tryptophan metabolism and plant hormone signal transduction. We investigated the possibility that ERF109 acts as a “master switch” mediator of a cascade of consecutive events across these three pathways initially by driving expression of ASA1 and YUC2 genes and possibly driving GST, IGPS and LAX2 genes. Action of downstream auxin-regulator, auxin-responsive as well as auxin carrier genes promotes plant cell growth under adverse conditions.
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Affiliation(s)
- Ahmed Bahieldin
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589, Saudi Arabia.
| | - Ahmed Atef
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589, Saudi Arabia
| | - Sherif Edris
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589, Saudi Arabia.,Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt.,Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Nour O Gadalla
- Department of Arid Land Agriculture, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia.,Genetics and Cytology Department, Genetic Engineering and Biotechnology Division, National Research Center, Dokki, Egypt
| | - Ahmed M Ramadan
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589, Saudi Arabia.,Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza, Egypt
| | - Sabah M Hassan
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589, Saudi Arabia.,Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Sanaa G Al Attas
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589, Saudi Arabia
| | - Magdy A Al-Kordy
- Genetics and Cytology Department, Genetic Engineering and Biotechnology Division, National Research Center, Dokki, Egypt
| | - Abdulrahman S M Al-Hajar
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589, Saudi Arabia
| | - Jamal S M Sabir
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589, Saudi Arabia
| | - Mahmoud E Nasr
- Faculty of Agriculture, Menofia University, Shebeen Elkom, Egypt
| | - Gamal H Osman
- Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza, Egypt. .,Department of Biology, Umm Al-Qura University, Makkah, Saudi Arabia.
| | - Fotouh M El-Domyati
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
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17
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Heyman J, Canher B, Bisht A, Christiaens F, De Veylder L. Emerging role of the plant ERF transcription factors in coordinating wound defense responses and repair. J Cell Sci 2018; 131:jcs.208215. [PMID: 29242229 DOI: 10.1242/jcs.208215] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 09/28/2017] [Indexed: 12/22/2022] Open
Abstract
Plants react to wounding through the activation of both defense and repair pathways, but how these two responses are coordinated is unclear. Here, we put forward the hypothesis that diverse members of the subfamily X of the plant-specific ethylene response factor (ERF) transcription factors coordinate stress signaling with the activation of wound repair mechanisms. Moreover, we highlight the observation that tissue repair is strongly boosted through the formation of a heterodimeric protein complex that comprises ERF and transcription factors of the GRAS domain type. This interaction turns ERFs into highly potent and stress-responsive activators of cell proliferation. The potency to induce stem cell identity suggests that these heterodimeric transcription factor complexes could become valuable tools to increase crop regeneration and transformation efficiency.
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Affiliation(s)
- Jefri Heyman
- Center for Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Balkan Canher
- Center for Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Anchal Bisht
- Center for Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Fien Christiaens
- Center for Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Lieven De Veylder
- Center for Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium .,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
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18
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Vahabi K, Reichelt M, Scholz SS, Furch ACU, Matsuo M, Johnson JM, Sherameti I, Gershenzon J, Oelmüller R. Alternaria Brassicae Induces Systemic Jasmonate Responses in Arabidopsis Which Travel to Neighboring Plants via a Piriformsopora Indica Hyphal Network and Activate Abscisic Acid Responses. FRONTIERS IN PLANT SCIENCE 2018; 9:626. [PMID: 29868082 PMCID: PMC5952412 DOI: 10.3389/fpls.2018.00626] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 04/20/2018] [Indexed: 05/20/2023]
Abstract
Stress information received by a particular local plant tissue is transferred to other tissues and neighboring plants, but how the information travels is not well understood. Application of Alternaria Brassicae spores to Arabidopsis leaves or roots stimulates local accumulation of jasmonic acid (JA), the expression of JA-responsive genes, as well as of NITRATE TRANSPORTER (NRT)2.5 and REDOX RESPONSIVE TRANSCRIPTION FACTOR1 (RRTF1). Infection information is systemically spread over the entire seedling and propagates radially from infected to non-infected leaves, axially from leaves to roots, and vice versa. The local and systemic NRT2.5 responses are reduced in the jar1 mutant, and the RRTF1 response in the rbohD mutant. Information about A. brassicae infection travels slowly to uninfected neighboring plants via a Piriformospora Indica hyphal network, where NRT2.5 and RRTF1 are up-regulated. The systemic A. brassicae-induced JA response in infected plants is converted to an abscisic acid (ABA) response in the neighboring plant where ABA and ABA-responsive genes are induced. We propose that the local threat information induced by A. brassicae infection is spread over the entire plant and transferred to neighboring plants via a P. indica hyphal network. The JA-specific response is converted to a general ABA-mediated stress response in the neighboring plant.
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Affiliation(s)
- Khabat Vahabi
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller-University Jena, Jena, Germany
| | - Michael Reichelt
- Department of Biochemistry, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Sandra S. Scholz
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller-University Jena, Jena, Germany
| | - Alexandra C. U. Furch
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller-University Jena, Jena, Germany
| | - Mitsuhiro Matsuo
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller-University Jena, Jena, Germany
| | - Joy M. Johnson
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller-University Jena, Jena, Germany
| | - Irena Sherameti
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller-University Jena, Jena, Germany
| | - Jonathan Gershenzon
- Department of Biochemistry, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Ralf Oelmüller
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller-University Jena, Jena, Germany
- *Correspondence: Ralf Oelmüller
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19
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Zhang L, Xu B, Wu T, Wen MX, Fan LX, Feng ZZ, Paoletti E. Transcriptomic analysis of Pak Choi under acute ozone exposure revealed regulatory mechanism against ozone stress. BMC PLANT BIOLOGY 2017; 17:236. [PMID: 29216819 PMCID: PMC5721698 DOI: 10.1186/s12870-017-1202-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 12/01/2017] [Indexed: 05/23/2023]
Abstract
BACKGROUND Ground-level ozone (O3) is one of the major air pollutants, which cause oxidative injury to plants. The physiological and biochemical mechanisms underlying the responses of plants to O3 stress have been well investigated. However, there are limited reports about the molecular basis of plant responses to O3. In this study, a comparative transcriptomic analysis of Pak Choi (Brassica campestris ssp. chinensis) exposed to different O3 concentrations was conducted for the first time. RESULTS Seedlings of Pak Choi with five leaves were exposed to non-filtered air (NF, 31 ppb) or elevated O3 (E-O3, 252 ppb) for 2 days (8 h per day, from 9:00-17:00). Compared with plants in the NF, a total of 675 differentially expressed genes (DEGs) were identified in plants under E-O3, including 219 DEGs with decreased expressions and 456 DEGs with increased expressions. Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that O3 stress invoked multiple cellular defense pathways to mitigate the impaired cellular integrity and metabolism, including 'glutathione metabolism', 'phenylpropanoid biosynthesis', 'sulfur metabolism', 'glucosinolate biosynthesis', 'cutin, suberine and wax biosynthesis' and others. Transcription factors potentially involved in this cellular regulation were also found, such as AP2-ERF, WRKY, JAZ, MYB etc. Based on the RNA-Seq data and previous studies, a working model was proposed integrating O3 caused reactive oxygen burst, oxidation-reduction regulation, jasmonic acid and downstream functional genes for the regulation of cellular homeostasis after acute O3 stress. CONCLUSION The present results provide a valuable insight into the molecular responses of Pak Choi to acute O3 stress and the specific DEGs revealed in this study could be used for further functional identification of key allelic genes determining the O3 sensitivity of Pak Choi.
