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Proteins Adsorbed during Intraoperative Hemoadsorption and Their In Vitro Effects on Endothelium. Healthcare (Basel) 2023; 11:healthcare11030310. [PMID: 36766885 PMCID: PMC9914797 DOI: 10.3390/healthcare11030310] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/21/2023] Open
Abstract
(1) Background: Hemoadsorption is a method of blood purification with a wide spectrum of indications. Pre-emptive use of hemoadsorption in patients undergoing heart surgery with cardiopulmonary bypass is considered to reduce the risk of postoperative systemic inflammatory response syndrome. The current study aimed to identify the spectrum of blood proteins adsorbed on the polymer matrix of the CytoSorb hemoadsorption system and to investigate their influence on cultured endothelial cells in vitro. (2) Methods: Adsorbers used for intraoperative hemoadsorption were obtained from patients undergoing on-pump valve surgery in acute endocarditis. Proteins were extracted from the adsorbers, purified, identified with mass-spectrometry and applied to cultured human aortic endothelial cells. (3) Results: A broad range of blood proteins were identified in the material eluted from the CytoSorb adsorber. When added to cultured ECs, these protein extracts caused severe reduction in cell viability and migration. After 24 h exposure, transcriptional changes with up-regulation of multiple metabolic regulators were observed and verified on the protein level. Genes responsible for control of mitosis were significantly down-regulated. (4) Conclusions: In summary, our data reveal that intraoperative hemoadsorption allows broad spectrum removal of a wide range of molecules eliciting endothelial damage.
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Dominguez PG, Conti G, Duffy T, Insani M, Alseekh S, Asurmendi S, Fernie AR, Carrari F. Multiomics analyses reveal the roles of the ASR1 transcription factor in tomato fruits. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6490-6509. [PMID: 34100923 DOI: 10.1093/jxb/erab269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 06/05/2021] [Indexed: 06/12/2023]
Abstract
The transcription factor ASR1 (ABA, STRESS, RIPENING 1) plays multiple roles in plant responses to abiotic stresses as well as being involved in the regulation of central metabolism in several plant species. However, despite the high expression of ASR1 in tomato fruits, large scale analyses to uncover its function in fruits are still lacking. In order to study its function in the context of fruit ripening, we performed a multiomics analysis of ASR1-antisense transgenic tomato fruits at the transcriptome and metabolome levels. Our results indicate that ASR1 is involved in several pathways implicated in the fruit ripening process, including cell wall, amino acid, and carotenoid metabolism, as well as abiotic stress pathways. Moreover, we found that ASR1-antisense fruits are more susceptible to the infection by the necrotrophic fungus Botrytis cinerea. Given that ASR1 could be regulated by fruit ripening regulators such as FRUITFULL1/FRUITFULL2 (FUL1/FUL2), NON-RIPENING (NOR), and COLORLESS NON-RIPENING (CNR), we positioned it in the regulatory cascade of red ripe tomato fruits. These data extend the known range of functions of ASR1 as an important auxiliary regulator of tomato fruit ripening.
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Affiliation(s)
- Pia Guadalupe Dominguez
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
| | - Gabriela Conti
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
- Facultad de Agronomía. Cátedra de Genética. Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Tomás Duffy
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
| | - Marina Insani
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Sebastián Asurmendi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Fernando Carrari
- Facultad de Agronomía. Cátedra de Genética. Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
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Loreti E, Betti F, Ladera-Carmona MJ, Fontana F, Novi G, Valeri MC, Perata P. ARGONAUTE1 and ARGONAUTE4 Regulate Gene Expression and Hypoxia Tolerance. PLANT PHYSIOLOGY 2020; 182:287-300. [PMID: 31358683 PMCID: PMC6945874 DOI: 10.1104/pp.19.00741] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 07/23/2019] [Indexed: 05/05/2023]
Abstract
In plants, hypoxia can be induced by submergence, and the lack of oxygen impairs mitochondrial respiration, thus affecting the plant's energy status. Hypoxia has major effects on gene expression; these changes induce key responses that help meet the needs of the stressed plant. However, little is known about the possible role of RNA signaling in the regulation of gene expression under limited oxygen availability. Here, we report the contribution of ARGONAUTE1 (AGO1) to hypoxia-induced gene regulation in Arabidopsis (Arabidopsis thaliana). Submergence induced changes in levels of the microRNAs miR2936 and miR398, but this had no obvious effects on their putative target mRNA levels. However, we found that ago1-27 plants are intolerant to submergence and transcriptome analysis identified genes whose regulation requires functional AGO1. Analysis of mutants affected in various branches of RNA signaling highlighted the convergence of AGO1 signaling with the AGO4-dependent RNA-directed DNA methylation (RdDM) pathway. AGO4-dependent RdDM represses the expression of HOMOLOG OF RPW8 4 (HR4) and alters its response to submergence. Remarkably, methylation of the second exon of HR4 is not only reduced in ago4-1 but also in plants overexpressing a constitutively stable version of the oxygen sensor RELATED TO APETALA2 12 (RAP2.12), indicating convergence of oxygen signaling with epigenetic regulation of gene expression. Therefore, our results identify a role for AGO1 and AGO4 RNA-silencing pathways in low-oxygen signaling in Arabidopsis.
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Affiliation(s)
- Elena Loreti
- Institute of Agricultural Biology and Biotechnology, CNR, National Research Council, Via Moruzzi, 56124 Pisa, Italy
| | - Federico Betti
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Via Guidiccioni 10, San Giuliano Terme,56017 Pisa, Italy
| | - Maria Jose Ladera-Carmona
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Via Guidiccioni 10, San Giuliano Terme,56017 Pisa, Italy
| | - Fabrizia Fontana
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Via Guidiccioni 10, San Giuliano Terme,56017 Pisa, Italy
| | - Giacomo Novi
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Via Guidiccioni 10, San Giuliano Terme,56017 Pisa, Italy
| | - Maria Cristina Valeri
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Via Guidiccioni 10, San Giuliano Terme,56017 Pisa, Italy
| | - Pierdomenico Perata
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Via Guidiccioni 10, San Giuliano Terme,56017 Pisa, Italy
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D'Angelo M, Zanor MI, Burgos E, Asprelli PD, Boggio SB, Carrari F, Peralta IE, Valle EM. Fruit metabolic and transcriptional programs differentiate among Andean tomato (Solanum lycopersicum L.) accessions. PLANTA 2019; 250:1927-1940. [PMID: 31529400 DOI: 10.1007/s00425-019-03274-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 09/05/2019] [Indexed: 06/10/2023]
Abstract
Andean tomatoes differed from the wild ancestor in the metabolic composition and the expression of genes related with mitochondrial functions, and environmental stresses, making them potentially suitable for breeding programmes. Traditional landraces or "criollo" tomatoes (Solanum lycopersicum L.) from Andean areas of Argentina, selected for their fruit quality, were analysed in this study. We explored the metabolome and transcriptome of the ripe fruit in nine landrace accessions representing the seven genetic groups and compared them to the mature fruit of the wild progenitor Solanum pimpinellifolium. The content of branched- (isoleucine and valine) and aromatic (phenylalanine and tryptophan) amino acids, citrate and sugars were significantly different in the fruit of several "criollo" tomatoes compared to S. pimpinellifolium. The transcriptomic profile of the ripe fruit showed several genes significantly and highly regulated in all varieties compared to S. pimpinellifolium, like genes encoding histones and mitochondrial proteins. Additionally, network analysis including transcripts and metabolites identified major hubs with the largest number of connections such as constitutive photomorphogenic protein 1 (a RING finger-type ubiquitin E3 ligase), five Zn finger transcription factors, ascorbate peroxidase, acetolactate synthase, and sucrose non-fermenting 1 kinase. Co-expression analysis of these genes revealed a potential function in acquiring tomato fruit quality during domestication.
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Affiliation(s)
- Matilde D'Angelo
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR), Rosario, Argentina
- Animal Nutrition and Welfare Service, Animal and Food Science Department, Universitat Autónoma de Barcelona, 08193, Bellaterra, Spain
| | - María I Zanor
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR), Rosario, Argentina
| | - Estanislao Burgos
- Instituto de Fisiología Biología Molecular y Neurociencias (IFIBYNE-CONICET-UBA), Buenos Aires, Argentina
| | - Pablo D Asprelli
- Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Silvana B Boggio
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR), Rosario, Argentina
| | - Fernando Carrari
- Instituto de Fisiología Biología Molecular y Neurociencias (IFIBYNE-CONICET-UBA), Buenos Aires, Argentina
| | - Iris E Peralta
- Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Mendoza, Argentina
- IADIZA CCT-CONICET, Mendoza, Argentina
| | - Estela M Valle
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR), Rosario, Argentina.
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Bartling B, Zunkel K, Al-Robaiy S, Dehghani F, Simm A. Gene doubling increases glyoxalase 1 expression in RAGE knockout mice. Biochim Biophys Acta Gen Subj 2019; 1864:129438. [PMID: 31526867 DOI: 10.1016/j.bbagen.2019.129438] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/09/2019] [Accepted: 09/12/2019] [Indexed: 01/10/2023]
Abstract
BACKGROUND The receptor for advanced glycation end-products (RAGE) is a multifunctional protein. Its function as pattern recognition receptor able to interact with various extracellular ligands is well described. Genetically modified mouse models, especially the RAGE knockout (RAGE-KO) mouse, identified the amplification of the immune response as an important function of RAGE. Pro-inflammatory ligands of RAGE are also methylglyoxal-derived advanced glycation end-products, which depend in their quantity, at least in part, on the activity of the methylglyoxal-detoxifying enzyme glyoxalase-1 (Glo1). Therefore, we studied the potential interaction of RAGE and Glo1 by use of RAGE-KO mice. METHODS Various tissues (lung, liver, kidney, heart, spleen, and brain) and blood cells from RAGE-KO and wildtype mice were analyzed for Glo1 expression and activity by biochemical assays and the Glo1 gene status by PCR techniques. RESULTS We identified an about two-fold up-regulation of Glo1 expression and activity in all tissues of RAGE-KO mice. This was result of a copy number variation of the Glo1 gene on mouse chromosome 17. In liver tissue and blood cells, the Glo1 expression and activity was additionally influenced by sex with higher values for male than female animals. As the genomic region containing Glo1 also contains the full-length sequence of another gene, namely Dnahc8, both genes were duplicated in RAGE-KO mice. CONCLUSION A genetic variance in RAGE-KO mice falsely suggests an interaction of RAGE and Glo1 function. GENERAL SIGNIFICANCE RAGE-independent up-regulation of Glo1 in RAGE-KO mice might be as another explanation for, at least some, effects attributed to RAGE before.
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Affiliation(s)
- Babett Bartling
- Department of Cardiac Surgery, Middle German Heart Center, University Hospital Halle (Saale), Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.
| | - Katja Zunkel
- Department of Cardiac Surgery, Middle German Heart Center, University Hospital Halle (Saale), Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Samiya Al-Robaiy
- Department of Cardiac Surgery, Middle German Heart Center, University Hospital Halle (Saale), Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Faramarz Dehghani
- Institute of Anatomy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Andreas Simm
- Department of Cardiac Surgery, Middle German Heart Center, University Hospital Halle (Saale), Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
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Patil M, Seifert S, Seiler F, Soll J, Schwenkert S. FZL is primarily localized to the inner chloroplast membrane however influences thylakoid maintenance. PLANT MOLECULAR BIOLOGY 2018; 97:421-433. [PMID: 29951988 DOI: 10.1007/s11103-018-0748-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 06/05/2018] [Indexed: 06/08/2023]
Abstract
FZL is primarily localized to the chloroplast inner envelope and not to the thylakoids, but nevertheless affects the maintenance of thylakoid membranes and photosynthetic protein complexes. The fuzzy-onion-like protein (FZL) is a membrane-bound dynamin-like GTPase located in the chloroplast. We have investigated the chloroplast sub-localization of the endogenous FZL protein and found it to be primarily localized to the inner envelope. Moreover, we observed that mature leaves of fzl mutants start to turn pale, especially in the midvein area of the leaves, 11 days after germination. We therefore assessed their photosynthetic performance as well as the accumulation of thylakoid membrane proteins and complexes after the initial appearance of the phenotype. Interestingly, we could observe a significant decrease in amounts of the cytochrome b6f complex in 20-day-old mutants, which was also reflected in an impaired electron transport rate as well as a more oxidized P700 redox state. Analysis of differences in transcriptome datasets obtained before and after onset of the phenotype, revealed large-scale changes in gene expression after the phenotype became visible. In summary, we propose that FZL, despite its localization in the inner chloroplast envelope has an important role in thylakoid maintenance in mature and aging leaves.