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Affiliation(s)
- Lu Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Bin Xu
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Tao Wu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Mu-xuan Wen
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Lian-xue Fan
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Zhao-zhong Feng
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Elena Paoletti
- Institute of Sustainable Plant Protection, National Research Council, Florence, Italy
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Pomiès L, Decourteix M, Franchel J, Moulia B, Leblanc-Fournier N. Poplar stem transcriptome is massively remodelled in response to single or repeated mechanical stimuli. BMC Genomics 2017; 18:300. [PMID: 28412928 PMCID: PMC5392906 DOI: 10.1186/s12864-017-3670-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 03/29/2017] [Indexed: 11/26/2022] Open
Abstract
Background Trees experience mechanical stimuli -like wind- that trigger thigmomorphogenetic syndrome, leading to modifications of plant growth and wood quality. This syndrome affects tree productivity but is also believed to improve tree acclimation to chronic wind. Wind is particularly challenging for trees, because of their stature and perenniality. Climate change forecasts are predicting that the occurrence of high wind will worsen, making it increasingly vital to understand the mechanisms regulating thigmomorphogenesis, especially in perennial plants. By extension, this also implies factoring in the recurring nature of wind episodes. However, data on the molecular processes underpinning mechanoperception and transduction of mechanical signals, and their dynamics, are still dramatically lacking in trees. Results Here we performed a genome-wide and time-series analysis of poplar transcriptional responsiveness to transitory and recurring controlled stem bending, mimicking wind. The study revealed that 6% of the poplar genome is differentially expressed after a single transient bending. The combination of clustering, Gene Ontology categorization and time-series expression approaches revealed the diversity of gene expression patterns and biological processes affected by stem bending. Short-term transcriptomic responses entailed a rapid stimulation of plant defence and abiotic stress signalling pathways, including ethylene and jasmonic acid signalling but also photosynthesis process regulation. Late transcriptomic responses affected genes involved in cell wall organization and/or wood development. An analysis of the molecular impact of recurring bending found that the vast majority (96%) of the genes differentially expressed after a first bending presented reduced or even net-zero amplitude regulation after the second exposure to bending. Conclusion This study constitutes the first dynamic characterization of the molecular processes affected by single or repeated stem bending in poplar. Moreover, the global attenuation of the transcriptional responses, observed from as early as after a second bending, indicates the existence of a mechanism governing a fine tuning of plant responsiveness. This points toward several mechanistic pathways that can now be targeted to elucidate the complex dynamics of wind acclimation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3670-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lise Pomiès
- Université Clermont Auvergne, INRA, PIAF, F-63000, Clermont-Ferrand, France
| | - Mélanie Decourteix
- Université Clermont Auvergne, INRA, PIAF, F-63000, Clermont-Ferrand, France
| | - Jérôme Franchel
- Université Clermont Auvergne, INRA, PIAF, F-63000, Clermont-Ferrand, France
| | - Bruno Moulia
- Université Clermont Auvergne, INRA, PIAF, F-63000, Clermont-Ferrand, France
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Zhang Y, Leclercq J, Montoro P. Reactive oxygen species in Hevea brasiliensis latex and relevance to Tapping Panel Dryness. TREE PHYSIOLOGY 2017; 37:261-269. [PMID: 27903918 PMCID: PMC5928795 DOI: 10.1093/treephys/tpw106] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 08/16/2016] [Accepted: 10/01/2016] [Indexed: 05/27/2023]
Abstract
Environmental stress can lead to oxidative stress resulting from an increase in reactive oxygen species (ROS) and involves redox adjustments. Natural rubber is synthesized in laticifers, which is a non-photosynthetic tissue particularly prone to oxidative stress. This paper reviews the current state of knowledge on the ROS production and ROS-scavenging systems in laticifers. These regulations have been the subject of intense research into a physiological syndrome, called Tapping Panel Dryness (TPD), affecting latex production in Hevea brasiliensis. In order to prevent TPD occurrence, monitoring thiol content appeared to be a crucial factor of latex diagnosis. Thiols, ascorbate and γ-tocotrienol are the major antioxidants in latex. They are involved in membrane protection from ROS and likely have an effect on the quality of raw rubber. Some transcription factors might play a role in the redox regulatory network in Hevea, in particular ethylene response factors, which have been the most intensively studied given the role of ethylene on rubber production. Current challenges for rubber research and development with regard to redox systems will involve improving antioxidant capacity using natural genetic variability.
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Affiliation(s)
- Yi Zhang
- CIRAD, UMR AGAP, F-34398 Montpellier, France
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22
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Phukan UJ, Jeena GS, Tripathi V, Shukla RK. Regulation of Apetala2/Ethylene Response Factors in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:150. [PMID: 28270817 PMCID: PMC5318435 DOI: 10.3389/fpls.2017.00150] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/25/2017] [Indexed: 05/18/2023]
Abstract
Multiple environmental stresses affect growth and development of plants. Plants try to adapt under these unfavorable condition through various evolutionary mechanisms like physiological and biochemical alterations connecting various network of regulatory processes. Transcription factors (TFs) like APETALA2/ETHYLENE RESPONSE FACTORS (AP2/ERFs) are an integral component of these signaling cascades because they regulate expression of a wide variety of down stream target genes related to stress response and development through different mechanism. This downstream regulation of transcript does not always positively or beneficially affect the plant but also they display some developmental defects like senescence and reduced growth under normal condition or sensitivity to stress condition. Therefore, tight auto/cross regulation of these TFs at transcriptional, translational and domain level is crucial to understand. The present manuscript discuss the multiple regulation and advantage of plasticity and specificity of these family of TFs to a wide or single downstream target(s) respectively. We have also discussed the concern which comes with the unwanted associated traits, which could only be averted by further study and exploration of these AP2/ERFs.
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Affiliation(s)
- Ujjal J. Phukan
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic PlantsLucknow, India
| | - Gajendra S. Jeena
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic PlantsLucknow, India
| | - Vineeta Tripathi
- Botany Division, CSIR-Central Drug Research InstituteLucknow, India
| | - Rakesh K. Shukla
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic PlantsLucknow, India
- *Correspondence: Rakesh K. Shukla
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Bahieldin A, Atef A, Edris S, Gadalla NO, Ali HM, Hassan SM, Al-Kordy MA, Ramadan AM, Makki RM, Al-Hajar ASM, El-Domyati FM. Ethylene responsive transcription factor ERF109 retards PCD and improves salt tolerance in plant. BMC PLANT BIOLOGY 2016; 16:216. [PMID: 27716054 PMCID: PMC5053207 DOI: 10.1186/s12870-016-0908-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 09/27/2016] [Indexed: 05/21/2023]
Abstract
BACKGROUND The ultimate goal of this work was to detect the role of transcription factors (TFs) concordantly expressed with genes related to programmed cell death (PCD) during PCD and salt stress. This work was based on the hypothesis that TFs and their driven genes likely co-express under different stimuli. The conserved superfamily ethylene responsive factor (AP2/ERF) draw attention of the present study as it participates in the response to biotic and abiotic stimuli as well as to program cell death (PCD). RESULTS RNA-Seq analysis was done for tobacco (N. benthamiana) leaves exposed to oxalic acid (OA) at 20 mM for 0, 2, 6, 12 and 24 h to induce PCD. Genes up-regulated after 2 h of OA treatment with known function during PCD were utilized as landmarks to select TFs with concordant expression. Knockdown mutants of these TFs were generated in tobacco via virus induced gene silencing (VIGS) in order to detect their roles during PCD. Based on the results of PCD assay, knockout (KO) T-DNA insertion mutants of Arabidopsis as well as over-expression lines of two selected TFs, namely ERF109 and TFIID5, analogs to those in tobacco, were tested under salt stress (0, 100, 150 and 200 mM NaCl). CONCLUSIONS Results of knockdown mutant tobacco cells confirmed the influence of these two TFs during PCD. Knockout insertion mutants and over-expression lines indicated the role of ERF109 in conferring salt tolerance in Arabidopsis.
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Affiliation(s)
- Ahmed Bahieldin
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
| | - Ahmed Atef
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
| | - Sherif Edris
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
- Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Nour O. Gadalla
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
| | - Hani M. Ali
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
| | - Sabah M. Hassan
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
| | - Magdy A. Al-Kordy
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
| | - Ahmed M. Ramadan
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
| | - Rania M. Makki
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
| | - Abdulrahman S. M. Al-Hajar
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
| | - Fotouh M. El-Domyati
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589 Saudi Arabia
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24
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Harvey CM, Sharkey TD. Exogenous isoprene modulates gene expression in unstressed Arabidopsis thaliana plants. PLANT, CELL & ENVIRONMENT 2016; 39:1251-1263. [PMID: 26477606 DOI: 10.1111/pce.12660] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/30/2015] [Accepted: 10/07/2015] [Indexed: 06/05/2023]
Abstract
Isoprene is a well-studied volatile hemiterpene that protects plants from abiotic stress through mechanisms that are not fully understood. The antioxidant and membrane stabilizing potential of isoprene are the two most commonly invoked mechanisms. However, isoprene also affects phenylpropanoid metabolism, suggesting an additional role as a signalling molecule. In this study, microarray-based gene expression profiling reveals transcriptional reprogramming of Arabidopsis thaliana plants fumigated for 24 h with a physiologically relevant concentration of isoprene. Functional enrichment analysis of fumigated plants revealed enhanced heat- and light-stress-responsive processes in response to isoprene. Isoprene induced a network enriched in ERF and WRKY transcription factors, which may play a role in stress tolerance. The isoprene-induced up-regulation of phenylpropanoid biosynthetic genes was specifically confirmed using quantitative reverse transcription polymerase chain reaction. These results support a role for isoprene as a signalling molecule, in addition to its possible roles as an antioxidant and membrane thermoprotectant.
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Affiliation(s)
- Christopher M Harvey
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Rd., East Lansing, MI, 48824, USA
| | - Thomas D Sharkey
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Rd., East Lansing, MI, 48824, USA
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25
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Bode R, Ivanov AG, Hüner NPA. Global transcriptome analyses provide evidence that chloroplast redox state contributes to intracellular as well as long-distance signalling in response to stress and acclimation in Arabidopsis. PHOTOSYNTHESIS RESEARCH 2016; 128:287-312. [PMID: 27021769 DOI: 10.1007/s11120-016-0245-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 03/10/2016] [Indexed: 05/03/2023]
Abstract
Global transcriptome analyses were used to assess the interactive effects of short-term stress versus long-term acclimation to high light (HL), low temperature (LT) and excitation pressure in Arabidopsis. Microarray analyses indicated that exposure to stress resulted in two times as many modulated transcripts in both, high-light-treated and low-temperature-treated plants, compared to plants that were fully acclimated to either one of these conditions. We showed that 10.9 % of all transcripts were regulated in the same way by both stress conditions, and hence, were categorized as excitation pressure regulated, rather than regulated by either high-light or low-temperature stress per se. This group of chloroplast redox-sensitive genes included various photosynthetic genes as well as genes known to be associated with cold acclimation (cbf3, cor15A, cor15B) and gibberellic acid (GA) metabolism and signalling (ga2ox1, gai). Chemical inhibition of the photosynthetic electron transport by either DCMU or DBMIB indicated that although the plastoquinone pool contributes significantly to redox regulation of the transcriptome (8.6 %), it appears that PSI represents the major source of redox signals (89 %), whereas PSII appears to contribute only 3.1 %. A comparison of the gene expression profiles between stress and acclimated plants indicated that 10 % of the genes induced by a short, 1-h stress were also associated with long-term acclimation to high excitation pressure. This included the APETALA2/ETHYLENE-RESPONSIVE-BINDING PROTEIN family, the MYB domain- and MYB-related transcription factor family as well as the GRAS transcription factor family important in GA signalling confirming that acclimation to stress is a time-nested phenomenon. We suggest that acclimation to photosynthetic redox imbalance extends beyond the chloroplast and the leaf cell to systemic ROS signalling. This is discussed in terms of the control of plant phenotype through regulation of the nuclear encoded cbf regulon and GA metabolism.
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Affiliation(s)
- Rainer Bode
- Department of Biology and The Biotron Centre for Experimental Climate Change Research, Western University, London, ON, N6A 5B7, Canada
- Department of Biology, Chemistry and Pharmacy, Institute of Biology - Physiology of Plants, Freie Universität Berlin, Königin-Luise-Straße 12-16, 14195, Berlin, Germany
| | - Alexander G Ivanov
- Department of Biology and The Biotron Centre for Experimental Climate Change Research, Western University, London, ON, N6A 5B7, Canada
| | - Norman P A Hüner
- Department of Biology and The Biotron Centre for Experimental Climate Change Research, Western University, London, ON, N6A 5B7, Canada.
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26
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Zermiani M, Zonin E, Nonis A, Begheldo M, Ceccato L, Vezzaro A, Baldan B, Trentin A, Masi A, Pegoraro M, Fadanelli L, Teale W, Palme K, Quintieri L, Ruperti B. Ethylene negatively regulates transcript abundance of ROP-GAP rheostat-encoding genes and affects apoplastic reactive oxygen species homeostasis in epicarps of cold stored apple fruits. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:7255-70. [PMID: 26428066 PMCID: PMC4765793 DOI: 10.1093/jxb/erv422] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Apple (Malus×domestica Borkh) fruits are stored for long periods of time at low temperatures (1 °C) leading to the occurrence of physiological disorders. 'Superficial scald' of Granny Smith apples, an economically important ethylene-dependent disorder, was used as a model to study relationships among ethylene action, the regulation of the ROP-GAP rheostat, and maintenance of H2O2 homeostasis in fruits during prolonged cold exposure. The ROP-GAP rheostat is a key module for adaptation to low oxygen in Arabidopsis through Respiratory Burst NADPH Oxidase Homologs (RBOH)-mediated and ROP GTPase-dependent regulation of reactive oxygen species (ROS) homeostasis. Here, it was shown that the transcriptional expression of several components of the apple ROP-GAP machinery, including genes encoding RBOHs, ROPs, and their ancillary proteins ROP-GEFs and ROP-GAPs, is coordinately and negatively regulated by ethylene in conjunction with the progressive impairment of apoplastic H2O2 homeostatic levels. RNA sequencing analyses showed that several components of the known ROP- and ROS-associated transcriptional networks are regulated along with the ROP-GAP rheostat in response to ethylene perception. These findings may extend the role of the ROP-GAP rheostat beyond hypoxic responses and suggest that it may be a functional regulatory node involved in the integration of ethylene and ROS signalling pathways in abiotic stress.
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Affiliation(s)
- Monica Zermiani
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, 35020 Legnaro, Italy
| | - Elisabetta Zonin
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, 35020 Legnaro, Italy
| | - Alberto Nonis
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, 35020 Legnaro, Italy
| | - Maura Begheldo
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, 35020 Legnaro, Italy
| | - Luca Ceccato
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, 35020 Legnaro, Italy
| | - Alice Vezzaro
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, 35020 Legnaro, Italy
| | - Barbara Baldan
- Department of Biology, University of Padova, 35121 Padova, Italy
| | - Annarita Trentin
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, 35020 Legnaro, Italy
| | - Antonio Masi
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, 35020 Legnaro, Italy
| | - Marco Pegoraro
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, 35020 Legnaro, Italy
| | - Livio Fadanelli
- Edmund Mach Foundation, San Michele all'Adige, 38123 Trento, Italy
| | - William Teale
- Institute of Biology II/Molecular Plant Physiology, Faculty of Biology, Albert-Ludwigs-University of Freiburg, D-79104 Freiburg, Germany
| | - Klaus Palme
- Institute of Biology II/Molecular Plant Physiology, Faculty of Biology, Albert-Ludwigs-University of Freiburg, D-79104 Freiburg, Germany Centre for Biological Systems Analysis, Albert-Ludwigs-University of Freiburg, D-79104 Freiburg, Germany Freiburg Institute for Advanced Sciences (FRIAS), Albert-Ludwigs-University of Freiburg, D-79104 Freiburg, Germany Centre for Biological Signalling Studies (bioss), Albert-Ludwigs-University of Freiburg, D-79104 Freiburg, Germany Freiburg Initiative for Systems Biology (FRISYS), Albert-Ludwigs-University of Freiburg, D-79104 Freiburg, Germany
| | - Luigi Quintieri
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, 35131 Padova, Italy
| | - Benedetto Ruperti
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, 35020 Legnaro, Italy
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27
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Chuang HW, Feng JH, Feng YL, Wei MJ. An Arabidopsis WDR protein coordinates cellular networks involved in light, stress response and hormone signals. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 241:23-31. [PMID: 26706055 DOI: 10.1016/j.plantsci.2015.09.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 09/25/2015] [Accepted: 09/25/2015] [Indexed: 06/05/2023]
Abstract
The WD-40 repeat (WDR) protein acts as a scaffold for protein interactions in various cellular events. An Arabidopsis WDR protein exhibited sequence similarity with human WDR26, a scaffolding protein implicated in H2O2-induced cell death in neural cells. The AtWDR26 transcript was induced by auxin, abscisic acid (ABA), ethylene (ET), osmostic stress and salinity. The expression of AtWDR26 was regulated by light, and seed germination of the AtWDR26 overexpression (OE) and seedling growth of the T-DNA knock-out (KO) exhibited altered sensitivity to light. Root growth of the OE seedlings increased tolerance to ZnSO4 and NaCl stresses and were hypersensitive to inhibition of osmotic stress. Seedlings of OE and KO altered sensitivities to multiple hormones. Transcriptome analysis of the transgenic plants overexpressing AtWDR26 showed that genes involved in the chloroplast-related metabolism constituted the largest group of the up-regulated genes. AtWDR26 overexpression up-regulated a large number of genes related to defense cellular events including biotic and abiotic stress response. Furthermore, several members of genes functioning in the regulation of Zn homeostasis, and hormone synthesis and perception of auxin and JA were strongly up-regulated in the transgenic plants. Our data provide physiological and transcriptional evidence for AtWDR26 role in hormone, light and abiotic stress cellular events.
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Affiliation(s)
- Huey-Wen Chuang
- Department of Bioagricultural Sciences, National Chiayi University, Chiayi, Taiwan.
| | - Ji-Huan Feng
- Department of Bioagricultural Sciences, National Chiayi University, Chiayi, Taiwan
| | - Yung-Lin Feng
- Department of Bioagricultural Sciences, National Chiayi University, Chiayi, Taiwan
| | - Miam-Ju Wei
- Department of Bioagricultural Sciences, National Chiayi University, Chiayi, Taiwan
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28
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Bertea CM, Narayana R, Agliassa C, Rodgers CT, Maffei ME. Geomagnetic Field (Gmf) and Plant Evolution: Investigating the Effects of Gmf Reversal on Arabidopsis thaliana Development and Gene Expression. J Vis Exp 2015. [PMID: 26649488 PMCID: PMC4692770 DOI: 10.3791/53286] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
One of the most stimulating observations in plant evolution is a correlation between the occurrence of geomagnetic field (GMF) reversals (or excursions) and the moment of the radiation of Angiosperms. This led to the hypothesis that alterations in GMF polarity may play a role in plant evolution. Here, we describe a method to test this hypothesis by exposing Arabidopsis thaliana to artificially reversed GMF conditions. We used a three-axis magnetometer and the collected data were used to calculate the magnitude of the GMF. Three DC power supplies were connected to three Helmholtz coil pairs and were controlled by a computer to alter the GMF conditions. Plants grown in Petri plates were exposed to both normal and reversed GMF conditions. Sham exposure experiments were also performed. Exposed plants were photographed during the experiment and images were analyzed to calculate root length and leaf areas. Arabidopsis total RNA was extracted and Quantitative Real Time-PCR (qPCR) analyses were performed on gene expression of CRUCIFERIN 3 (CRU3), copper transport protein1 (COTP1), Redox Responsive Transcription Factor1 (RRTF1), Fe Superoxide Dismutase 1, (FSD1), Catalase3 (CAT3), Thylakoidal Ascorbate Peroxidase (TAPX), a cytosolic Ascorbate Peroxidase1 (APX1), and NADPH/respiratory burst oxidase protein D (RbohD). Four different reference genes were analysed to normalize the results of the qPCR. The best of the four genes was selected and the most stable gene for normalization was used. Our data show for the first time that reversing the GMF polarity using triaxial coils has significant effects on plant growth and gene expression. This supports the hypothesis that GMF reversal contributes to inducing changes in plant development that might justify a higher selective pressure, eventually leading to plant evolution.