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Affiliation(s)
- Manali Patil
- Department Biologie I, Botanik, Ludwig-Maximilians-Universität, Großhaderner Strasse. 2-4, 82152, Planegg-Martinsried, Germany
- Munich Center for Integrated Protein Science CiPSM, Ludwig-Maximilians-Universität, Feodor-Lynen-Strasse 25, 81377, Munich, Germany
| | - Stephanie Seifert
- Department Biologie I, Botanik, Ludwig-Maximilians-Universität, Großhaderner Strasse. 2-4, 82152, Planegg-Martinsried, Germany
| | - Franka Seiler
- Department Biologie I, Botanik, Ludwig-Maximilians-Universität, Großhaderner Strasse. 2-4, 82152, Planegg-Martinsried, Germany
| | - Jürgen Soll
- Department Biologie I, Botanik, Ludwig-Maximilians-Universität, Großhaderner Strasse. 2-4, 82152, Planegg-Martinsried, Germany
- Munich Center for Integrated Protein Science CiPSM, Ludwig-Maximilians-Universität, Feodor-Lynen-Strasse 25, 81377, Munich, Germany
| | - Serena Schwenkert
- Department Biologie I, Botanik, Ludwig-Maximilians-Universität, Großhaderner Strasse. 2-4, 82152, Planegg-Martinsried, Germany.
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Zuther E, Lee YP, Erban A, Kopka J, Hincha DK. Natural Variation in Freezing Tolerance and Cold Acclimation Response in Arabidopsis thaliana and Related Species. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1081:81-98. [DOI: 10.1007/978-981-13-1244-1_5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Patharkar OR, Gassmann W, Walker JC. Leaf shedding as an anti-bacterial defense in Arabidopsis cauline leaves. PLoS Genet 2017; 13:e1007132. [PMID: 29253890 PMCID: PMC5749873 DOI: 10.1371/journal.pgen.1007132] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 01/02/2018] [Accepted: 11/28/2017] [Indexed: 01/04/2023] Open
Abstract
Plants utilize an innate immune system to protect themselves from disease. While many molecular components of plant innate immunity resemble the innate immunity of animals, plants also have evolved a number of truly unique defense mechanisms, particularly at the physiological level. Plant's flexible developmental program allows them the unique ability to simply produce new organs as needed, affording them the ability to replace damaged organs. Here we develop a system to study pathogen-triggered leaf abscission in Arabidopsis. Cauline leaves infected with the bacterial pathogen Pseudomonas syringae abscise as part of the defense mechanism. Pseudomonas syringae lacking a functional type III secretion system fail to elicit an abscission response, suggesting that the abscission response is a novel form of immunity triggered by effectors. HAESA/HAESA-like 2, INFLORESCENCE DEFICIENT IN ABSCISSION, and NEVERSHED are all required for pathogen-triggered abscission to occur. Additionally phytoalexin deficient 4, enhanced disease susceptibility 1, salicylic acid induction-deficient 2, and senescence-associated gene 101 plants with mutations in genes necessary for bacterial defense and salicylic acid signaling, and NahG transgenic plants with low levels of salicylic acid fail to abscise cauline leaves normally. Bacteria that physically contact abscission zones trigger a strong abscission response; however, long-distance signals are also sent from distal infected tissue to the abscission zone, alerting the abscission zone of looming danger. We propose a threshold model regulating cauline leaf defense where minor infections are handled by limiting bacterial growth, but when an infection is deemed out of control, cauline leaves are shed. Together with previous results, our findings suggest that salicylic acid may regulate both pathogen- and drought-triggered leaf abscission.
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Affiliation(s)
- O. Rahul Patharkar
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States of America
| | - Walter Gassmann
- Division of Plant Sciences, CS Bond Life Sciences Center and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States of America
| | - John C. Walker
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States of America
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Hu Y, Depaepe T, Smet D, Hoyerova K, Klíma P, Cuypers A, Cutler S, Buyst D, Morreel K, Boerjan W, Martins J, Petrášek J, Vandenbussche F, Van Der Straeten D. ACCERBATIN, a small molecule at the intersection of auxin and reactive oxygen species homeostasis with herbicidal properties. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4185-4203. [PMID: 28922768 PMCID: PMC5853866 DOI: 10.1093/jxb/erx242] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 06/22/2017] [Indexed: 05/30/2023]
Abstract
The volatile two-carbon hormone ethylene acts in concert with an array of signals to affect etiolated seedling development. From a chemical screen, we isolated a quinoline carboxamide designated ACCERBATIN (AEX) that exacerbates the 1-aminocyclopropane-1-carboxylic acid-induced triple response, typical for ethylene-treated seedlings in darkness. Phenotypic analyses revealed distinct AEX effects including inhibition of root hair development and shortening of the root meristem. Mutant analysis and reporter studies further suggested that AEX most probably acts in parallel to ethylene signaling. We demonstrated that AEX functions at the intersection of auxin metabolism and reactive oxygen species (ROS) homeostasis. AEX inhibited auxin efflux in BY-2 cells and promoted indole-3-acetic acid (IAA) oxidation in the shoot apical meristem and cotyledons of etiolated seedlings. Gene expression studies and superoxide/hydrogen peroxide staining further revealed that the disrupted auxin homeostasis was accompanied by oxidative stress. Interestingly, in light conditions, AEX exhibited properties reminiscent of the quinoline carboxylate-type auxin-like herbicides. We propose that AEX interferes with auxin transport from its major biosynthesis sites, either as a direct consequence of poor basipetal transport from the shoot meristematic region, or indirectly, through excessive IAA oxidation and ROS accumulation. Further investigation of AEX can provide new insights into the mechanisms connecting auxin and ROS homeostasis in plant development and provide useful tools to study auxin-type herbicides.
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Affiliation(s)
- Yuming Hu
- Laboratory of Functional Plant Biology, Department of Biology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat, Ghent, Belgium
| | - Thomas Depaepe
- Laboratory of Functional Plant Biology, Department of Biology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat, Ghent, Belgium
| | - Dajo Smet
- Laboratory of Functional Plant Biology, Department of Biology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat, Ghent, Belgium
| | - Klara Hoyerova
- Institute of Experimental Botany ASCR, Praha, Czech Republic
| | - Petr Klíma
- Institute of Experimental Botany ASCR, Praha, Czech Republic
| | - Ann Cuypers
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, Diepenbeek, Belgium
| | - Sean Cutler
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Dieter Buyst
- NMR and Structure Analysis, Department of Organic Chemistry, Krijgslaan, Ghent, Belgium
| | - Kris Morreel
- Department of Plant Systems Biology, VIB (Flanders Institute for Biotechnology), Technologiepark, Ghent, Belgium
| | - Wout Boerjan
- Department of Plant Systems Biology, VIB (Flanders Institute for Biotechnology), Technologiepark, Ghent, Belgium
| | - José Martins
- NMR and Structure Analysis, Department of Organic Chemistry, Krijgslaan, Ghent, Belgium
| | - Jan Petrášek
- Institute of Experimental Botany ASCR, Praha, Czech Republic
| | - Filip Vandenbussche
- Laboratory of Functional Plant Biology, Department of Biology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat, Ghent, Belgium
| | - Dominique Van Der Straeten
- Laboratory of Functional Plant Biology, Department of Biology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat, Ghent, Belgium
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Comparative Phenotypical and Molecular Analyses of Arabidopsis Grown under Fluorescent and LED Light. PLANTS 2017; 6:plants6020024. [PMID: 28608805 PMCID: PMC5489796 DOI: 10.3390/plants6020024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 06/08/2017] [Accepted: 06/11/2017] [Indexed: 12/05/2022]
Abstract
Comparative analyses of phenotypic and molecular traits of Arabidopsis thaliana grown under standardised conditions is still a challenge using climatic devices supplied with common light sources. These are in most cases fluorescent lights, which have several disadvantages such as heat production at higher light intensities, an invariable spectral output, and relatively rapid “ageing”. This results in non-desired variations of growth conditions and lowers the comparability of data acquired over extended time periods. In this study, we investigated the growth behaviour of Arabidopsis Col0 under different light conditions, applying fluorescent compared to LED lamps, and we conducted physiological as well as gene expression analyses. By changing the spectral composition and/or light intensity of LEDs we can clearly influence the growth behaviour of Arabidopsis and thereby study phenotypic attributes under very specific light conditions that are stable and reproducible, which is not necessarily given for fluorescent lamps. By using LED lights, we can also roughly mimic the sun light emission spectrum, enabling us to study plant growth in a more natural-like light set-up. We observed distinct growth behaviour under the different light regimes which was reflected by physiological properties of the plants. In conclusion, LEDs provide variable emission spectra for studying plant growth under defined, stable light conditions.
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11
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From plant genomes to phenotypes. J Biotechnol 2017; 261:46-52. [PMID: 28602791 DOI: 10.1016/j.jbiotec.2017.06.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/27/2017] [Accepted: 06/07/2017] [Indexed: 12/21/2022]
Abstract
Recent advances in sequencing technologies have greatly accelerated the rate of plant genome and applied breeding research. Despite this advancing trend, plant genomes continue to present numerous difficulties to the standard tools and pipelines not only for genome assembly but also gene annotation and downstream analysis. Here we give a perspective on tools, resources and services necessary to assemble and analyze plant genomes and link them to plant phenotypes.
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12
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Ntatsi G, Savvas D, Papasotiropoulos V, Katsileros A, Zrenner RM, Hincha DK, Zuther E, Schwarz D. Rootstock Sub-Optimal Temperature Tolerance Determines Transcriptomic Responses after Long-Term Root Cooling in Rootstocks and Scions of Grafted Tomato Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:911. [PMID: 28642763 PMCID: PMC5462977 DOI: 10.3389/fpls.2017.00911] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 05/15/2017] [Indexed: 05/21/2023]
Abstract
Grafting of elite cultivars onto tolerant rootstocks is an advanced strategy to increase tomato tolerance to sub-optimal temperature. However, a detailed understanding of adaptive mechanisms to sub-optimal temperature in rootstocks and scions of grafting combinations on a physiological and molecular level is lacking. Here, the commercial cultivar Kommeet was grafted either onto 'Moneymaker' (sensitive) or onto the line accession LA 1777 of Solanum habrochaites (tolerant). Grafted plants were grown in NFT-system at either optimal (25°C) or sub-optimal (15°C) temperatures in the root environment with optimal air temperature (25°C) for 22 days. Grafting onto the differently tolerant rootstocks caused differences in shoot fresh and dry weight, total leaf area and dry matter content of roots, in stomatal conductance and intercellular CO2 and guaiacol peroxidase activity but not in net photosynthesis, sugar, starch and amino acid content, lipid peroxidation and antioxidant enzyme activity. In leaves, comparative transcriptome analysis identified 361 differentially expressed genes (DEG) responding to sub-optimal root temperature when 'Kommeet' was grafted onto the sensitive but no when grafted onto the tolerant rootstock. 1509 and 2036 DEG responding to sub-optimal temperature were identified in LA 1777 and 'Moneymaker' rootstocks, respectively. In tolerant rootstocks down-regulated genes were enriched in main stress-responsive functional categories and up-regulated genes in cellulose synthesis suggesting that cellulose synthesis may be one of the main adaptation mechanisms to long-term sub-optimal temperature. Down-regulated genes of the sensitive rootstock showed a similar response, but functional categories of up-regulated genes pointed to induced stress responses. Rootstocks of the sensitive cultivar Moneymaker showed in addition an enrichment of up-regulated genes in the functional categories fatty acid desaturation, phenylpropanoids, biotic stress, cytochrome P450 and protein degradation, indicating that the sensitive cultivar showed more transcriptional adaptation to low temperature than the tolerant cultivar that did not show these changes. Mainly defense-related genes were highly differentially expressed between the tolerant and sensitive rootstock genotypes under sub-optimal temperature in the root environment. These results provide new insights into the molecular mechanisms of long-term sub-optimal temperature tolerance of tomato.
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Affiliation(s)
- Georgia Ntatsi
- Laboratory of Vegetable Crops, Department of Crop Science, Agricultural University of AthensAthens, Greece
| | - Dimitrios Savvas
- Laboratory of Vegetable Crops, Department of Crop Science, Agricultural University of AthensAthens, Greece
| | - Vassilis Papasotiropoulos
- Department of Agricultural Technology, Technological Education Institute of Western GreeceAmaliada, Greece
| | - Anastasios Katsileros
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of AthensAthens, Greece
| | - Rita M. Zrenner
- Leibniz Institute of Vegetable and Ornamental CropsGroßbeeren, Germany
| | - Dirk K. Hincha
- Central Infrastructure Group Genomics and Transcript Profiling, Max-Planck-Institute of Molecular Plant PhysiologyPotsdam, Germany
| | - Ellen Zuther
- Central Infrastructure Group Genomics and Transcript Profiling, Max-Planck-Institute of Molecular Plant PhysiologyPotsdam, Germany
| | - Dietmar Schwarz
- Leibniz Institute of Vegetable and Ornamental CropsGroßbeeren, Germany
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13
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Espinoza C, Liang Y, Stacey G. Chitin receptor CERK1 links salt stress and chitin-triggered innate immunity in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:984-995. [PMID: 27888535 DOI: 10.1111/tpj.13437] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/18/2016] [Accepted: 11/22/2016] [Indexed: 05/18/2023]
Abstract
In nature, plants need to respond to multiple environmental stresses that require the involvement and fine-tuning of different stress signaling pathways. Cross-tolerance, in which plants pre-treated with chitin (a fungal microbe-associated molecular pattern) have improved salt tolerance, was observed in Arabidopsis, but is not well understood. Here, we show a unique link between chitin and salt signaling mediated by the chitin receptor CHITIN ELICITOR RECEPTOR KINASE 1 (CERK1). Transcriptome analysis revealed that salt stress-induced genes are highly correlated with chitin-induced genes, although this was not observed with other microbe-associated molecular patterns (MAMPs) or with other abiotic stresses. The cerk1 mutant was more susceptible to NaCl than was the wild type. cerk1 plants had an irregular increase of cytosolic calcium ([Ca2+ ]cyt ) after NaCl treatment. Bimolecular fluorescence complementation (BiFC) and co-immunoprecipitation experiments indicated that CERK1 physically interacts with ANNEXIN 1 (ANN1), which was reported to form a calcium-permeable channel that contributes to the NaCl-induced [Ca2+ ]cyt signal. In turn, ann1 mutants showed elevated chitin-induced rapid responses. In short, molecular components previously shown to function in chitin or salt signaling physically interact and intimately link the downstream responses to fungal attack and salt stress.