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Affiliation(s)
- Cinzia M Bertea
- Department of Life Sciences and Systems Biology, University of Turin
| | | | - Chiara Agliassa
- Department of Life Sciences and Systems Biology, University of Turin
| | | | - Massimo E Maffei
- Department of Life Sciences and Systems Biology, University of Turin;
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29
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Rutowicz K, Puzio M, Halibart-Puzio J, Lirski M, Kotliński M, Kroteń MA, Knizewski L, Lange B, Muszewska A, Śniegowska-Świerk K, Kościelniak J, Iwanicka-Nowicka R, Buza K, Janowiak F, Żmuda K, Jõesaar I, Laskowska-Kaszub K, Fogtman A, Kollist H, Zielenkiewicz P, Tiuryn J, Siedlecki P, Swiezewski S, Ginalski K, Koblowska M, Archacki R, Wilczynski B, Rapacz M, Jerzmanowski A. A Specialized Histone H1 Variant Is Required for Adaptive Responses to Complex Abiotic Stress and Related DNA Methylation in Arabidopsis. PLANT PHYSIOLOGY 2015; 169:2080-101. [PMID: 26351307 PMCID: PMC4634048 DOI: 10.1104/pp.15.00493] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 09/07/2015] [Indexed: 05/18/2023]
Abstract
Linker (H1) histones play critical roles in chromatin compaction in higher eukaryotes. They are also the most variable of the histones, with numerous nonallelic variants cooccurring in the same cell. Plants contain a distinct subclass of minor H1 variants that are induced by drought and abscisic acid and have been implicated in mediating adaptive responses to stress. However, how these variants facilitate adaptation remains poorly understood. Here, we show that the single Arabidopsis (Arabidopsis thaliana) stress-inducible variant H1.3 occurs in plants in two separate and most likely autonomous pools: a constitutive guard cell-specific pool and a facultative environmentally controlled pool localized in other tissues. Physiological and transcriptomic analyses of h1.3 null mutants demonstrate that H1.3 is required for both proper stomatal functioning under normal growth conditions and adaptive developmental responses to combined light and water deficiency. Using fluorescence recovery after photobleaching analysis, we show that H1.3 has superfast chromatin dynamics, and in contrast to the main Arabidopsis H1 variants H1.1 and H1.2, it has no stable bound fraction. The results of global occupancy studies demonstrate that, while H1.3 has the same overall binding properties as the main H1 variants, including predominant heterochromatin localization, it differs from them in its preferences for chromatin regions with epigenetic signatures of active and repressed transcription. We also show that H1.3 is required for a substantial part of DNA methylation associated with environmental stress, suggesting that the likely mechanism underlying H1.3 function may be the facilitation of chromatin accessibility by direct competition with the main H1 variants.
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Affiliation(s)
- Kinga Rutowicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Marcin Puzio
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Joanna Halibart-Puzio
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Maciej Lirski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Maciej Kotliński
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Magdalena A Kroteń
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Lukasz Knizewski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Bartosz Lange
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Katarzyna Śniegowska-Świerk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Janusz Kościelniak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Roksana Iwanicka-Nowicka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Krisztián Buza
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Franciszek Janowiak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Katarzyna Żmuda
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Indrek Jõesaar
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Katarzyna Laskowska-Kaszub
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Anna Fogtman
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Hannes Kollist
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Piotr Zielenkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Jerzy Tiuryn
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Paweł Siedlecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Szymon Swiezewski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Krzysztof Ginalski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Marta Koblowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Rafał Archacki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Bartek Wilczynski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Marcin Rapacz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Andrzej Jerzmanowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
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30
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Matsuo M, Johnson JM, Hieno A, Tokizawa M, Nomoto M, Tada Y, Godfrey R, Obokata J, Sherameti I, Yamamoto YY, Böhmer FD, Oelmüller R. High REDOX RESPONSIVE TRANSCRIPTION FACTOR1 Levels Result in Accumulation of Reactive Oxygen Species in Arabidopsis thaliana Shoots and Roots. MOLECULAR PLANT 2015; 8:1253-73. [PMID: 25882345 DOI: 10.1016/j.molp.2015.03.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 03/17/2015] [Accepted: 03/19/2015] [Indexed: 05/07/2023]
Abstract
Redox Responsive Transcription Factor1 (RRTF1) in Arabidopsis is rapidly and transiently upregulated by H2O2, as well as biotic- and abiotic-induced redox signals. RRTF1 is highly conserved in angiosperms, but its physiological role remains elusive. Here we show that inactivation of RRTF1 restricts and overexpression promotes reactive oxygen species (ROS) accumulation in response to stress. Transgenic lines overexpressing RRTF1 are impaired in root and shoot development, light sensitive, and susceptible to Alternaria brassicae infection. These symptoms are diminished by the beneficial root endophyte Piriformospora indica, which reduces ROS accumulation locally in roots and systemically in shoots, and by antioxidants and ROS inhibitors that scavenge ROS. More than 800 genes were detected in mature leaves and seedlings of transgenic lines overexpressing RRTF1; ∼ 40% of them have stress-, redox-, ROS-regulated-, ROS-scavenging-, defense-, cell death- and senescence-related functions. Bioinformatic analyses and in vitro DNA binding assays demonstrate that RRTF1 binds to GCC-box-like sequences in the promoter of RRTF1-responsive genes. Upregulation of RRTF1 by stress stimuli and H2O2 requires WRKY18/40/60. RRTF1 is co-regulated with the phylogenetically related RAP2.6, which contains a GCC-box-like sequence in its promoter, but transgenic lines overexpressing RAP2.6 do not accumulate higher ROS levels. RRTF1 also stimulates systemic ROS accumulation in distal non-stressed leaves. We conclude that the elevated levels of the highly conserved RRTF1 induce ROS accumulation in response to ROS and ROS-producing abiotic and biotic stress signals.
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Affiliation(s)
- Mitsuhiro Matsuo
- Institute of Plant Physiology, Friedrich-Schiller University Jena, Dornburger Straße 159, 07743 Jena, Germany; Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Joy Michal Johnson
- Institute of Plant Physiology, Friedrich-Schiller University Jena, Dornburger Straße 159, 07743 Jena, Germany
| | - Ayaka Hieno
- Faculty of Applied Biological Sciences, Gifu University, Yanagido 1-1, Gifu City 501-1193, Japan
| | - Mutsutomo Tokizawa
- Faculty of Applied Biological Sciences, Gifu University, Yanagido 1-1, Gifu City 501-1193, Japan
| | - Mika Nomoto
- Center for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Yasuomi Tada
- Center for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Rinesh Godfrey
- Institute of Molecular Cell Biology, Center for Molecular Biomedicine, Jena University Hospital, 00743 Jena, Germany; Molecular Cardiology, Department of Cardiovascular Medicine, University Hospital Münster, 48149 Münster, Germany
| | - Junichi Obokata
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Irena Sherameti
- Institute of Plant Physiology, Friedrich-Schiller University Jena, Dornburger Straße 159, 07743 Jena, Germany
| | - Yoshiharu Y Yamamoto
- Faculty of Applied Biological Sciences, Gifu University, Yanagido 1-1, Gifu City 501-1193, Japan
| | - Frank-D Böhmer
- Institute of Molecular Cell Biology, Center for Molecular Biomedicine, Jena University Hospital, 00743 Jena, Germany
| | - Ralf Oelmüller
- Institute of Plant Physiology, Friedrich-Schiller University Jena, Dornburger Straße 159, 07743 Jena, Germany.
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31
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Baldacci-Cresp F, Moussawi J, Leplé JC, Van Acker R, Kohler A, Candiracci J, Twyffels L, Spokevicius AV, Bossinger G, Laurans F, Brunel N, Vermeersch M, Boerjan W, El Jaziri M, Baucher M. PtaRHE1, a Populus tremula × Populus alba RING-H2 protein of the ATL family, has a regulatory role in secondary phloem fibre development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:978-990. [PMID: 25912812 DOI: 10.1111/tpj.12867] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 04/21/2015] [Accepted: 04/21/2015] [Indexed: 06/04/2023]
Abstract
REALLY INTERESTING NEW GENE (RING) proteins play important roles in the regulation of many processes by recognizing target proteins for ubiquitination. Previously, we have shown that the expression of PtaRHE1, encoding a Populus tremula × Populus alba RING-H2 protein with E3 ubiquitin ligase activity, is associated with tissues undergoing secondary growth. To further elucidate the role of PtaRHE1 in vascular tissues, we have undertaken a reverse genetic analysis in poplar. Within stem secondary vascular tissues, PtaRHE1 and its corresponding protein are expressed predominantly in the phloem. The downregulation of PtaRHE1 in poplar by artificial miRNA triggers alterations in phloem fibre patterning, characterized by an increased portion of secondary phloem fibres that have a reduced cell wall thickness and a change in lignin composition, with lower levels of syringyl units as compared with wild-type plants. Following an RNA-seq analysis, a biological network involving hormone stress signalling, as well as developmental processes, could be delineated. Several candidate genes possibly associated with the altered phloem fibre phenotype observed in amiRPtaRHE1 poplar were identified. Altogether, our data suggest a regulatory role for PtaRHE1 in secondary phloem fibre development.
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Affiliation(s)
- Fabien Baldacci-Cresp
- Laboratoire de Biotechnologie Végétale, Université Libre de Bruxelles (ULB), 6041, Gosselies, Belgium
| | - Jihad Moussawi
- Laboratoire de Biotechnologie Végétale, Université Libre de Bruxelles (ULB), 6041, Gosselies, Belgium
| | - Jean-Charles Leplé
- Unité de Recherche Amélioration Génétique et Physiologie Forestières (UR0588), Institut National de la Recherche Agronomique (INRA), 45075, Orléans Cedex 02, France
| | - Rebecca Van Acker
- Department of Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
| | - Annegret Kohler
- Unité Mixte de Recherche 1136, Interactions Arbres-Microorganismes, Laboratory of Excellence ARBRE, INRA, 54280, Champenoux, France
- Unité Mixte de Recherche 1136, Interactions Arbres-Microorganismes, Laboratory of Excellence ARBRE, Lorraine University, 54500, Vandoeuvre-lès-Nancy, France
| | - Julie Candiracci
- Laboratoire de Biotechnologie Végétale, Université Libre de Bruxelles (ULB), 6041, Gosselies, Belgium
| | - Laure Twyffels
- Center for Microscopy and Molecular Imaging-CMMI, Université Libre de Bruxelles (ULB), 6041, Gosselies, Belgium
| | - Antanas V Spokevicius
- School of Ecosystem and Forest Sciences, The University of Melbourne, Water Street, Creswick, Vic., 3363, Australia
| | - Gerd Bossinger
- School of Ecosystem and Forest Sciences, The University of Melbourne, Water Street, Creswick, Vic., 3363, Australia
| | - Françoise Laurans
- Unité de Recherche Amélioration Génétique et Physiologie Forestières (UR0588), Institut National de la Recherche Agronomique (INRA), 45075, Orléans Cedex 02, France
| | - Nicole Brunel
- UMR A547 PIAF, Clermont Université, Université Blaise Pascal, BP 10448, 63000, Clermont-Ferrand, France
- UMR A547 PIAF, INRA, 63100, Clermont-Ferrand, France
| | - Marjorie Vermeersch
- Center for Microscopy and Molecular Imaging-CMMI, Université Libre de Bruxelles (ULB), 6041, Gosselies, Belgium
- Laboratoire de Parasitologie Moléculaire, IBMM, Université Libre de Bruxelles (ULB), 6041, Gosselies, Belgium
| | - Wout Boerjan
- Department of Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
| | - Mondher El Jaziri
- Laboratoire de Biotechnologie Végétale, Université Libre de Bruxelles (ULB), 6041, Gosselies, Belgium
| | - Marie Baucher
- Laboratoire de Biotechnologie Végétale, Université Libre de Bruxelles (ULB), 6041, Gosselies, Belgium
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Dietz KJ. Efficient high light acclimation involves rapid processes at multiple mechanistic levels. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:2401-14. [PMID: 25573858 DOI: 10.1093/jxb/eru505] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Like no other chemical or physical parameter, the natural light environment of plants changes with high speed and jumps of enormous intensity. To cope with this variability, photosynthetic organisms have evolved sensing and response mechanisms that allow efficient acclimation. Most signals originate from the chloroplast itself. In addition to very fast photochemical regulation, intensive molecular communication is realized within the photosynthesizing cell, optimizing the acclimation process. Current research has opened up new perspectives on plausible but mostly unexpected complexity in signalling events, crosstalk, and process adjustments. Within seconds and minutes, redox states, levels of reactive oxygen species, metabolites, and hormones change and transmit information to the cytosol, modifying metabolic activity, gene expression, translation activity, and alternative splicing events. Signalling pathways on an intermediate time scale of several minutes to a few hours pave the way for long-term acclimation. Thereby, a new steady state of the transcriptome, proteome, and metabolism is realized within rather short time periods irrespective of the previous acclimation history to shade or sun conditions. This review provides a time line of events during six hours in the 'stressful' life of a plant.
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Affiliation(s)
- Karl-Josef Dietz
- Biochemistry and Physiology of Plants, Faculty of Biology, W5-134, Bielefeld University, University Street 25, 33501 Bielefeld, Germany
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Ethylene Response Factors Are Controlled by Multiple Harvesting Stresses in Hevea brasiliensis. PLoS One 2015; 10:e0123618. [PMID: 25906196 PMCID: PMC4408094 DOI: 10.1371/journal.pone.0123618] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 02/25/2015] [Indexed: 11/25/2022] Open
Abstract
Tolerance of recurrent mechanical wounding and exogenous ethylene is a feature of the rubber tree. Latex harvesting involves tapping of the tree bark and ethephon is applied to increase latex flow. Ethylene is an essential element in controlling latex production. The ethylene signalling pathway leads to the activation of Ethylene Response Factor (ERF) transcription factors. This family has been identified in Hevea brasiliensis. This study set out to understand the regulation of ERF genes during latex harvesting in relation to abiotic stress and hormonal treatments. Analyses of the relative transcript abundance were carried out for 35 HbERF genes in latex, in bark from mature trees and in leaves from juvenile plants under multiple abiotic stresses. Twenty-one HbERF genes were regulated by harvesting stress in laticifers, revealing an overrepresentation of genes in group IX. Transcripts of three HbERF-IX genes from HbERF-IXc4, HbERF-IXc5 and HbERF-IXc6 were dramatically accumulated by combining wounding, methyl jasmonate and ethylene treatments. When an ethylene inhibitor was used, the transcript accumulation for these three genes was halted, showing ethylene-dependent induction. Subcellular localization and transactivation experiments confirmed that several members of HbERF-IX are activator-type transcription factors. This study suggested that latex harvesting induces mechanisms developed for the response to abiotic stress. These mechanisms probably depend on various hormonal signalling pathways. Several members of HbERF-IX could be essential integrators of complex hormonal signalling pathways in Hevea.
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Campbell MT, Proctor CA, Dou Y, Schmitz AJ, Phansak P, Kruger GR, Zhang C, Walia H. Genetic and molecular characterization of submergence response identifies Subtol6 as a major submergence tolerance locus in maize. PLoS One 2015; 10:e0120385. [PMID: 25806518 PMCID: PMC4373911 DOI: 10.1371/journal.pone.0120385] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 01/21/2015] [Indexed: 11/22/2022] Open
Abstract
Maize is highly sensitive to short term flooding and submergence. Early season flooding reduces germination, survival and growth rate of maize seedlings. We aimed to discover genetic variation for submergence tolerance in maize and elucidate the genetic basis of submergence tolerance through transcriptional profiling and linkage analysis of contrasting genotypes. A diverse set of maize nested association mapping (NAM) founder lines were screened, and two highly tolerant (Mo18W and M162W) and sensitive (B97 and B73) genotypes were identified. Tolerant lines exhibited delayed senescence and lower oxidative stress levels compared to sensitive lines. Transcriptome analysis was performed on these inbreds to provide genome level insights into the molecular responses to submergence. Tolerant lines had higher transcript abundance of several fermentation-related genes and an unannotated Pyrophosphate-Dependent Fructose-6-Phosphate 1-Phosphotransferase gene during submergence. A coexpression network enriched for CBF (C-REPEAT/DRE BINDING FACTOR: C-REPEAT/DRE BINDING FACTOR) genes, was induced by submergence in all four inbreds, but was more activated in the tolerant Mo18W. A recombinant inbred line (RIL) population derived from Mo18W and B73 was screened for submergence tolerance. A major QTL named Subtol6 was mapped to chromosome 6 that explains 22% of the phenotypic variation within the RIL population. We identified two candidate genes (HEMOGLOBIN2 and RAV1) underlying Subtol6 based on contrasting expression patterns observed in B73 and Mo18W. Sources of tolerance identified in this study (Subtol6) can be useful to increase survival rate during flooding events that are predicted to increase in frequency with climate change.
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Affiliation(s)
- Malachy T. Campbell
- University of Nebraska-Lincoln, Department of Agronomy and Horticulture, Lincoln, Nebraska, United States of America
| | - Christopher A. Proctor
- University of Nebraska-Lincoln, Department of Agronomy and Horticulture, Lincoln, Nebraska, United States of America
| | - Yongchao Dou
- University of Nebraska-Lincoln, School of Biological Sciences, Lincoln, Nebraska, United States of America
| | - Aaron J. Schmitz
- University of Nebraska-Lincoln, Department of Agronomy and Horticulture, Lincoln, Nebraska, United States of America
| | - Piyaporn Phansak
- University of Nebraska-Lincoln, Department of Agronomy and Horticulture, Lincoln, Nebraska, United States of America
- Nakhon Phanom University, Muang District, Thailand
| | - Greg R. Kruger
- University of Nebraska-Lincoln, Department of Agronomy and Horticulture, Lincoln, Nebraska, United States of America
| | - Chi Zhang
- University of Nebraska-Lincoln, School of Biological Sciences, Lincoln, Nebraska, United States of America
| | - Harkamal Walia
- University of Nebraska-Lincoln, Department of Agronomy and Horticulture, Lincoln, Nebraska, United States of America
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Benina M, Ribeiro DM, Gechev TS, Mueller-Roeber B, Schippers JHM. A cell type-specific view on the translation of mRNAs from ROS-responsive genes upon paraquat treatment of Arabidopsis thaliana leaves. PLANT, CELL & ENVIRONMENT 2015; 38:349-63. [PMID: 24738758 DOI: 10.1111/pce.12355] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 03/21/2014] [Accepted: 03/24/2014] [Indexed: 05/10/2023]
Abstract
Oxidative stress causes dramatic changes in the expression levels of many genes. The formation of a functional protein through successful mRNA translation is central to a coordinated cellular response. To what extent the response towards reactive oxygen species (ROS) is regulated at the translational level is poorly understood. Here we analysed leaf- and tissue-specific translatomes using a set of transgenic Arabidopsis thaliana lines expressing a FLAG-tagged ribosomal protein to immunopurify polysome-bound mRNAs before and after oxidative stress. We determined transcript levels of 171 ROS-responsive genes upon paraquat treatment, which causes formation of superoxide radicals, at the whole-organ level. Furthermore, the translation of mRNAs was determined for five cell types: mesophyll, bundle sheath, phloem companion, epidermal and guard cells. Mesophyll and bundle sheath cells showed the strongest response to paraquat treatment. Interestingly, several ROS-responsive transcription factors displayed cell type-specific translation patterns, while others were translated in all cell types. In part, cell type-specific translation could be explained by the length of the 5'-untranslated region (5'-UTR) and the presence of upstream open reading frames (uORFs). Our analysis reveals insights into the translational regulation of ROS-responsive genes, which is important to understanding cell-specific responses and functions during oxidative stress.