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Affiliation(s)
- Catherine Espinoza
- Divisions of Plant Sciences and Biochemistry, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Yan Liang
- Divisions of Plant Sciences and Biochemistry, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
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14
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Izadi F, Zarrini HN, Kiani G, Jelodar NB. A comparative analytical assay of gene regulatory networks inferred using microarray and RNA-seq datasets. Bioinformation 2016; 12:340-346. [PMID: 28293077 PMCID: PMC5320930 DOI: 10.6026/97320630012340] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 08/05/2016] [Accepted: 08/06/2016] [Indexed: 01/16/2023] Open
Abstract
A Gene Regulatory Network (GRN) is a collection of interactions between molecular regulators and their targets in cells governing gene expression level. Omics data explosion generated from high-throughput genomic assays such as microarray and RNA-Seq technologies and the emergence of a number of pre-processing methods demands suitable guidelines to determine the impact of transcript data platforms and normalization procedures on describing associations in GRNs. In this study exploiting publically available microarray and RNA-Seq datasets and a gold standard of transcriptional interactions in Arabidopsis, we performed a comparison between six GRNs derived by RNA-Seq and microarray data and different normalization procedures. As a result we observed that compared algorithms were highly data-specific and Networks reconstructed by RNA-Seq data revealed a considerable accuracy against corresponding networks captured by microarrays. Topological analysis showed that GRNs inferred from two platforms were similar in several of topological features although we observed more connectivity in RNA-Seq derived genes network. Taken together transcriptional regulatory networks obtained by Robust Multiarray Averaging (RMA) and Variance-Stabilizing Transformed (VST) normalized data demonstrated predicting higher rate of true edges over the rest of methods used in this comparison.
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Affiliation(s)
- Fereshteh Izadi
- Plant Breeding Department, Sari Agricultural Sciences and Natural Resources, Iran
| | - Hamid Najafi Zarrini
- Plant Breeding Department, Sari Agricultural Sciences and Natural Resources, Iran
| | - Ghaffar Kiani
- Plant Breeding Department, Sari Agricultural Sciences and Natural Resources, Iran
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15
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Li Z, Omranian N, Neumetzler L, Wang T, Herter T, Usadel B, Demura T, Giavalisco P, Nikoloski Z, Persson S. A Transcriptional and Metabolic Framework for Secondary Wall Formation in Arabidopsis. PLANT PHYSIOLOGY 2016; 172:1334-1351. [PMID: 27566165 PMCID: PMC5047112 DOI: 10.1104/pp.16.01100] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 08/23/2016] [Indexed: 05/02/2023]
Abstract
Plant cell walls are essential for plant growth and development. The cell walls are traditionally divided into primary walls, which surround growing cells, and secondary walls, which provide structural support to certain cell types and promote their functions. While much information is available about the enzymes and components that contribute to the production of these two types of walls, much less is known about the transition from primary to secondary wall synthesis. To address this question, we made use of a transcription factor system in Arabidopsis (Arabidopsis thaliana) in which an overexpressed master secondary wall-inducing transcription factor, VASCULAR-RELATED NAC DOMAIN PROTEIN7, can be redirected into the nucleus by the addition of dexamethasone. We established the time frame during which primary wall synthesis changed into secondary wall production in dexamethasone-treated seedlings and measured transcript and metabolite abundance at eight time points after induction. Using cluster- and network-based analyses, we integrated the data sets to explore coordination between transcripts, metabolites, and the combination of the two across the time points. We provide the raw data as well as a range of network-based analyses. These data reveal links between hormone signaling and metabolic processes during the formation of secondary walls and provide a framework toward a deeper understanding of how primary walls transition into secondary walls.
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Affiliation(s)
- Zheng Li
- School of BioSciences (Z.L., S.P.) and Australian Research Council Centre of Excellence in Plant Cell Walls (S.P.), University of Melbourne, Parkville, Victoria 3010, Australia;Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (Z.L., N.O., L.N., T.W., T.H., P.G., Z.N., S.P.);Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52056 Aachen, Germany (B.U.); andGraduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (T.D.)
| | - Nooshin Omranian
- School of BioSciences (Z.L., S.P.) and Australian Research Council Centre of Excellence in Plant Cell Walls (S.P.), University of Melbourne, Parkville, Victoria 3010, Australia;Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (Z.L., N.O., L.N., T.W., T.H., P.G., Z.N., S.P.);Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52056 Aachen, Germany (B.U.); andGraduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (T.D.)
| | - Lutz Neumetzler
- School of BioSciences (Z.L., S.P.) and Australian Research Council Centre of Excellence in Plant Cell Walls (S.P.), University of Melbourne, Parkville, Victoria 3010, Australia;Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (Z.L., N.O., L.N., T.W., T.H., P.G., Z.N., S.P.);Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52056 Aachen, Germany (B.U.); andGraduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (T.D.)
| | - Ting Wang
- School of BioSciences (Z.L., S.P.) and Australian Research Council Centre of Excellence in Plant Cell Walls (S.P.), University of Melbourne, Parkville, Victoria 3010, Australia;Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (Z.L., N.O., L.N., T.W., T.H., P.G., Z.N., S.P.);Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52056 Aachen, Germany (B.U.); andGraduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (T.D.)
| | - Thomas Herter
- School of BioSciences (Z.L., S.P.) and Australian Research Council Centre of Excellence in Plant Cell Walls (S.P.), University of Melbourne, Parkville, Victoria 3010, Australia;Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (Z.L., N.O., L.N., T.W., T.H., P.G., Z.N., S.P.);Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52056 Aachen, Germany (B.U.); andGraduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (T.D.)
| | - Bjoern Usadel
- School of BioSciences (Z.L., S.P.) and Australian Research Council Centre of Excellence in Plant Cell Walls (S.P.), University of Melbourne, Parkville, Victoria 3010, Australia;Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (Z.L., N.O., L.N., T.W., T.H., P.G., Z.N., S.P.);Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52056 Aachen, Germany (B.U.); andGraduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (T.D.)
| | - Taku Demura
- School of BioSciences (Z.L., S.P.) and Australian Research Council Centre of Excellence in Plant Cell Walls (S.P.), University of Melbourne, Parkville, Victoria 3010, Australia;Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (Z.L., N.O., L.N., T.W., T.H., P.G., Z.N., S.P.);Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52056 Aachen, Germany (B.U.); andGraduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (T.D.)
| | - Patrick Giavalisco
- School of BioSciences (Z.L., S.P.) and Australian Research Council Centre of Excellence in Plant Cell Walls (S.P.), University of Melbourne, Parkville, Victoria 3010, Australia;Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (Z.L., N.O., L.N., T.W., T.H., P.G., Z.N., S.P.);Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52056 Aachen, Germany (B.U.); andGraduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (T.D.)
| | - Zoran Nikoloski
- School of BioSciences (Z.L., S.P.) and Australian Research Council Centre of Excellence in Plant Cell Walls (S.P.), University of Melbourne, Parkville, Victoria 3010, Australia;Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (Z.L., N.O., L.N., T.W., T.H., P.G., Z.N., S.P.);Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52056 Aachen, Germany (B.U.); andGraduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (T.D.)
| | - Staffan Persson
- School of BioSciences (Z.L., S.P.) and Australian Research Council Centre of Excellence in Plant Cell Walls (S.P.), University of Melbourne, Parkville, Victoria 3010, Australia;Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (Z.L., N.O., L.N., T.W., T.H., P.G., Z.N., S.P.);Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52056 Aachen, Germany (B.U.); andGraduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (T.D.)
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16
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Czedik-Eysenberg A, Arrivault S, Lohse MA, Feil R, Krohn N, Encke B, Nunes-Nesi A, Fernie AR, Lunn JE, Sulpice R, Stitt M. The Interplay between Carbon Availability and Growth in Different Zones of the Growing Maize Leaf. PLANT PHYSIOLOGY 2016; 172:943-967. [PMID: 27582314 PMCID: PMC5047066 DOI: 10.1104/pp.16.00994] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 08/26/2016] [Indexed: 05/18/2023]
Abstract
Plants assimilate carbon in their photosynthetic tissues in the light. However, carbon is required during the night and in nonphotosynthetic organs. It is therefore essential that plants manage their carbon resources spatially and temporally and coordinate growth with carbon availability. In growing maize (Zea mays) leaf blades, a defined developmental gradient facilitates analyses in the cell division, elongation, and mature zones. We investigated the responses of the metabolome and transcriptome and polysome loading, as a qualitative proxy for protein synthesis, at dusk, dawn, and 6, 14, and 24 h into an extended night, and tracked whole-leaf elongation over this time course. Starch and sugars are depleted by dawn in the mature zone, but only after an extension of the night in the elongation and division zones. Sucrose (Suc) recovers partially between 14 and 24 h into the extended night in the growth zones, but not the mature zone. The global metabolome and transcriptome track these zone-specific changes in Suc. Leaf elongation and polysome loading in the growth zones also remain high at dawn, decrease between 6 and 14 h into the extended night, and then partially recover, indicating that growth processes are determined by local carbon status. The level of Suc-signaling metabolite trehalose-6-phosphate, and the trehalose-6-phosphate:Suc ratio are much higher in growth than mature zones at dusk and dawn but fall in the extended night. Candidate genes were identified by searching for transcripts that show characteristic temporal response patterns or contrasting responses to carbon starvation in growth and mature zones.
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Affiliation(s)
- Angelika Czedik-Eysenberg
- Gregor-Mendel-Institute of Molecular Plant Biology, 1030 Vienna, Austria (A.C.-E.);Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (S.A., R.F., N.K., B.E., A.R.F., J.E.L., M.S.);Targenomix GmbH, 14476 Potsdam, Germany (M.A.L.);Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais State, Brasil (A.N.-N.); andPlant Systems Biology Lab, Plant AgriBiosciences, C314 Aras de Brun, National University of Ireland, Galway, Ireland (R.S.)
| | - Stéphanie Arrivault
- Gregor-Mendel-Institute of Molecular Plant Biology, 1030 Vienna, Austria (A.C.-E.);Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (S.A., R.F., N.K., B.E., A.R.F., J.E.L., M.S.);Targenomix GmbH, 14476 Potsdam, Germany (M.A.L.);Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais State, Brasil (A.N.-N.); andPlant Systems Biology Lab, Plant AgriBiosciences, C314 Aras de Brun, National University of Ireland, Galway, Ireland (R.S.)
| | - Marc A Lohse
- Gregor-Mendel-Institute of Molecular Plant Biology, 1030 Vienna, Austria (A.C.-E.);Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (S.A., R.F., N.K., B.E., A.R.F., J.E.L., M.S.);Targenomix GmbH, 14476 Potsdam, Germany (M.A.L.);Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais State, Brasil (A.N.-N.); andPlant Systems Biology Lab, Plant AgriBiosciences, C314 Aras de Brun, National University of Ireland, Galway, Ireland (R.S.)
| | - Regina Feil
- Gregor-Mendel-Institute of Molecular Plant Biology, 1030 Vienna, Austria (A.C.-E.);Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (S.A., R.F., N.K., B.E., A.R.F., J.E.L., M.S.);Targenomix GmbH, 14476 Potsdam, Germany (M.A.L.);Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais State, Brasil (A.N.-N.); andPlant Systems Biology Lab, Plant AgriBiosciences, C314 Aras de Brun, National University of Ireland, Galway, Ireland (R.S.)
| | - Nicole Krohn
- Gregor-Mendel-Institute of Molecular Plant Biology, 1030 Vienna, Austria (A.C.-E.);Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (S.A., R.F., N.K., B.E., A.R.F., J.E.L., M.S.);Targenomix GmbH, 14476 Potsdam, Germany (M.A.L.);Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais State, Brasil (A.N.-N.); andPlant Systems Biology Lab, Plant AgriBiosciences, C314 Aras de Brun, National University of Ireland, Galway, Ireland (R.S.)