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Affiliation(s)
- Maria Benina
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 4000, Plovdiv, Bulgaria; Institute of Molecular Biology and Biotechnology, 4000, Plovdiv, Bulgaria
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Mata-Pérez C, Sánchez-Calvo B, Begara-Morales JC, Luque F, Jiménez-Ruiz J, Padilla MN, Fierro-Risco J, Valderrama R, Fernández-Ocaña A, Corpas FJ, Barroso JB. Transcriptomic profiling of linolenic acid-responsive genes in ROS signaling from RNA-seq data in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2015; 6:122. [PMID: 25852698 PMCID: PMC4362301 DOI: 10.3389/fpls.2015.00122] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 02/14/2015] [Indexed: 05/20/2023]
Abstract
Linolenic acid (Ln) released from chloroplast membrane galactolipids is a precursor of the phytohormone jasmonic acid (JA). The involvement of this hormone in different plant biological processes, such as responses to biotic stress conditions, has been extensively studied. However, the role of Ln in the regulation of gene expression during abiotic stress situations mediated by cellular redox changes and/or by oxidative stress processes remains poorly understood. An RNA-seq approach has increased our knowledge of the interplay among Ln, oxidative stress and ROS signaling that mediates abiotic stress conditions. Transcriptome analysis with the aid of RNA-seq in the absence of oxidative stress revealed that the incubation of Arabidopsis thaliana cell suspension cultures (ACSC) with Ln resulted in the modulation of 7525 genes, of which 3034 genes had a 2-fold-change, being 533 up- and 2501 down-regulated genes, respectively. Thus, RNA-seq data analysis showed that an important set of these genes were associated with the jasmonic acid biosynthetic pathway including lypoxygenases (LOXs) and Allene oxide cyclases (AOCs). In addition, several transcription factor families involved in the response to biotic stress conditions (pathogen attacks or herbivore feeding), such as WRKY, JAZ, MYC, and LRR were also modified in response to Ln. However, this study also shows that Ln has the capacity to modulate the expression of genes involved in the response to abiotic stress conditions, particularly those mediated by ROS signaling. In this regard, we were able to identify new targets such as galactinol synthase 1 (GOLS1), methionine sulfoxide reductase (MSR) and alkenal reductase in ACSC. It is therefore possible to suggest that, in the absence of any oxidative stress, Ln is capable of modulating new sets of genes involved in the signaling mechanism mediated by additional abiotic stresses (salinity, UV and high light intensity) and especially in stresses mediated by ROS.
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Affiliation(s)
- Capilla Mata-Pérez
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Area of Biochemistry and Molecular Biology, University of JaénJaén, Spain
| | - Beatriz Sánchez-Calvo
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Area of Biochemistry and Molecular Biology, University of JaénJaén, Spain
| | - Juan C. Begara-Morales
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Area of Biochemistry and Molecular Biology, University of JaénJaén, Spain
| | - Francisco Luque
- Department of Experimental Biology, Center for Advanced Studies in Olive Grove and Olive Oils, University of JaénJaén, Spain
| | - Jaime Jiménez-Ruiz
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Area of Biochemistry and Molecular Biology, University of JaénJaén, Spain
| | - María N. Padilla
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Area of Biochemistry and Molecular Biology, University of JaénJaén, Spain
| | - Jesús Fierro-Risco
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Area of Biochemistry and Molecular Biology, University of JaénJaén, Spain
| | - Raquel Valderrama
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Area of Biochemistry and Molecular Biology, University of JaénJaén, Spain
| | - Ana Fernández-Ocaña
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Area of Biochemistry and Molecular Biology, University of JaénJaén, Spain
| | - Francisco J. Corpas
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Biochemistry, Cellular and Molecular Biology of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranada, Spain
| | - Juan B. Barroso
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Area of Biochemistry and Molecular Biology, University of JaénJaén, Spain
- Department of Experimental Biology, Center for Advanced Studies in Olive Grove and Olive Oils, University of JaénJaén, Spain
- *Correspondence: Juan B. Barroso, Department of Experimental Biology, Area of Biochemistry and Molecular Biology, University of Jaén, Campus Las Lagunillas s/n, Jaén 23071, Spain e-mail:
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Matsuo M, Oelmüller R. REDOX RESPONSIVE TRANSCRIPTION FACTOR1 is involved in age-dependent and systemic stress signaling. PLANT SIGNALING & BEHAVIOR 2015; 10:e1051279. [PMID: 26479402 PMCID: PMC4883954 DOI: 10.1080/15592324.2015.1051279] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
REDOX RESPONSIVE TRANSCRIPTION FACTOR1 (RRTF1) regulates redox homeostasis under stress, however the mechanism is mainly unknown. In a recent publication, we analyzed rrtf1 knockout (ko) and RRTF1 overexpressor lines of Arabidopsis thaliana and showed that RRTF1 plays a crucial role in reactive oxygen species (ROS) production. Ko line produces less and overexpressor lines constitutively high levels of ROS under stress, and the amount of ROS increases with increase in stress and the RRTF1 level in the plant. The transcription factor also activates systemic ROS signaling under stress. (1) In this report, we show that RRTF1 exerts different roles in young and old leaves. While RRTF1 enhances defense responses to high light (HL) stress in young leaves, it induces senescence and chlorosis in older leaves. These findings suggest that RRTF1 and/or RRTF1-mediated ROS signaling induce stress responses in an age-dependent manner, and the age-dependent alteration in the RRTF1 function might be important for plants' acclimation to the stress environment.
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Affiliation(s)
- Mitsuhiro Matsuo
- Graduate School of Life and Environmental Sciences; Kyoto Prefectural University; Shimogamo, Sakyo-ku, Kyoto, Japan
| | - Ralf Oelmüller
- Institute of Plant Physiology; Friedrich-Schiller University Jena; Jena, Germany
- Correspondence to: Ralf Oelmüller;
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Arabidopsis ERF109 mediates cross-talk between jasmonic acid and auxin biosynthesis during lateral root formation. Nat Commun 2014; 5:5833. [PMID: 25524530 DOI: 10.1038/ncomms6833] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 11/12/2014] [Indexed: 11/08/2022] Open
Abstract
Jasmonic acid (JA) is well known to promote lateral root formation but the mechanisms by which JA signalling is integrated into the pathways responsible for lateral root formation, and how it interacts with auxin in this process remains poorly understood. Here, we report that the highly JA-responsive ethylene response factor 109 (ERF109) mediates cross-talk between JA signalling and auxin biosynthesis to regulate lateral root formation in Arabidopsis. erf109 mutants have fewer lateral roots under MeJA treatments compared with wild type whereas ERF109 overexpression causes a root phenotype that resembles those of auxin overproduction mutants. ERF109 binds directly to GCC-boxes in the promoters of ASA1 and YUC2, which encode two key enzymes in auxin biosynthesis. Thus, our study reveals a molecular mechanism for JA and auxin cross-talk during JA-induced lateral root formation.
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Cui H, Kong D, Wei P, Hao Y, Torii KU, Lee JS, Li J. SPINDLY, ERECTA, and its ligand STOMAGEN have a role in redox-mediated cortex proliferation in the Arabidopsis root. MOLECULAR PLANT 2014; 7:1727-39. [PMID: 25267734 PMCID: PMC4261839 DOI: 10.1093/mp/ssu106] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Reactive oxygen species (ROS) are harmful to all living organisms and therefore they must be removed to ensure normal growth and development. ROS are also signaling molecules, but so far little is known about the mechanisms of ROS perception and developmental response in plants. We here report that hydrogen peroxide induces cortex proliferation in the Arabidopsis root and that SPINDLY (SPY), an O-linked glucosamine acetyltransferase, regulates cortex proliferation by maintaining cellular redox homeostasis. We also found that mutation in the leucine-rich receptor kinase ERECTA and its putative peptide ligand STOMAGEN block the effect of hydrogen peroxide on root cortex proliferation. However, ERECTA and STOMAGEN are expressed in the vascular tissue, whereas extra cortex cells are produced from the endodermis, suggesting the involvement of intercellular signaling. SPY appears to act downstream of ERECTA, because the spy mutation still caused cortex proliferation in the erecta mutant background. We therefore have not only gained insight into the mechanism by which SPY regulates root development but also uncovered a novel pathway for ROS signaling in plants. The importance of redox-mediated cortex proliferation as a protective mechanism against oxidative stress is also discussed.
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Affiliation(s)
- Hongchang Cui
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA
| | - Danyu Kong
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA
| | - Pengcheng Wei
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA Present address: Biotechnical Group, Institute of Rice Research, Anhui Agricultural Academy of Science, 40#, Nongke South Road, Hefei, Anhui, 230031, China
| | - Yueling Hao
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA
| | - Keiko U Torii
- Howard Hughes Medical Institute, Department of Biology, University of Washington, Seattle, WA 98195-1800, USA
| | - Jin Suk Lee
- Howard Hughes Medical Institute, Department of Biology, University of Washington, Seattle, WA 98195-1800, USA
| | - Jie Li
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA
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Li Y, Xu J, Haq NU, Zhang H, Zhu XG. Was low CO2 a driving force of C4 evolution: Arabidopsis responses to long-term low CO2 stress. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:3657-67. [PMID: 24855683 PMCID: PMC4085967 DOI: 10.1093/jxb/eru193] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The responses of long-term growth of plants under elevated CO2 have been studied extensively. Comparatively, the responses of plants to subambient CO2 concentrations have not been well studied. This study aims to investigate the responses of the model C3 plant, Arabidopsis thaliana, to low CO2 at the molecular level. Results showed that low CO2 dramatically decreased biomass productivity, together with delayed flowering and increased stomatal density. Furthermore, alteration of thylakoid stacking in both bundle sheath and mesophyll cells, upregulation of PEPC and PEPC-K together with altered expression of a number of regulators known involved in photosynthesis development were observed. These responses to low CO2 are discussed with regard to the fitness of C3 plants under low CO2. This work also briefly discusses the relevance of the data to C4 photosynthesis evolution.