| | - Beatrice Encke
- Gregor-Mendel-Institute of Molecular Plant Biology, 1030 Vienna, Austria (A.C.-E.);Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (S.A., R.F., N.K., B.E., A.R.F., J.E.L., M.S.);Targenomix GmbH, 14476 Potsdam, Germany (M.A.L.);Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais State, Brasil (A.N.-N.); andPlant Systems Biology Lab, Plant AgriBiosciences, C314 Aras de Brun, National University of Ireland, Galway, Ireland (R.S.)
| | - Adriano Nunes-Nesi
- Gregor-Mendel-Institute of Molecular Plant Biology, 1030 Vienna, Austria (A.C.-E.);Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (S.A., R.F., N.K., B.E., A.R.F., J.E.L., M.S.);Targenomix GmbH, 14476 Potsdam, Germany (M.A.L.);Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais State, Brasil (A.N.-N.); andPlant Systems Biology Lab, Plant AgriBiosciences, C314 Aras de Brun, National University of Ireland, Galway, Ireland (R.S.)
| | - Alisdair R Fernie
- Gregor-Mendel-Institute of Molecular Plant Biology, 1030 Vienna, Austria (A.C.-E.);Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (S.A., R.F., N.K., B.E., A.R.F., J.E.L., M.S.);Targenomix GmbH, 14476 Potsdam, Germany (M.A.L.);Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais State, Brasil (A.N.-N.); andPlant Systems Biology Lab, Plant AgriBiosciences, C314 Aras de Brun, National University of Ireland, Galway, Ireland (R.S.)
| | - John E Lunn
- Gregor-Mendel-Institute of Molecular Plant Biology, 1030 Vienna, Austria (A.C.-E.);Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (S.A., R.F., N.K., B.E., A.R.F., J.E.L., M.S.);Targenomix GmbH, 14476 Potsdam, Germany (M.A.L.);Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais State, Brasil (A.N.-N.); andPlant Systems Biology Lab, Plant AgriBiosciences, C314 Aras de Brun, National University of Ireland, Galway, Ireland (R.S.)
| | - Ronan Sulpice
- Gregor-Mendel-Institute of Molecular Plant Biology, 1030 Vienna, Austria (A.C.-E.);Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (S.A., R.F., N.K., B.E., A.R.F., J.E.L., M.S.);Targenomix GmbH, 14476 Potsdam, Germany (M.A.L.);Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais State, Brasil (A.N.-N.); andPlant Systems Biology Lab, Plant AgriBiosciences, C314 Aras de Brun, National University of Ireland, Galway, Ireland (R.S.)
| | - Mark Stitt
- Gregor-Mendel-Institute of Molecular Plant Biology, 1030 Vienna, Austria (A.C.-E.);Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany (S.A., R.F., N.K., B.E., A.R.F., J.E.L., M.S.);Targenomix GmbH, 14476 Potsdam, Germany (M.A.L.);Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais State, Brasil (A.N.-N.); andPlant Systems Biology Lab, Plant AgriBiosciences, C314 Aras de Brun, National University of Ireland, Galway, Ireland (R.S.)
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17
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Huang LJ, Li N, Thurow C, Wirtz M, Hell R, Gatz C. Ectopically expressed glutaredoxin ROXY19 negatively regulates the detoxification pathway in Arabidopsis thaliana. BMC PLANT BIOLOGY 2016; 16:200. [PMID: 27624344 PMCID: PMC5022239 DOI: 10.1186/s12870-016-0886-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 09/01/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND Glutaredoxins (GRXs) are small proteins which bind glutathione to either reduce disulfide bonds or to coordinate iron sulfur clusters. Whereas these well-established functions are associated with ubiquitously occurring GRXs that encode variants of a CPYC or a CGFS motif in the active center, land plants also possess CCxC/S-type GRXs (named ROXYs) for which the biochemical functions are yet unknown. ROXYs physically and genetically interact with bZIP transcription factors of the TGA family. In Arabidopsis, ectopically expressed ROXY19 (originally named GRX480 or GRXC9) negatively regulates expression of jasmonic acid/ethylene-induced defense genes through an unknown mechanism that requires at least one of the redundant transcription factors TGA2, TGA5 or TGA6. RESULTS Ectopically expressed ROXY19 interferes with the activation of TGA-dependent detoxification genes. Similar to the tga2 tga5 tga6 mutant, 35S:ROXY19 plants are more susceptible to the harmful chemical TIBA (2,3,5-triiodobenzoic acid). The repressive function of ROXY19 depends on the integrity of the active site, which can be either CCMC or CPYC but not SSMS. Ectopic expression of the related GRX ROXY18/GRXS13 also led to increased susceptibility to TIBA, indicating potential functional redundancy of members of the ROXY gene family. This redundancy might explain why roxy19 knock-out plants did not show a phenotype with respect to the regulation of the TIBA-induced detoxification program. Complementation of the tga2 tga5 tga6 mutant with either TGA5 or TGA5C186S, in which the single potential target-site of ROXY19 had been eliminated, did not reveal any evidence for a critical redox modification that might be important for controlling the detoxification program. CONCLUSIONS ROXY19 and related proteins of the ROXY gene family can function as negative regulators of TGA-dependent promoters controlling detoxification genes.
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Affiliation(s)
- Li-Jun Huang
- Albrecht-von-Haller-Institute for Plant Sciences, Molecular Biology and Physiology, Georg-August-University Göttingen, Julia-Lermontowa-Weg 3, 37077 Göttingen, Germany
| | - Ning Li
- Albrecht-von-Haller-Institute for Plant Sciences, Molecular Biology and Physiology, Georg-August-University Göttingen, Julia-Lermontowa-Weg 3, 37077 Göttingen, Germany
| | - Corinna Thurow
- Albrecht-von-Haller-Institute for Plant Sciences, Molecular Biology and Physiology, Georg-August-University Göttingen, Julia-Lermontowa-Weg 3, 37077 Göttingen, Germany
| | - Markus Wirtz
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Rüdiger Hell
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Christiane Gatz
- Albrecht-von-Haller-Institute for Plant Sciences, Molecular Biology and Physiology, Georg-August-University Göttingen, Julia-Lermontowa-Weg 3, 37077 Göttingen, Germany
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18
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Patharkar OR, Walker JC. Core Mechanisms Regulating Developmentally Timed and Environmentally Triggered Abscission. PLANT PHYSIOLOGY 2016; 172:510-20. [PMID: 27468996 PMCID: PMC5074626 DOI: 10.1104/pp.16.01004] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 07/27/2016] [Indexed: 05/21/2023]
Abstract
Drought-triggered abscission is a strategy used by plants to avoid the full consequences of drought; however, it is poorly understood at the molecular genetic level. Here, we show that Arabidopsis (Arabidopsis thaliana) can be used to elucidate the pathway controlling drought-triggered leaf shedding. We further show that much of the pathway regulating developmentally timed floral organ abscission is conserved in regulating drought-triggered leaf abscission. Gene expression of HAESA (HAE) and INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) is induced in cauline leaf abscission zones when the leaves become wilted in response to limited water and HAE continues to accumulate in the leaf abscission zones through the abscission process. The genes that encode HAE/HAESA-LIKE2, IDA, NEVERSHED, and MAPK KINASE4 and 5 are all necessary for drought-induced leaf abscission. Our findings offer a molecular mechanism explaining drought-triggered leaf abscission. Furthermore, the ability to study leaf abscission in Arabidopsis opens up a new avenue to tease apart mechanisms involved in abscission that have been difficult to separate from flower development as well as for understanding the mechanistic role of water and turgor pressure in abscission.
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Affiliation(s)
- O Rahul Patharkar
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211
| | - John C Walker
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211
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Flis A, Sulpice R, Seaton DD, Ivakov AA, Liput M, Abel C, Millar AJ, Stitt M. Photoperiod-dependent changes in the phase of core clock transcripts and global transcriptional outputs at dawn and dusk in Arabidopsis. PLANT, CELL & ENVIRONMENT 2016; 39:1955-81. [PMID: 27075884 DOI: 10.1111/pce.12754] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 04/01/2016] [Indexed: 05/06/2023]
Abstract
Plants use the circadian clock to sense photoperiod length. Seasonal responses like flowering are triggered at a critical photoperiod when a light-sensitive clock output coincides with light or darkness. However, many metabolic processes, like starch turnover, and growth respond progressively to photoperiod duration. We first tested the photoperiod response of 10 core clock genes and two output genes. qRT-PCR analyses of transcript abundance under 6, 8, 12 and 18 h photoperiods revealed 1-4 h earlier peak times under short photoperiods and detailed changes like rising PRR7 expression before dawn. Clock models recapitulated most of these changes. We explored the consequences for global gene expression by performing transcript profiling in 4, 6, 8, 12 and 18 h photoperiods. There were major changes in transcript abundance at dawn, which were as large as those between dawn and dusk in a given photoperiod. Contributing factors included altered timing of the clock relative to dawn, light signalling and changes in carbon availability at night as a result of clock-dependent regulation of starch degradation. Their interaction facilitates coordinated transcriptional regulation of key processes like starch turnover, anthocyanin, flavonoid and glucosinolate biosynthesis and protein synthesis and underpins the response of metabolism and growth to photoperiod.
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Affiliation(s)
- Anna Flis
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Golm, Potsdam, Germany
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, GPO Box 475, Canberra, Australian Capital Territory, 2601, Australia
| | - Ronan Sulpice
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Golm, Potsdam, Germany
- Plant Systems Biology Lab, Plant and AgriBiosciences Research Centre, Botany and Plant Science, NUIG, Galway, Ireland
| | - Daniel D Seaton
- SynthSys and School of Biological Sciences, C.H. Waddington Building, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Alexander A Ivakov
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Golm, Potsdam, Germany
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, GPO Box 475, Canberra, Australian Capital Territory, 2601, Australia
| | - Magda Liput
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Golm, Potsdam, Germany
| | - Christin Abel
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Golm, Potsdam, Germany
| | - Andrew J Millar
- SynthSys and School of Biological Sciences, C.H. Waddington Building, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Golm, Potsdam, Germany
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Lee YP, Funk C, Erban A, Kopka J, Köhl KI, Zuther E, Hincha DK. Salt stress responses in a geographically diverse collection of Eutrema/Thellungiella spp. accessions. FUNCTIONAL PLANT BIOLOGY : FPB 2016; 43:590-606. [PMID: 32480489 DOI: 10.1071/fp15285] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 12/10/2015] [Indexed: 05/13/2023]
Abstract
Salinity strongly impairs plant growth and development. Natural genetic variation can be used to dissect complex traits such as plant salt tolerance. We used 16 accessions of the halophytic species Eutrema salsugineum (previously called Thellungiella salsuginea (Pallas) O.E.Schulz, Thellungiella halophila (C.A.Meyer) O.E. Schulz and Thellungiella botschantzevii D.A.German to investigate their natural variation in salinity tolerance. Although all accessions showed survival and growth up to 700mM NaCl in hydroponic culture, their relative salt tolerance varied considerably. All accessions accumulated the compatible solutes proline, sucrose, glucose and fructose and the polyamines putrescine and spermine. Relative salt tolerance was not correlated with the content of any of the investigated solutes. We compared the metabolomes and transcriptomes of Arabidopsis thaliana (L. Heynh.) Col-0 and E. salsugineum Yukon under control and salt stress conditions. Higher content of several metabolites in Yukon compared with Col-0 under control conditions indicated metabolic pre-adaptation to salinity in the halophyte. Most metabolic salt responses in Yukon took place at 200mM NaCl, whereas few additional changes were observed between 200 and 500mM. The opposite trend was observed for the transcriptome, with only little overlap between salt-regulated genes in the two species. In addition, only about half of the salt-regulated Yukon unigenes had orthologues in Col-0.