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Affiliation(s)
- Yuanyuan Li
- State Key Laboratory of Hybrid Rice Research, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China Key Laboratory of Computational Biology and Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jiajia Xu
- State Key Laboratory of Hybrid Rice Research, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China Key Laboratory of Computational Biology and Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Noor Ul Haq
- Key Laboratory of Computational Biology and Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hui Zhang
- Key Laboratory of Computational Biology and Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai 200031, China Shandong Normal University, Jinan, Shandong 250014, China
| | - Xin-Guang Zhu
- State Key Laboratory of Hybrid Rice Research, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China Key Laboratory of Computational Biology and Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai 200031, China
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41
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Sequence and expression analyses of ethylene response factors highly expressed in latex cells from Hevea brasiliensis. PLoS One 2014; 9:e99367. [PMID: 24971876 PMCID: PMC4074046 DOI: 10.1371/journal.pone.0099367] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 05/05/2014] [Indexed: 11/21/2022] Open
Abstract
The AP2/ERF superfamily encodes transcription factors that play a key role in plant development and responses to abiotic and biotic stress. In Hevea brasiliensis, ERF genes have been identified by RNA sequencing. This study set out to validate the number of HbERF genes, and identify ERF genes involved in the regulation of latex cell metabolism. A comprehensive Hevea transcriptome was improved using additional RNA reads from reproductive tissues. Newly assembled contigs were annotated in the Gene Ontology database and were assigned to 3 main categories. The AP2/ERF superfamily is the third most represented compared with other transcription factor families. A comparison with genomic scaffolds led to an estimation of 114 AP2/ERF genes and 1 soloist in Hevea brasiliensis. Based on a phylogenetic analysis, functions were predicted for 26 HbERF genes. A relative transcript abundance analysis was performed by real-time RT-PCR in various tissues. Transcripts of ERFs from group I and VIII were very abundant in all tissues while those of group VII were highly accumulated in latex cells. Seven of the thirty-five ERF expression marker genes were highly expressed in latex. Subcellular localization and transactivation analyses suggested that HbERF-VII candidate genes encoded functional transcription factors.
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42
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Petrillo E, Godoy Herz MA, Fuchs A, Reifer D, Fuller J, Yanovsky MJ, Simpson C, Brown JWS, Barta A, Kalyna M, Kornblihtt AR. A chloroplast retrograde signal regulates nuclear alternative splicing. Science 2014; 344:427-30. [PMID: 24763593 DOI: 10.1126/science.1250322] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Light is a source of energy and also a regulator of plant physiological adaptations. We show here that light/dark conditions affect alternative splicing of a subset of Arabidopsis genes preferentially encoding proteins involved in RNA processing. The effect requires functional chloroplasts and is also observed in roots when the communication with the photosynthetic tissues is not interrupted, suggesting that a signaling molecule travels through the plant. Using photosynthetic electron transfer inhibitors with different mechanisms of action, we deduce that the reduced pool of plastoquinones initiates a chloroplast retrograde signaling that regulates nuclear alternative splicing and is necessary for proper plant responses to varying light conditions.
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Affiliation(s)
- Ezequiel Petrillo
- Laboratorio de Fisiología y Biología Molecular, Departamento de Fisiología, Biología Molecular y Celular, IFIBYNE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
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43
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Foyer CH, Karpinska B, Krupinska K. The functions of WHIRLY1 and REDOX-RESPONSIVE TRANSCRIPTION FACTOR 1 in cross tolerance responses in plants: a hypothesis. Philos Trans R Soc Lond B Biol Sci 2014; 369:20130226. [PMID: 24591713 DOI: 10.1098/rstb.2013.0226] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Chloroplasts are important sensors of environment change, fulfilling key roles in the regulation of plant growth and development in relation to environmental cues. Photosynthesis produces a repertoire of reductive and oxidative (redox) signals that provide information to the nucleus facilitating appropriate acclimation to a changing light environment. Redox signals are also recognized by the cellular innate immune system allowing activation of non-specific, stress-responsive pathways that underpin cross tolerance to biotic-abiotic stresses. While these pathways have been intensively studied in recent years, little is known about the different components that mediate chloroplast-to-nucleus signalling and facilitate cross tolerance phenomena. Here, we consider the properties of the WHIRLY family of proteins and the REDOX-RESPONSIVE TRANSCRIPTION FACTOR 1 (RRTF1) in relation to chloroplast redox signals that facilitate the synergistic co-activation of gene expression pathways and confer cross tolerance to abiotic and biotic stresses. We propose a new hypothesis for the role of WHIRLY1 as a redox sensor in chloroplast-to-nucleus retrograde signalling leading to cross tolerance, including acclimation and immunity responses. By virtue of its association with chloroplast nucleoids and with nuclear DNA, WHIRLY1 is an attractive candidate coordinator of the expression of photosynthetic genes in the nucleus and chloroplasts. We propose that the redox state of the photosynthetic electron transport chain triggers the movement of WHIRLY1 from the chloroplasts to the nucleus, and draw parallels with the regulation of NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1).
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Affiliation(s)
- Christine H Foyer
- Centre for Plant Sciences, Faculty of Biology, University of Leeds, , Leeds LS2 9JT, UK
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44
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Vogel MO, Moore M, König K, Pecher P, Alsharafa K, Lee J, Dietz KJ. Fast retrograde signaling in response to high light involves metabolite export, MITOGEN-ACTIVATED PROTEIN KINASE6, and AP2/ERF transcription factors in Arabidopsis. THE PLANT CELL 2014; 26:1151-65. [PMID: 24668746 PMCID: PMC4001375 DOI: 10.1105/tpc.113.121061] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 01/31/2014] [Accepted: 02/28/2014] [Indexed: 05/18/2023]
Abstract
Regulation of the expression of nuclear genes encoding chloroplast proteins allows for metabolic adjustment in response to changing environmental conditions. This regulation is linked to retrograde signals that transmit information on the metabolic state of the chloroplast to the nucleus. Transcripts of several APETALA2/ETHYLENE RESPONSE FACTOR transcription factors (AP2/ERF-TFs) were found to respond within 10 min after transfer of low-light-acclimated Arabidopsis thaliana plants to high light. Initiation of this transcriptional response was completed within 1 min after transfer to high light. The fast responses of four AP2/ERF genes, ERF6, RRTF1, ERF104, and ERF105, were entirely deregulated in triose phosphate/phosphate translocator (tpt) mutants. Similarly, activation of MITOGEN-ACTIVATED PROTEIN KINASE6 (MPK6) was upregulated after 1 min in the wild type but not in the tpt mutant. Based on this, together with altered transcript regulation in mpk6 and erf6 mutants, a retrograde signal transmission model is proposed starting with metabolite export through the triose phosphate/phosphate translocator with subsequent MPK6 activation leading to initiation of AP2/ERF-TF gene expression and other downstream gene targets. The results show that operational retrograde signaling in response to high light involves a metabolite-linked pathway in addition to previously described redox and hormonal pathways.
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Affiliation(s)
- Marc Oliver Vogel
- Biochemistry and Physiology of Plants, Bielefeld University, 33501 Bielefeld, Germany
| | - Marten Moore
- Biochemistry and Physiology of Plants, Bielefeld University, 33501 Bielefeld, Germany
| | - Katharina König
- Biochemistry and Physiology of Plants, Bielefeld University, 33501 Bielefeld, Germany
| | - Pascal Pecher
- Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany
| | - Khalid Alsharafa
- Biochemistry and Physiology of Plants, Bielefeld University, 33501 Bielefeld, Germany
| | - Justin Lee
- Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany
| | - Karl-Josef Dietz
- Biochemistry and Physiology of Plants, Bielefeld University, 33501 Bielefeld, Germany
- Address correspondence to
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Sewelam N, Kazan K, Thomas-Hall SR, Kidd BN, Manners JM, Schenk PM. Ethylene response factor 6 is a regulator of reactive oxygen species signaling in Arabidopsis. PLoS One 2013; 8:e70289. [PMID: 23940555 PMCID: PMC3734174 DOI: 10.1371/journal.pone.0070289] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 06/18/2013] [Indexed: 11/18/2022] Open
Abstract
Reactive oxygen species (ROS) are produced in plant cells in response to diverse biotic and abiotic stresses as well as during normal growth and development. Although a large number of transcription factor (TF) genes are up- or down-regulated by ROS, currently very little is known about the functions of these TFs during oxidative stress. In this work, we examined the role of ERF6 (ETHYLENE RESPONSE FACTOR6), an AP2/ERF domain-containing TF, during oxidative stress responses in Arabidopsis. Mutant analyses showed that NADPH oxidase (RbohD) and calcium signaling are required for ROS-responsive expression of ERF6. erf6 insertion mutant plants showed reduced growth and increased H2O2 and anthocyanin levels. Expression analyses of selected ROS-responsive genes during oxidative stress identified several differentially expressed genes in the erf6 mutant. In particular, a number of ROS responsive genes, such as ZAT12, HSFs, WRKYs, MAPKs, RBOHs, DHAR1, APX4, and CAT1 were more strongly induced by H2O2 in erf6 plants than in wild-type. In contrast, MDAR3, CAT3, VTC2 and EX1 showed reduced expression levels in the erf6 mutant. Taken together, our results indicate that ERF6 plays an important role as a positive antioxidant regulator during plant growth and in response to biotic and abiotic stresses.
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Affiliation(s)
- Nasser Sewelam
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Kemal Kazan
- Commonwealth Scientific and Industrial Research Organization Plant Industry, Queensland Bioscience Precinct, Brisbane, Queensland, Australia
| | - Skye R. Thomas-Hall
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Brendan N. Kidd
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland, Australia
- Commonwealth Scientific and Industrial Research Organization Plant Industry, Queensland Bioscience Precinct, Brisbane, Queensland, Australia
| | - John M. Manners
- Commonwealth Scientific and Industrial Research Organization Plant Industry, Queensland Bioscience Precinct, Brisbane, Queensland, Australia
| | - Peer M. Schenk
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland, Australia
- * E-mail:
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Schön M, Töller A, Diezel C, Roth C, Westphal L, Wiermer M, Somssich IE. Analyses of wrky18 wrky40 plants reveal critical roles of SA/EDS1 signaling and indole-glucosinolate biosynthesis for Golovinomyces orontii resistance and a loss-of resistance towards Pseudomonas syringae pv. tomato AvrRPS4. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2013; 26:758-67. [PMID: 23617415 DOI: 10.1094/mpmi-11-12-0265-r] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Simultaneous mutation of two WRKY-type transcription factors, WRKY18 and WRKY40, renders otherwise susceptible wild-type Arabidopsis plants resistant towards the biotrophic powdery mildew fungus Golovinomyces orontii. Resistance in wrky18 wrky40 double mutant plants is accompanied by massive transcriptional reprogramming, imbalance in salicylic acid (SA) and jasmonic acid (JA) signaling, altered ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1) expression, and accumulation of the phytoalexin camalexin. Genetic analyses identified SA biosynthesis and EDS1 signaling as well as biosynthesis of the indole-glucosinolate 4MI3G as essential components required for loss-of-WRKY18 WRKY40-mediated resistance towards G. orontii. The analysis of wrky18 wrky40 pad3 mutant plants impaired in camalexin biosynthesis revealed an uncoupling of pre- from postinvasive resistance against G. orontii. Comprehensive infection studies demonstrated the specificity of wrky18 wrky40-mediated G. orontii resistance. Interestingly, WRKY18 and WRKY40 act as positive regulators in effector-triggered immunity, as the wrky18 wrky40 double mutant was found to be strongly susceptible towards the bacterial pathogen Pseudomonas syringae DC3000 expressing the effector AvrRPS4 but not against other tested Pseudomonas strains. We hypothesize that G. orontii depends on the function of WRKY18 and WRKY40 to successfully infect Arabidopsis wild-type plants while, in the interaction with P. syringae AvrRPS4, they are required to mediate effector-triggered immunity.
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Affiliation(s)
- Moritz Schön
- Department of Plant Microbe Interaction, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
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Kerchev PI, Karpińska B, Morris JA, Hussain A, Verrall SR, Hedley PE, Fenton B, Foyer CH, Hancock RD. Vitamin C and the abscisic acid-insensitive 4 transcription factor are important determinants of aphid resistance in Arabidopsis. Antioxid Redox Signal 2013; 18:2091-105. [PMID: 23343093 DOI: 10.1089/ars.2012.5097] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
AIMS Aphids, like other insects, are probably unable to synthesize vitamin C (ascorbic acid), which is therefore an essential dietary nutrient that has to be obtained from the host plant. Plant responses to aphids involve hormones such as salicylic acid (SA), jasmonic acid (JA), and abscisic acid (ABA), but hormone/redox interactions remain poorly characterized. We therefore investigated hormone/redox signaling in the response of Arabidopsis thaliana to infestation by the aphid Myzus persicae, focusing on the interactions between ascorbic acid and ABA, together with the influence of altered ascorbate and ABA signaling on the SA- and JA-dependent pathways. RESULTS Whole-genome microarray analysis revealed highly dynamic transcriptional responses to aphid infestation with extensive differences between transcript profiles of infested and systemic leaves, revealing aphid-dependent effects on the suites of transcripts involved in the redox, SA, and ABA responses. Central roles for ascorbate, ABA-insensitive 4 (ABI4), and oxidative signal-inducible 1 in plant resistance to aphids were demonstrated by altered fecundity on respective mutants. However, ABA had a negative effect on aphid resistance, as did ABI4 or redox-responsive transcription factor 1. The decrease in aphid fecundity observed in mutants defective in ascorbate accumulation (vtc2) was absent from abi4vtc2 double mutants that are also deficient in ABA signaling (abi4). Aphid-dependent transcriptome responses reveal a role for ascorbate-regulated receptor-like kinases in plant defenses against aphids. INNOVATION Vitamin C deficiency enhances plant resistance to aphids through redox signaling pathways rather than dietary requirements. CONCLUSION ABI4 is a linchpin of redox regulation of the innate immune response to aphids.
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Affiliation(s)
- Pavel I Kerchev
- Faculty of Biology, Centre for Plant Sciences, University of Leeds, Leeds, United Kingdom
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48
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Iyer NJ, Tang Y, Mahalingam R. Physiological, biochemical and molecular responses to a combination of drought and ozone in Medicago truncatula. PLANT, CELL & ENVIRONMENT 2013; 36:706-20. [PMID: 22946485 DOI: 10.1111/pce.12008] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Drought and tropospheric ozone are escalating climate change problems that can co-occur. In this study, we observed Medicago truncatula cultivar Jemalong that is sensitive to ozone and drought stress when applied singly, showed tolerance when subjected to a combined application of these stresses. Lowered stomatal conductance may be a vital tolerance mechanism to overcome combined ozone and drought. Sustained increases in both reduced ascorbate and glutathione in response to combined stress may play a role in lowering reactive oxygen species and nitric oxide toxicity. Transcriptome analysis indicated that genes associated with glucan metabolism, responses to temperature and light signalling may play a role in dampening ozone responses due to drought-induced stomatal closure during combined occurrence of these two stresses. Gene ontologies for jasmonic acid signalling and innate immunity were enriched among the 300 differentially expressed genes unique to combined stress. Differential expression of transcription factors associated with redox, defence signalling, jasmonate responses and chromatin modifications may be important for evoking novel gene networks during combined occurrence of drought and ozone. The alterations in redox milieu and distinct transcriptome changes in response to combined stress could aid in tweaking the metabolome and proteome to annul the detrimental effects of ozone and drought in Jemalong.
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Affiliation(s)
- Niranjani J Iyer
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, USA
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49
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Piyatrakul P, Putranto RA, Martin F, Rio M, Dessailly F, Leclercq J, Dufayard JF, Lardet L, Montoro P. Some ethylene biosynthesis and AP2/ERF genes reveal a specific pattern of expression during somatic embryogenesis in Hevea brasiliensis. BMC PLANT BIOLOGY 2012; 12:244. [PMID: 23268714 PMCID: PMC3561283 DOI: 10.1186/1471-2229-12-244] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 11/30/2012] [Indexed: 05/05/2023]
Abstract
BACKGROUND Ethylene production and signalling play an important role in somatic embryogenesis, especially for species that are recalcitrant in in vitro culture. The AP2/ERF superfamily has been identified and classified in Hevea brasiliensis. This superfamily includes the ERFs involved in response to ethylene. The relative transcript abundance of ethylene biosynthesis genes and of AP2/ERF genes was analysed during somatic embryogenesis for callus lines with different regeneration potential, in order to identify genes regulated during that process. RESULTS The analysis of relative transcript abundance was carried out by real-time RT-PCR for 142 genes. The transcripts of ERFs from group I, VII and VIII were abundant at all stages of the somatic embryogenesis process. Forty genetic expression markers for callus regeneration capacity were identified. Fourteen markers were found for proliferating calli and 35 markers for calli at the end of the embryogenesis induction phase. Sixteen markers discriminated between normal and abnormal embryos and, lastly, there were 36 markers of conversion into plantlets. A phylogenetic analysis comparing the sequences of the AP2 domains of Hevea and Arabidopsis genes enabled us to predict the function of 13 expression marker genes. CONCLUSIONS This first characterization of the AP2/ERF superfamily in Hevea revealed dramatic regulation of the expression of AP2/ERF genes during the somatic embryogenesis process. The gene expression markers of proliferating callus capacity to regenerate plants by somatic embryogenesis should make it possible to predict callus lines suitable to be used for multiplication. Further functional characterization of these markers opens up prospects for discovering specific AP2/ERF functions in the Hevea species for which somatic embryogenesis is difficult.
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Affiliation(s)
- Piyanuch Piyatrakul
- CIRAD, UMR AGAP, F-34398, Montpellier, France
- Rubber Research Institute, Chatuchak, Bangkok, 10900, Thailand
| | - Riza-Arief Putranto
- CIRAD, UMR AGAP, F-34398, Montpellier, France
- Indonesian Biotechnology Research Institute for Estate Crops, Bogor, Indonesia
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50
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Tripathy BC, Oelmüller R. Reactive oxygen species generation and signaling in plants. PLANT SIGNALING & BEHAVIOR 2012; 7:1621-33. [PMID: 23072988 PMCID: PMC3578903 DOI: 10.4161/psb.22455] [Citation(s) in RCA: 318] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The introduction of molecular oxygen into the atmosphere was accompanied by the generation of reactive oxygen species (ROS) as side products of many biochemical reactions. ROS are permanently generated in plastids, peroxisomes, mitochiondria, the cytosol and the apoplast. Imbalance between ROS generation and safe detoxification generates oxidative stress and the accumulating ROS are harmful for the plants. On the other hand, specific ROS function as signaling molecules and activate signal transduction processes in response to various stresses. Here, we summarize the generation of ROS in the different cellular compartments and the signaling processes which are induced by ROS.
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