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Affiliation(s)
- Yang Ping Lee
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | - Christian Funk
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | - Alexander Erban
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | - Joachim Kopka
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | - Karin I Köhl
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | - Ellen Zuther
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | - Dirk K Hincha
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam, Germany
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Neugart S, Krumbein A, Zrenner R. Influence of Light and Temperature on Gene Expression Leading to Accumulation of Specific Flavonol Glycosides and Hydroxycinnamic Acid Derivatives in Kale (Brassica oleracea var. sabellica). FRONTIERS IN PLANT SCIENCE 2016; 7:326. [PMID: 27066016 PMCID: PMC4812050 DOI: 10.3389/fpls.2016.00326] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 03/03/2016] [Indexed: 05/05/2023]
Abstract
Light intensity and temperature are very important signals for the regulation of plant growth and development. Plants subjected to less favorable light or temperature conditions often respond with accumulation of secondary metabolites. Some of these metabolites have been identified as bioactive compounds, considered to exert positive effects on human health when consumed regularly. In order to test a typical range of growth parameters for the winter crop Brassica oleracea var. sabellica, plants were grown either at 400 μmol m(-2) s(-1) or 100 μmol m(-2) s(-1) at 10°C, or at 400 μmol m(-2) s(-1) with 5 or 15°C. The higher light intensity overall increased flavonol content of leaves, favoring the main quercetin glycosides, a caffeic acid monoacylated kaempferol triglycoside, and disinapoyl-gentiobiose. The higher temperature mainly increased the hydroxycinnamic acid derivative disinapoyl-gentiobiose, while at lower temperature synthesis is in favor of very complex sinapic acid acylated flavonol tetraglycosides such as kaempferol-3-O-sinapoyl-sophoroside-7-O-diglucoside. A global analysis of light and temperature dependent alterations of gene expression in B. oleracea var. sabellica leaves was performed with the most comprehensive Brassica microarray. When compared to the light experiment much less genes were differentially expressed in kale leaves grown at 5 or 15°C. A structured evaluation of differentially expressed genes revealed the expected enrichment in the functional categories of e.g. protein degradation at different light intensities or phytohormone metabolism at different temperature. Genes of the secondary metabolism namely phenylpropanoids are significantly enriched with both treatments. Thus, the genome of B. oleracea was screened for predicted genes putatively involved in the biosynthesis of flavonoids and hydroxycinnamic acid derivatives. All identified B. oleracea genes were analyzed for their most specific 60-mer oligonucleotides present on the 2 × 105 K format Brassica microarray. Expression differences were correlated to the structure-dependent response of flavonoid glycosides and hydroxycinnamic acid derivatives to alterations in either light or temperature. The altered metabolite accumulation was mainly reflected on gene expression level of core biosynthetic pathway genes and gave further hints to an isoform specific functional specialization.
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Hohnjec N, Czaja-Hasse LF, Hogekamp C, Küster H. Pre-announcement of symbiotic guests: transcriptional reprogramming by mycorrhizal lipochitooligosaccharides shows a strict co-dependency on the GRAS transcription factors NSP1 and RAM1. BMC Genomics 2015; 16:994. [PMID: 26597293 PMCID: PMC4657205 DOI: 10.1186/s12864-015-2224-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 11/16/2015] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND More than 80 % of all terrestrial plant species establish an arbuscular mycorrhiza (AM) symbiosis with Glomeromycota fungi. This plant-microbe interaction primarily improves phosphate uptake, but also supports nitrogen, mineral, and water aquisition. During the pre-contact stage, the AM symbiosis is controled by an exchange of diffusible factors from either partner. Amongst others, fungal signals were identified as a mix of sulfated and non-sulfated lipochitooligosaccharides (LCOs), being structurally related to rhizobial nodulation (Nod)-factor LCOs that in legumes induce the formation of nitrogen-fixing root nodules. LCO signals are transduced via a common symbiotic signaling pathway (CSSP) that activates a group of GRAS transcription factors (TFs). Using complex gene expression fingerprints as molecular phenotypes, this study primarily intended to shed light on the importance of the GRAS TFs NSP1 and RAM1 for LCO-activated gene expression during pre-symbiotic signaling. RESULTS We investigated the genome-wide transcriptional responses in 5 days old primary roots of the Medicago truncatula wild type and four symbiotic mutants to a 6 h challenge with LCO signals supplied at 10(-7/-8) M. We were able to show that during the pre-symbiotic stage, sulfated Myc-, non-sulfated Myc-, and Nod-LCO-activated gene expression almost exclusively depends on the LysM receptor kinase NFP and is largely controled by the CSSP, although responses independent of this pathway exist. Our results show that downstream of the CSSP, gene expression activation by Myc-LCOs supplied at 10(-7/-8) M strictly required both the GRAS transcription factors RAM1 and NSP1, whereas those genes either co- or specifically activated by Nod-LCOs displayed a preferential NSP1-dependency. RAM1, a central regulator of root colonization by AM fungi, controled genes activated by non-sulfated Myc-LCOs during the pre-symbiotic stage that are also up-regulated in areas with early physical contact, e.g. hyphopodia and infecting hyphae; linking responses to externally applied LCOs with early root colonization. CONCLUSIONS Since both RAM1 and NSP1 were essential for the pre-symbiotic transcriptional reprogramming by Myc-LCOs, we propose that downstream of the CSSP, these GRAS transcription factors act synergistically in the transduction of those diffusible signals that pre-announce the presence of symbiotic fungi.
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Affiliation(s)
- Natalija Hohnjec
- Institut für Pflanzengenetik, Abt. IV - Pflanzengenomforschung, Leibniz Universität Hannover, Herrenhäuser Str. 2, D-30419, Hannover, Germany.
| | - Lisa F Czaja-Hasse
- Institut für Pflanzengenetik, Abt. IV - Pflanzengenomforschung, Leibniz Universität Hannover, Herrenhäuser Str. 2, D-30419, Hannover, Germany.
- Present address: Max Planck Genome Centre Cologne, Carl-von-Linné-Weg 10, D-50829, Köln, Germany.
| | - Claudia Hogekamp
- Institut für Pflanzengenetik, Abt. IV - Pflanzengenomforschung, Leibniz Universität Hannover, Herrenhäuser Str. 2, D-30419, Hannover, Germany.
| | - Helge Küster
- Institut für Pflanzengenetik, Abt. IV - Pflanzengenomforschung, Leibniz Universität Hannover, Herrenhäuser Str. 2, D-30419, Hannover, Germany.
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Wang T, Tohge T, Ivakov A, Mueller-Roeber B, Fernie AR, Mutwil M, Schippers JHM, Persson S. Salt-Related MYB1 Coordinates Abscisic Acid Biosynthesis and Signaling during Salt Stress in Arabidopsis. PLANT PHYSIOLOGY 2015; 169:1027-41. [PMID: 26243618 PMCID: PMC4587467 DOI: 10.1104/pp.15.00962] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/03/2015] [Indexed: 05/18/2023]
Abstract
Abiotic stresses, such as salinity, cause global yield loss of all major crop plants. Factors and mechanisms that can aid in plant breeding for salt stress tolerance are therefore of great importance for food and feed production. Here, we identified a MYB-like transcription factor, Salt-Related MYB1 (SRM1), that negatively affects Arabidopsis (Arabidopsis thaliana) seed germination under saline conditions by regulating the levels of the stress hormone abscisic acid (ABA). Accordingly, several ABA biosynthesis and signaling genes act directly downstream of SRM1, including SALT TOLERANT1/NINE-CIS-EPOXYCAROTENOID DIOXYGENASE3, RESPONSIVE TO DESICCATION26, and Arabidopsis NAC DOMAIN CONTAINING PROTEIN19. Furthermore, SRM1 impacts vegetative growth and leaf shape. We show that SRM1 is an important transcriptional regulator that directly targets ABA biosynthesis and signaling-related genes and therefore may be regarded as an important regulator of ABA-mediated salt stress tolerance.
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Affiliation(s)
- Ting Wang
- Max-Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (T.W., T.T., A.I., B.M.-R., A.R.F., M.M., J.H.M.S., S.P.);Molecular Biology, University of Potsdam, 14476 Potsdam, Germany (B.M.-R.);Institute of Biology I, Rheinisch-Westfälische Technische Hochschule Aachen University, 52074 Aachen, Germany (J.H.M.S.); andSchool of Biosciences, University of Melbourne, Parkville, Victoria 3010, Australia (S.P.)
| | - Takayuki Tohge
- Max-Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (T.W., T.T., A.I., B.M.-R., A.R.F., M.M., J.H.M.S., S.P.);Molecular Biology, University of Potsdam, 14476 Potsdam, Germany (B.M.-R.);Institute of Biology I, Rheinisch-Westfälische Technische Hochschule Aachen University, 52074 Aachen, Germany (J.H.M.S.); andSchool of Biosciences, University of Melbourne, Parkville, Victoria 3010, Australia (S.P.)
| | - Alexander Ivakov
- Max-Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (T.W., T.T., A.I., B.M.-R., A.R.F., M.M., J.H.M.S., S.P.);Molecular Biology, University of Potsdam, 14476 Potsdam, Germany (B.M.-R.);Institute of Biology I, Rheinisch-Westfälische Technische Hochschule Aachen University, 52074 Aachen, Germany (J.H.M.S.); andSchool of Biosciences, University of Melbourne, Parkville, Victoria 3010, Australia (S.P.)
| | - Bernd Mueller-Roeber
- Max-Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (T.W., T.T., A.I., B.M.-R., A.R.F., M.M., J.H.M.S., S.P.);Molecular Biology, University of Potsdam, 14476 Potsdam, Germany (B.M.-R.);Institute of Biology I, Rheinisch-Westfälische Technische Hochschule Aachen University, 52074 Aachen, Germany (J.H.M.S.); andSchool of Biosciences, University of Melbourne, Parkville, Victoria 3010, Australia (S.P.)
| | - Alisdair R Fernie
- Max-Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (T.W., T.T., A.I., B.M.-R., A.R.F., M.M., J.H.M.S., S.P.);Molecular Biology, University of Potsdam, 14476 Potsdam, Germany (B.M.-R.);Institute of Biology I, Rheinisch-Westfälische Technische Hochschule Aachen University, 52074 Aachen, Germany (J.H.M.S.); andSchool of Biosciences, University of Melbourne, Parkville, Victoria 3010, Australia (S.P.)
| | - Marek Mutwil
- Max-Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (T.W., T.T., A.I., B.M.-R., A.R.F., M.M., J.H.M.S., S.P.);Molecular Biology, University of Potsdam, 14476 Potsdam, Germany (B.M.-R.);Institute of Biology I, Rheinisch-Westfälische Technische Hochschule Aachen University, 52074 Aachen, Germany (J.H.M.S.); andSchool of Biosciences, University of Melbourne, Parkville, Victoria 3010, Australia (S.P.)
| | - Jos H M Schippers
- Max-Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (T.W., T.T., A.I., B.M.-R., A.R.F., M.M., J.H.M.S., S.P.);Molecular Biology, University of Potsdam, 14476 Potsdam, Germany (B.M.-R.);Institute of Biology I, Rheinisch-Westfälische Technische Hochschule Aachen University, 52074 Aachen, Germany (J.H.M.S.); andSchool of Biosciences, University of Melbourne, Parkville, Victoria 3010, Australia (S.P.)
| | - Staffan Persson
- Max-Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (T.W., T.T., A.I., B.M.-R., A.R.F., M.M., J.H.M.S., S.P.);Molecular Biology, University of Potsdam, 14476 Potsdam, Germany (B.M.-R.);Institute of Biology I, Rheinisch-Westfälische Technische Hochschule Aachen University, 52074 Aachen, Germany (J.H.M.S.); andSchool of Biosciences, University of Melbourne, Parkville, Victoria 3010, Australia (S.P.)
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Li X, Lawas LMF, Malo R, Glaubitz U, Erban A, Mauleon R, Heuer S, Zuther E, Kopka J, Hincha DK, Jagadish KSV. Metabolic and transcriptomic signatures of rice floral organs reveal sugar starvation as a factor in reproductive failure under heat and drought stress. PLANT, CELL & ENVIRONMENT 2015; 38:2171-92. [PMID: 25828772 DOI: 10.1111/pce.12545] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 03/22/2015] [Indexed: 05/18/2023]
Abstract
Heat and drought stress are projected to become major challenges to sustain rice (Oryza sativa L.) yields with global climate change. Both stresses lead to yield losses when they coincide with flowering. A significant knowledge gap exists in the mechanistic understanding of the responses of rice floral organs that determine reproductive success under stress. Our work connects the metabolomic and transcriptomic changes in anthers, pistils before pollination and pollinated pistils in a heat-tolerant (N22) and a heat-sensitive (Moroberekan) cultivar. Systematic analysis of the floral organs revealed contrasts in metabolic profiles across anthers and pistils. Constitutive metabolic markers were identified that can define reproductive success in rice under stress. Six out of nine candidate metabolites identified by intersection analysis of stressed anthers were differentially accumulated in N22 compared with Moroberekan under non-stress conditions. Sugar metabolism was identified to be the crucial metabolic and transcriptional component that differentiated floral organ tolerance or susceptibility to stress. While susceptible Moroberekan specifically showed high expression of the Carbon Starved Anthers (CSA) gene under combined heat and drought, tolerant N22 responded with high expression of genes encoding a sugar transporter (MST8) and a cell wall invertase (INV4) as markers of high sink strength.
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Affiliation(s)
- Xia Li
- Max-Planck-Institute of Molecular Plant Physiology, D-14476, Potsdam, Germany
| | - Lovely M F Lawas
- International Rice Research Institute, DAPO BOX. 7777, Manila, The Philippines
| | - Richard Malo
- International Rice Research Institute, DAPO BOX. 7777, Manila, The Philippines
| | - Ulrike Glaubitz
- Max-Planck-Institute of Molecular Plant Physiology, D-14476, Potsdam, Germany
| | - Alexander Erban
- Max-Planck-Institute of Molecular Plant Physiology, D-14476, Potsdam, Germany
| | - Ramil Mauleon
- International Rice Research Institute, DAPO BOX. 7777, Manila, The Philippines
| | - Sigrid Heuer
- International Rice Research Institute, DAPO BOX. 7777, Manila, The Philippines
| | - Ellen Zuther
- Max-Planck-Institute of Molecular Plant Physiology, D-14476, Potsdam, Germany
| | - Joachim Kopka
- Max-Planck-Institute of Molecular Plant Physiology, D-14476, Potsdam, Germany
| | - Dirk K Hincha
- Max-Planck-Institute of Molecular Plant Physiology, D-14476, Potsdam, Germany
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Gao Y, Zhang D, Li J. TCP1 Modulates DWF4 Expression via Directly Interacting with the GGNCCC Motifs in the Promoter Region of DWF4 in Arabidopsis thaliana. J Genet Genomics 2015; 42:383-92. [DOI: 10.1016/j.jgg.2015.04.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 03/30/2015] [Accepted: 04/01/2015] [Indexed: 01/09/2023]
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Jia F, Wan X, Zhu W, Sun D, Zheng C, Liu P, Huang J. Overexpression of Mitochondrial Phosphate Transporter 3 Severely Hampers Plant Development through Regulating Mitochondrial Function in Arabidopsis. PLoS One 2015; 10:e0129717. [PMID: 26076137 PMCID: PMC4468087 DOI: 10.1371/journal.pone.0129717] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 05/12/2015] [Indexed: 12/22/2022] Open
Abstract
Mitochondria are abundant and important organelles present in nearly all eukaryotic cells, which maintain metabolic communication with the cytosol through mitochondrial carriers. The mitochondrial membrane localized phosphate transporter (MPT) plays vital roles in diverse development and signaling processes, especially the ATP biosynthesis. Among the three MPT genes in Arabidopsis genome, AtMPT3 was proven to be a major member, and its overexpression gave rise to multiple developmental defects including curly leaves with deep color, dwarfed stature, and reduced fertility. Transcript profiles revealed that genes involved in plant metabolism, cellular redox homeostasis, alternative respiration pathway, and leaf and flower development were obviously altered in AtMPT3 overexpression (OEMPT3) plants. Moreover, OEMPT3 plants also accumulated higher ATP content, faster respiration rate and more reactive oxygen species (ROS) than wild type plants. Overall, our studies showed that AtMPT3 was indispensable for Arabidopsis normal growth and development, and provided new sights to investigate its possible regulation mechanisms.
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Affiliation(s)
- Fengjuan Jia
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, P.R. China
| | - Xiaomin Wan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, P.R. China
| | - Wei Zhu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, P.R. China
| | - Dan Sun
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, P.R. China
| | - Chengchao Zheng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, P.R. China
| | - Pei Liu
- College of Food Science and Engineering, Shandong Agricultural University, Taian, Shandong, P.R. China
- * E-mail: (PL); (JH)
| | - Jinguang Huang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, P.R. China
- * E-mail: (PL); (JH)
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27
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Saladié M, Cañizares J, Phillips MA, Rodriguez-Concepcion M, Larrigaudière C, Gibon Y, Stitt M, Lunn JE, Garcia-Mas J. Comparative transcriptional profiling analysis of developing melon (Cucumis melo L.) fruit from climacteric and non-climacteric varieties. BMC Genomics 2015; 16:440. [PMID: 26054931 PMCID: PMC4460886 DOI: 10.1186/s12864-015-1649-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 05/20/2015] [Indexed: 11/14/2022] Open
Abstract
Background In climacteric fruit-bearing species, the onset of fruit ripening is marked by a transient rise in respiration rate and autocatalytic ethylene production, followed by rapid deterioration in fruit quality. In non-climacteric species, there is no increase in respiration or ethylene production at the beginning or during fruit ripening. Melon is unusual in having climacteric and non-climacteric varieties, providing an interesting model system to compare both ripening types. Transcriptomic analysis of developing melon fruits from Védrantais and Dulce (climacteric) and Piel de sapo and PI 161375 (non-climacteric) varieties was performed to understand the molecular mechanisms that differentiate the two fruit ripening types. Results Fruits were harvested at 15, 25, 35 days after pollination and at fruit maturity. Transcript profiling was performed using an oligo-based microarray with 75 K probes. Genes linked to characteristic traits of fruit ripening were differentially expressed between climacteric and non-climacteric types, as well as several transcription factor genes and genes encoding enzymes involved in sucrose catabolism. The expression patterns of some genes in PI 161375 fruits were either intermediate between. Piel de sapo and the climacteric varieties, or more similar to the latter. PI 161375 fruits also accumulated some carotenoids, a characteristic trait of climacteric varieties. Conclusions Simultaneous changes in transcript abundance indicate that there is coordinated reprogramming of gene expression during fruit development and at the onset of ripening in both climacteric and non-climacteric fruits. The expression patterns of genes related to ethylene metabolism, carotenoid accumulation, cell wall integrity and transcriptional regulation varied between genotypes and was consistent with the differences in their fruit ripening characteristics. There were differences between climacteric and non-climacteric varieties in the expression of genes related to sugar metabolism suggesting that they may be potential determinants of sucrose content and post-harvest stability of sucrose levels in fruit. Several transcription factor genes were also identified that were differentially expressed in both types, implicating them in regulation of ripening behaviour. The intermediate nature of PI 161375 suggested that classification of melon fruit ripening behaviour into just two distinct types is an over-simplification, and that in reality there is a continuous spectrum of fruit ripening behaviour. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1649-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Montserrat Saladié
- IRTA, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain. .,Present address: School of Chemistry and Biochemistry, Biochemistry and Molecular Biology, The University of Western Australia, Crawley, WA, 6009, Australia.
| | - Joaquin Cañizares
- COMAV, Institute for the Conservation and Breeding of Agricultural Biodiversity, Universitat Politècnica de València (UPV), Camino de Vera s/n, Valencia, 46022, Spain.
| | - Michael A Phillips
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain.
| | - Manuel Rodriguez-Concepcion
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain.
| | - Christian Larrigaudière
- IRTA, Parc Científic i Tecnològic Agroalimentari, Parc de Gardeny, Edifici Fruitcentre, Lleida, 25003, Spain.
| | - Yves Gibon
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, Potsdam, 14476, (OT) Golm, Germany. .,Present address: INRA Bordeaux, University of Bordeaux, UMR1332 Fruit Biology and Pathology, Villenave d'Ornon, F-33883, France.
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, Potsdam, 14476, (OT) Golm, Germany.
| | - John Edward Lunn
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, Potsdam, 14476, (OT) Golm, Germany.
| | - Jordi Garcia-Mas
- IRTA, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain.
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Boudichevskaia A, Heckwolf M, Althaus L, Kaldenhoff R. Transcriptome analysis of the aquaporin AtPIP1;2 deficient line in Arabidopsis thaliana. GENOMICS DATA 2015; 4:162-4. [PMID: 26484207 PMCID: PMC4535893 DOI: 10.1016/j.gdata.2015.04.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 04/21/2015] [Indexed: 11/28/2022]
Abstract
Atmospheric CO2 impacts all aspects of plant development. It has changed in the past and is predicted to change further on. Studies on the response of crop plants to low and elevated CO2 concerning growth, productivity and physiological processes are intense. In contrast, the molecular mechanisms of cellular CO2 exchange are still under discussion. At the same time it becomes more and more accepted that carbon dioxide is transported across cellular biomembranes by CO2 conducting aquaporins. Our recent study (Boudichevskaia et al., 2015) demonstrates that the lack of a single gene product – aquaporin AtPIP1;2 – resulted in massive transcriptional reprogramming in Arabidopsis as a consequence of reduced tissue CO2 diffusion rates. Therefore, the transcriptome data of the aquaporin AtPIP1;2 deficient line can be used in the comparative expression analyses for better understanding the role of aquaporins with regard to CO2 and water transport in plants. Here we describe a gene expression dataset generated for three biological replicates per genotype on Affymetrix platform. We provide detailed methods and analysis on microarray data which has been deposited in Gene Expression Omnibus (GEO): GSE62167. Additionally, we provide the R code for data preprocessing and quality control.
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Affiliation(s)
- Anastassia Boudichevskaia
- Darmstadt University of Technology, Applied Plant Science, Schnittspahnstr. 10, D-64287 Darmstadt, Germany
| | - Marlies Heckwolf
- Darmstadt University of Technology, Applied Plant Science, Schnittspahnstr. 10, D-64287 Darmstadt, Germany ; Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53703, USA ; Department of Agronomy, University of Wisconsin, Madison, WI 53703, USA
| | - Lea Althaus
- Darmstadt University of Technology, Applied Plant Science, Schnittspahnstr. 10, D-64287 Darmstadt, Germany
| | - Ralf Kaldenhoff
- Darmstadt University of Technology, Applied Plant Science, Schnittspahnstr. 10, D-64287 Darmstadt, Germany
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Lima JM, Nath M, Dokku P, Raman KV, Kulkarni KP, Vishwakarma C, Sahoo SP, Mohapatra UB, Mithra SVA, Chinnusamy V, Robin S, Sarla N, Seshashayee M, Singh K, Singh AK, Singh NK, Sharma RP, Mohapatra T. Physiological, anatomical and transcriptional alterations in a rice mutant leading to enhanced water stress tolerance. AOB PLANTS 2015; 7:plv023. [PMID: 25818072 PMCID: PMC4482838 DOI: 10.1093/aobpla/plv023] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 02/26/2015] [Indexed: 05/04/2023]
Abstract
Water stress is one of the most severe constraints to crop productivity. Plants display a variety of physiological and biochemical responses both at the cellular and whole organism level upon sensing water stress. Leaf rolling, stomatal closure, deeper root penetration, higher relative water content (RWC) and better osmotic adjustment are some of the mechanisms that plants employ to overcome water stress. In the current study, we report a mutant, enhanced water stress tolerant1 (ewst1) with enhanced water stress tolerance, identified from the ethyl methanesulfonate-induced mutant population of rice variety Nagina22 by field screening followed by withdrawal of irrigation in pots and hydroponics (PEG 6000). Though ewst1 was morphologically similar to the wild type (WT) for 35 of the 38 morphological descriptors (except chalky endosperm/expression of white core, decorticated grain colour and grain weight), it showed enhanced germination in polyethylene glycol-infused medium. It exhibited increase in maximum root length without any significant changes in its root weight, root volume and total root number on crown when compared with the WT under stress in PVC tube experiment. It also showed better performance for various physiological parameters such as RWC, cell membrane stability and chlorophyll concentration upon water stress in a pot experiment. Root anatomy and stomatal microscopic studies revealed changes in the number of xylem and phloem cells, size of central meta-xylem and number of closed stomata in ewst1. Comparative genome-wide transcriptome analysis identified genes related to exocytosis, secondary metabolites, tryptophan biosynthesis, protein phosphorylation and other signalling pathways to be playing a role in enhanced response to water stress in ewst1. The possible involvement of a candidate gene with respect to the observed morpho-physiological and transcriptional changes and its role in stress tolerance are discussed. The mutant identified and characterized in this study will be useful for further dissection of water stress tolerance in rice.
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Affiliation(s)
- John Milton Lima
- National Research Centre on Plant Biotechnology, IARI, New Delhi, India Department of Botany, North Orissa University, Baripada, Odisha, India
| | - Manoj Nath
- National Research Centre on Plant Biotechnology, IARI, New Delhi, India
| | - Prasad Dokku
- National Research Centre on Plant Biotechnology, IARI, New Delhi, India
| | - K V Raman
- National Research Centre on Plant Biotechnology, IARI, New Delhi, India
| | - K P Kulkarni
- National Research Centre on Plant Biotechnology, IARI, New Delhi, India
| | - C Vishwakarma
- National Research Centre on Plant Biotechnology, IARI, New Delhi, India
| | - S P Sahoo
- National Research Centre on Plant Biotechnology, IARI, New Delhi, India
| | - U B Mohapatra
- Department of Botany, North Orissa University, Baripada, Odisha, India
| | - S V Amitha Mithra
- National Research Centre on Plant Biotechnology, IARI, New Delhi, India
| | - V Chinnusamy
- Indian Agricultural Research Institute, New Delhi, India
| | - S Robin
- Tamil Nadu Agricultural University, Coimbatore, India
| | - N Sarla
- Directorate of Rice Research, Hyderabad, India
| | - M Seshashayee
- University of Agricultural Sciences, Bangalore, India
| | - K Singh
- Punjab Agricultural University, Ludhiana, India
| | - A K Singh
- Indian Agricultural Research Institute, New Delhi, India
| | - N K Singh
- National Research Centre on Plant Biotechnology, IARI, New Delhi, India
| | - R P Sharma
- National Research Centre on Plant Biotechnology, IARI, New Delhi, India
| | - T Mohapatra
- National Research Centre on Plant Biotechnology, IARI, New Delhi, India Present address: Central Rice Research Institute, Cuttack, Odisha, India
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Li N, Gügel IL, Giavalisco P, Zeisler V, Schreiber L, Soll J, Philippar K. FAX1, a novel membrane protein mediating plastid fatty acid export. PLoS Biol 2015; 13:e1002053. [PMID: 25646734 PMCID: PMC4344464 DOI: 10.1371/journal.pbio.1002053] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 12/19/2014] [Indexed: 11/23/2022] Open
Abstract
Fatty acid synthesis in plants occurs in plastids, and thus, export for subsequent acyl editing and lipid assembly in the cytosol and endoplasmatic reticulum is required. Yet, the transport mechanism for plastid fatty acids still remains enigmatic. We isolated FAX1 (fatty acid export 1), a novel protein, which inserts into the chloroplast inner envelope by α-helical membrane-spanning domains. Detailed phenotypic and ultrastructural analyses of FAX1 mutants in Arabidopsis thaliana showed that FAX1 function is crucial for biomass production, male fertility and synthesis of fatty acid-derived compounds such as lipids, ketone waxes, or pollen cell wall material. Determination of lipid, fatty acid, and wax contents by mass spectrometry revealed that endoplasmatic reticulum (ER)-derived lipids decreased when FAX1 was missing, but levels of several plastid-produced species increased. FAX1 over-expressing lines showed the opposite behavior, including a pronounced increase of triacyglycerol oils in flowers and leaves. Furthermore, the cuticular layer of stems from fax1 knockout lines was specifically reduced in C29 ketone wax compounds. Differential gene expression in FAX1 mutants as determined by DNA microarray analysis confirmed phenotypes and metabolic imbalances. Since in yeast FAX1 could complement for fatty acid transport, we concluded that FAX1 mediates fatty acid export from plastids. In vertebrates, FAX1 relatives are structurally related, mitochondrial membrane proteins of so-far unknown function. Therefore, this protein family might represent a powerful tool not only to increase lipid/biofuel production in plants but also to explore novel transport systems involved in vertebrate fatty acid and lipid metabolism. The novel protein FAX1 mediates the export of free fatty acids across the inner membrane of chloroplasts so that they can be processed in other plant cell organelles to generate oils, waxes, and other lipids. Fatty acid synthesis in plants occurs in chloroplasts—the organelle more commonly known for conducting photosynthesis. For subsequent lipid assembly to be possible in the endoplasmatic reticulum (ER), export of these fatty acids across the chloroplast envelope membranes is required. The mechanism of this transport until now has not been known. We isolated FAX1 (fatty acid export 1), a novel membrane protein in chloroplast inner envelopes. FAX1 function is crucial for biomass production, male fertility, and the synthesis of fatty acid-derived compounds like lipids, waxes, or cell wall material of pollen grains. Whereas ER-derived lipids decreased when FAX1 was missing, levels of plastid-produced lipids increased. FAX1 over-expressing mutants showed the opposite behavior, including an increase of triacyglycerol oils. Because FAX1 could complement for fatty acid transport in yeast, we concluded that FAX1 mediates the export of free fatty acids from chloroplasts. In vertebrates, FAX1 relatives are structurally related proteins of so-far unknown function in mitochondria. This protein family may thus represent a powerful tool not only to increase lipid oil and biofuel production in plants but also to explore novel transport systems in animals.
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Affiliation(s)
- Nannan Li
- Biochemie und Physiologie der Pflanzen, Department Biologie I - Botanik, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Research Center of Bioenergy and Bioremediation RCBB, College of Resources and Environment, Southwest University, Beibei Dist., Chongqing, P.R. China
| | - Irene Luise Gügel
- Biochemie und Physiologie der Pflanzen, Department Biologie I - Botanik, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Munich Centre for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, München, Germany
| | - Patrick Giavalisco
- Max Planck Institut für Molekulare Pflanzenphysiologie MPIMP, Potsdam-Golm, Germany
| | - Viktoria Zeisler
- Institute of Cellular and Molecular Botany, Department of Ecophysiology, University of Bonn, Bonn, Germany
| | - Lukas Schreiber
- Institute of Cellular and Molecular Botany, Department of Ecophysiology, University of Bonn, Bonn, Germany
| | - Jürgen Soll
- Biochemie und Physiologie der Pflanzen, Department Biologie I - Botanik, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Munich Centre for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, München, Germany
| | - Katrin Philippar
- Biochemie und Physiologie der Pflanzen, Department Biologie I - Botanik, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Munich Centre for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, München, Germany
- * E-mail:
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31
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Le MQ, Pagter M, Hincha DK. Global changes in gene expression, assayed by microarray hybridization and quantitative RT-PCR, during acclimation of three Arabidopsis thaliana accessions to sub-zero temperatures after cold acclimation. PLANT MOLECULAR BIOLOGY 2015; 87:1-15. [PMID: 25311197 DOI: 10.1007/s11103-014-0256-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 10/07/2014] [Indexed: 05/20/2023]
Abstract
During cold acclimation plants increase in freezing tolerance in response to low non-freezing temperatures. This is accompanied by many physiological, biochemical and molecular changes that have been extensively investigated. In addition, plants of many species, including Arabidopsis thaliana, become more freezing tolerant during exposure to mild, non-damaging sub-zero temperatures after cold acclimation. There is hardly any information available about the molecular basis of this adaptation. Here, we have used microarrays and a qRT-PCR primer platform covering 1,880 genes encoding transcription factors (TFs) to monitor changes in gene expression in the Arabidopsis accessions Columbia-0, Rschew and Tenela during the first 3 days of sub-zero acclimation at -3 °C. The results indicate that gene expression during sub-zero acclimation follows a tighly controlled time-course. Especially AP2/EREBP and WRKY TFs may be important regulators of sub-zero acclimation, although the CBF signal transduction pathway seems to be less important during sub-zero than during cold acclimation. Globally, we estimate that approximately 5% of all Arabidopsis genes are regulated during sub-zero acclimation. Particularly photosynthesis-related genes are down-regulated and genes belonging to the functional classes of cell wall biosynthesis, hormone metabolism and RNA regulation of transcription are up-regulated. Collectively, these data provide the first global analysis of gene expression during sub-zero acclimation and allow the identification of candidate genes for forward and reverse genetic studies into the molecular mechanisms of sub-zero acclimation.
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Affiliation(s)
- Mai Q Le
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam, Germany
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32
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Jin X, Zimmermann J, Polle A, Fischer U. Auxin is a long-range signal that acts independently of ethylene signaling on leaf abscission in Populus. FRONTIERS IN PLANT SCIENCE 2015; 6:634. [PMID: 26322071 PMCID: PMC4532917 DOI: 10.3389/fpls.2015.00634] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 07/31/2015] [Indexed: 05/04/2023]
Abstract
Timing of leaf abscission is an important trait for biomass production and seasonal acclimation in deciduous trees. The signaling leading to organ separation, from the external cue (decreasing photoperiod) to ethylene-regulated hydrolysis of the middle lamellae in the abscission zone, is only poorly understood. Data from annual species indicate that the formation of an auxin gradient spanning the abscission zone regulates the timing of abscission. We established an experimental system in Populus to induce leaf shedding synchronously under controlled greenhouse conditions in order to test the function of auxin in leaf abscission. Here, we show that exogenous auxin delayed abscission of dark-induced leaves over short and long distances and that a new auxin response maximum preceded the formation of an abscission zone. Several auxin transporters were down-regulated during abscission and inhibition of polar auxin transport delayed leaf shedding. Ethylene signaling was not involved in the regulation of these auxin transporters and in the formation of an abscission zone, but was required for the expression of hydrolytic enzymes associated with cell separation. Since exogenous auxin delayed abscission in absence of ethylene signaling auxin likely acts independently of ethylene signaling on cell separation.
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Affiliation(s)
- Xu Jin
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural SciencesUmeå, Sweden
- Forest Botany and Tree Physiology, Georg-August University of GöttingenGöttingen, Germany
| | - Jorma Zimmermann
- Forest Botany and Tree Physiology, Georg-August University of GöttingenGöttingen, Germany
| | - Andrea Polle
- Forest Botany and Tree Physiology, Georg-August University of GöttingenGöttingen, Germany
| | - Urs Fischer
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural SciencesUmeå, Sweden
- Forest Botany and Tree Physiology, Georg-August University of GöttingenGöttingen, Germany
- *Correspondence: Urs Fischer, Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden,
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Scott IM, Ward JL, Miller SJ, Beale MH. Opposite variations in fumarate and malate dominate metabolic phenotypes of Arabidopsis salicylate mutants with abnormal biomass under chilling. PHYSIOLOGIA PLANTARUM 2014; 152:660-674. [PMID: 24735077 DOI: 10.1111/ppl.12210] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 03/12/2014] [Accepted: 03/13/2014] [Indexed: 06/03/2023]
Abstract
In chilling conditions (5°C), salicylic acid (SA)-deficient mutants (sid2, eds5 and NahG) of Arabidopsis thaliana produced more biomass than wild type (Col-0), whereas the SA overproducer cpr1 was extremely stunted. The hypothesis that these phenotypes were reflected in metabolism was explored using 600 MHz (1) H nuclear magnetic resonance (NMR) analysis of unfractionated polar shoot extracts. Biomass-related metabolic phenotypes were identified as multivariate data models of these NMR 'fingerprints'. These included principal components that correlated with biomass. Also, partial least squares-regression models were found to predict the relative size of plants in previously unseen experiments in different light intensities, or relative size of one genotype from the others. The dominant signal in these models was fumarate, which was high in SA-deficient mutants, intermediate in Col-0 and low in cpr1 at 5°C. Among signals negatively correlated with biomass, malate was prominent. Abundance of transcripts of the FUM2 cytosolic fumarase (At5g50950) showed strong positive correlation with fumarate levels and with biomass, whereas no significant differences were found for the FUM1 mitochondrial fumarase (At2g47510). It was confirmed that the morphological effects of SA under chilling find expression in the metabolome, with a role of fumarate highlighted.
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Affiliation(s)
- Ian M Scott
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, UK
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Schommer C, Debernardi JM, Bresso EG, Rodriguez RE, Palatnik JF. Repression of cell proliferation by miR319-regulated TCP4. MOLECULAR PLANT 2014; 7:1533-44. [PMID: 25053833 DOI: 10.1093/mp/ssu084] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Leaf development has been extensively studied on a genetic level. However, little is known about the interplay between the developmental regulators and the cell cycle machinery--a link that ultimately affects leaf form and size. miR319 is a conserved microRNA that regulates TCP transcription factors involved in multiple developmental pathways, including leaf development and senescence, organ curvature, and hormone biosynthesis and signaling. Here, we analyze the participation of TCP4 in the control of cell proliferation. A small increase in TCP4 activity has an immediate impact on leaf cell number, by significantly reducing cell proliferation. Plants with high TCP4 levels have a strong reduction in the expression of genes known to be active in G2-M phase of the cell cycle. Part of these effects is mediated by induction of miR396, which represses Growth-Regulating Factor (GRF) transcription factors. Detailed analysis revealed TCP4 to be a direct regulator of MIR396b. However, we found that TCP4 can control cell proliferation through additional pathways, and we identified a direct connection between TCP4 and ICK1/KRP1, a gene involved in the progression of the cell cycle. Our results show that TCP4 can activate different pathways that repress cell proliferation.
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Affiliation(s)
- Carla Schommer
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Argentina
| | - Juan M Debernardi
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Argentina
| | - Edgardo G Bresso
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Argentina
| | - Ramiro E Rodriguez
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Argentina
| | - Javier F Palatnik
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Argentina
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Debernardi JM, Mecchia MA, Vercruyssen L, Smaczniak C, Kaufmann K, Inze D, Rodriguez RE, Palatnik JF. Post-transcriptional control of GRF transcription factors by microRNA miR396 and GIF co-activator affects leaf size and longevity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:413-26. [PMID: 24888433 DOI: 10.1111/tpj.12567] [Citation(s) in RCA: 182] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 05/08/2014] [Accepted: 05/21/2014] [Indexed: 05/20/2023]
Abstract
The growth-regulating factors (GRFs) are plant-specific transcription factors. They form complexes with GRF-interacting factors (GIFs), a small family of transcriptional co-activators. In Arabidopsis thaliana, seven out of the nine GRFs are controlled by microRNA miR396. Analysis of Arabidopsis plants carrying a GRF3 allele insensitive to miR396 revealed a strong boost in the number of cells in leaves, which was further enhanced synergistically by an additional increase of GIF1 levels. Genetic experiments revealed that GRF3 can still increase cell number in gif1 mutants, albeit to a much lesser extent. Genome-wide transcript profiling indicated that the simultaneous increase of GRF3 and GIF1 levels causes additional effects in gene expression compared to either of the transgenes alone. We observed that GIF1 interacts in vivo with GRF3, as well as with chromatin-remodeling complexes, providing a mechanistic explanation for the synergistic activities of a GRF3-GIF1 complex. Interestingly, we found that, in addition to the leaf size, the GRF system also affects the organ longevity. Genetic and molecular analysis revealed that the functions of GRFs in leaf growth and senescence can be uncoupled, demonstrating that the miR396-GRF-GIF network impinges on different stages of leaf development. Our results integrate the post-transcriptional control of the GRF transcription factors with the progression of leaf development.
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Affiliation(s)
- Juan M Debernardi
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda, Rosario, Argentina
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Zander M, Thurow C, Gatz C. TGA Transcription Factors Activate the Salicylic Acid-Suppressible Branch of the Ethylene-Induced Defense Program by Regulating ORA59 Expression. PLANT PHYSIOLOGY 2014; 165:1671-1683. [PMID: 24989234 PMCID: PMC4119047 DOI: 10.1104/pp.114.243360] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 06/26/2014] [Indexed: 05/18/2023]
Abstract
Salicylic acid (SA), a hormone essential for defense against biotrophic pathogens, triggers increased susceptibility of plants against necrotrophic attackers by suppressing the jasmonic acid-ethylene (ET) defense response. Here, we show that this disease-promoting SA effect is abolished in plants lacking the three related TGACG sequence-specific binding proteins TGA2, TGA5, and TGA6 (class II TGAs). After treatment of plants with the ET precursor 1-aminocyclopropane-1-carboxylic acid (ACC), activation of all those genes that are suppressed by SA depended on class II TGAs. Rather than TGA binding sites, GCC-box motifs were significantly enriched in the corresponding promoters. GCC-box motifs are recognized by members of the superfamily of APETALA2/ETHYLENE RESPONSE FACTORs (ERFs). Of 11 activating ACC-induced APETALA2/ERFs, only ORA59 (for OCTADECANOID-RESPONSIVE ARABIDOPSIS APETALA2/ETHYLENE RESPONSE FACTOR domain protein59) and ERF96 were strongly suppressed by SA. ORA59 is the master regulator of the jasmonic acid-ET-induced defense program. ORA59 transcript levels do not reach maximal levels in the tga2 tga5 tga6 triple mutant, and this residual activity cannot be suppressed by SA. The ORA59 promoter contains an essential TGA binding site and is a direct target of class II TGAs as revealed by chromatin immunoprecipitation experiments. We suggest that class II TGAs at the ORA59 promoter constitute an important regulatory hub for the activation and SA suppression of ACC-induced genes.
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Affiliation(s)
- Mark Zander
- Molecular Biology and Physiology of Plants, Albrecht-von-Haller-Institute, Georg-August-University Goettingen, D-37077 Goettingen, Germany
| | - Corinna Thurow
- Molecular Biology and Physiology of Plants, Albrecht-von-Haller-Institute, Georg-August-University Goettingen, D-37077 Goettingen, Germany
| | - Christiane Gatz
- Molecular Biology and Physiology of Plants, Albrecht-von-Haller-Institute, Georg-August-University Goettingen, D-37077 Goettingen, Germany
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Babuin MF, Campestre MP, Rocco R, Bordenave CD, Escaray FJ, Antonelli C, Calzadilla P, Gárriz A, Serna E, Carrasco P, Ruiz OA, Menendez AB. Response to long-term NaHCO3-derived alkalinity in model Lotus japonicus Ecotypes Gifu B-129 and Miyakojima MG-20: transcriptomic profiling and physiological characterization. PLoS One 2014; 9:e97106. [PMID: 24835559 PMCID: PMC4024010 DOI: 10.1371/journal.pone.0097106] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 04/14/2014] [Indexed: 11/19/2022] Open
Abstract
The current knowledge regarding transcriptomic changes induced by alkalinity on plants is scarce and limited to studies where plants were subjected to the alkaline salt for periods not longer than 48 h, so there is no information available regarding the regulation of genes involved in the generation of a new homeostatic cellular condition after long-term alkaline stress. Lotus japonicus is a model legume broadly used to study many important physiological processes including biotic interactions and biotic and abiotic stresses. In the present study, we characterized phenotipically the response to alkaline stress of the most widely used L. japonicus ecotypes, Gifu B-129 and MG-20, and analyzed global transcriptome of plants subjected to 10 mM NaHCO3 during 21 days, by using the Affymetrix Lotus japonicus GeneChip®. Plant growth assessment, gas exchange parameters, chlorophyll a fluorescence transient (OJIP) analysis and metal accumulation supported the notion that MG-20 plants displayed a higher tolerance level to alkaline stress than Gifu B-129. Overall, 407 and 459 probe sets were regulated in MG-20 and Gifu B-129, respectively. The number of probe sets differentially expressed in roots was higher than that of shoots, regardless the ecotype. Gifu B-129 and MG-20 also differed in their regulation of genes that could play important roles in the generation of a new Fe/Zn homeostatic cellular condition, synthesis of plant compounds involved in stress response, protein-degradation, damage repair and root senescence, as well as in glycolysis, gluconeogenesis and TCA. In addition, there were differences between both ecotypes in the expression patterns of putative transcription factors that could determine distinct arrangements of flavonoid and isoflavonoid compounds. Our results provided a set of selected, differentially expressed genes deserving further investigation and suggested that the L. japonicus ecotypes could constitute a useful model to search for common and distinct tolerance mechanisms to long-term alkaline stress response in plants.
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Affiliation(s)
- María Florencia Babuin
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús/Universidad Nacional de General San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas (IIB-INTECH/UNSAM-CONICET), Chascomús, Argentina
| | - María Paula Campestre
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús/Universidad Nacional de General San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas (IIB-INTECH/UNSAM-CONICET), Chascomús, Argentina
| | - Rubén Rocco
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús/Universidad Nacional de General San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas (IIB-INTECH/UNSAM-CONICET), Chascomús, Argentina
| | - Cesar D. Bordenave
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús/Universidad Nacional de General San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas (IIB-INTECH/UNSAM-CONICET), Chascomús, Argentina
| | - Francisco J. Escaray
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús/Universidad Nacional de General San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas (IIB-INTECH/UNSAM-CONICET), Chascomús, Argentina
| | - Cristian Antonelli
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús/Universidad Nacional de General San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas (IIB-INTECH/UNSAM-CONICET), Chascomús, Argentina
| | - Pablo Calzadilla
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús/Universidad Nacional de General San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas (IIB-INTECH/UNSAM-CONICET), Chascomús, Argentina
| | - Andrés Gárriz
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús/Universidad Nacional de General San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas (IIB-INTECH/UNSAM-CONICET), Chascomús, Argentina
| | - Eva Serna
- Unidad Central de Investigación en Medicina-INCLIVA, Universitat de Valencia, Valencia, Spain
| | - Pedro Carrasco
- Departamento de Bioquímica y Biología Vegetal-Universitat de Valencia, Valencia, Spain
| | - Oscar A. Ruiz
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús/Universidad Nacional de General San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas (IIB-INTECH/UNSAM-CONICET), Chascomús, Argentina
| | - Ana B. Menendez
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús/Universidad Nacional de General San Martín-Consejo Nacional de Investigaciones Científicas y Técnicas (IIB-INTECH/UNSAM-CONICET), Chascomús, Argentina
- Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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Wiesner M, Schreiner M, Zrenner R. Functional identification of genes responsible for the biosynthesis of 1-methoxy-indol-3-ylmethyl-glucosinolate in Brassica rapa ssp. chinensis. BMC PLANT BIOLOGY 2014; 14:124. [PMID: 24886080 PMCID: PMC4108037 DOI: 10.1186/1471-2229-14-124] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 04/24/2014] [Indexed: 05/29/2023]
Abstract
BACKGROUND Brassica vegetables contain a class of secondary metabolites, the glucosinolates (GS), whose specific degradation products determine the characteristic flavor and smell. While some of the respective degradation products of particular GS are recognized as health promoting substances for humans, recent studies also show evidence that namely the 1-methoxy-indol-3-ylmethyl GS might be deleterious by forming characteristic DNA adducts. Therefore, a deeper knowledge of aspects involved in the biosynthesis of indole GS is crucial to design vegetables with an improved secondary metabolite profile. RESULTS Initially the leafy Brassica vegetable pak choi (Brassica rapa ssp. chinensis) was established as suitable tool to elicit very high concentrations of 1-methoxy-indol-3-ylmethyl GS by application of methyl jasmonate. Differentially expressed candidate genes were discovered in a comparative microarray analysis using the 2 × 104 K format Brassica Array and compared to available gene expression data from the Arabidopsis AtGenExpress effort. Arabidopsis knock out mutants of the respective candidate gene homologs were subjected to a comprehensive examination of their GS profiles and confirmed the exclusive involvement of polypeptide 4 of the cytochrome P450 monooxygenase subfamily CYP81F in 1-methoxy-indol-3-ylmethyl GS biosynthesis. Functional characterization of the two identified isoforms coding for CYP81F4 in the Brassica rapa genome was performed using expression analysis and heterologous complementation of the respective Arabidopsis mutant. CONCLUSIONS Specific differences discovered in a comparative microarray and glucosinolate profiling analysis enables the functional attribution of Brassica rapa ssp. chinensis genes coding for polypeptide 4 of the cytochrome P450 monooxygenase subfamily CYP81F to their metabolic role in indole glucosinolate biosynthesis. These new identified Brassica genes will enable the development of genetic tools for breeding vegetables with improved GS composition in the near future.
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Affiliation(s)
- Melanie Wiesner
- Leibniz-Institute of Vegetable and Ornamental Crops Grossbeeren and Erfurt e.V., Theodor-Echtermeyer-Weg 1, 14979 Grossbeeren, Germany
| | - Monika Schreiner
- Leibniz-Institute of Vegetable and Ornamental Crops Grossbeeren and Erfurt e.V., Theodor-Echtermeyer-Weg 1, 14979 Grossbeeren, Germany
| | - Rita Zrenner
- Leibniz-Institute of Vegetable and Ornamental Crops Grossbeeren and Erfurt e.V., Theodor-Echtermeyer-Weg 1, 14979 Grossbeeren, Germany
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Mor A, Koh E, Weiner L, Rosenwasser S, Sibony-Benyamini H, Fluhr R. Singlet oxygen signatures are detected independent of light or chloroplasts in response to multiple stresses. PLANT PHYSIOLOGY 2014; 165:249-61. [PMID: 24599491 PMCID: PMC4012584 DOI: 10.1104/pp.114.236380] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 03/03/2014] [Indexed: 05/18/2023]
Abstract
The production of singlet oxygen is typically associated with inefficient dissipation of photosynthetic energy or can arise from light reactions as a result of accumulation of chlorophyll precursors as observed in fluorescent (flu)-like mutants. Such photodynamic production of singlet oxygen is thought to be involved in stress signaling and programmed cell death. Here we show that transcriptomes of multiple stresses, whether from light or dark treatments, were correlated with the transcriptome of the flu mutant. A core gene set of 118 genes, common to singlet oxygen, biotic and abiotic stresses was defined and confirmed to be activated photodynamically by the photosensitizer Rose Bengal. In addition, induction of the core gene set by abiotic and biotic selected stresses was shown to occur in the dark and in nonphotosynthetic tissue. Furthermore, when subjected to various biotic and abiotic stresses in the dark, the singlet oxygen-specific probe Singlet Oxygen Sensor Green detected rapid production of singlet oxygen in the Arabidopsis (Arabidopsis thaliana) root. Subcellular localization of Singlet Oxygen Sensor Green fluorescence showed its accumulation in mitochondria, peroxisomes, and the nucleus, suggesting several compartments as the possible origins or targets for singlet oxygen. Collectively, the results show that singlet oxygen can be produced by multiple stress pathways and can emanate from compartments other than the chloroplast in a light-independent manner. The results imply that the role of singlet oxygen in plant stress regulation and response is more ubiquitous than previously thought.
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Schmitz J, Heinrichs L, Scossa F, Fernie AR, Oelze ML, Dietz KJ, Rothbart M, Grimm B, Flügge UI, Häusler RE. The essential role of sugar metabolism in the acclimation response of Arabidopsis thaliana to high light intensities. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:1619-36. [PMID: 24523502 PMCID: PMC3967092 DOI: 10.1093/jxb/eru027] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Retrograde signals from chloroplasts are thought to control the expression of nuclear genes associated with plastidial processes such as acclimation to varying light conditions. Arabidopsis mutants altered in the day and night path of photoassimilate export from the chloroplasts served as tools to study the involvement of carbohydrates in high light (HL) acclimation. A double mutant impaired in the triose phosphate/phosphate translocator (TPT) and ADP-glucose pyrophosphorylase (AGPase) (adg1-1/tpt-2) exhibits a HL-dependent depletion in endogenous carbohydrates combined with a severe growth and photosynthesis phenotype. The acclimation response of mutant and wild-type plants has been assessed in time series after transfer from low light (LL) to HL by analysing photosynthetic performance, carbohydrates, MgProtoIX (a chlorophyll precursor), and the ascorbate/glutathione redox system, combined with microarray-based transcriptomic and GC-MS-based metabolomic approaches. The data indicate that the accumulation of soluble carbohydrates (predominantly glucose) acts as a short-term response to HL exposure in both mutant and wild-type plants. Only if carbohydrates are depleted in the long term (e.g. after 2 d) is the acclimation response impaired, as observed in the adg1-1/tpt-2 double mutant. Furthermore, meta-analyses conducted with in-house and publicly available microarray data suggest that, in the long term, reactive oxygen species such as H₂O₂ can replace carbohydrates as signals. Moreover, a cross-talk exists between genes associated with the regulation of starch and lipid metabolism. The involvement of genes responding to phytohormones in HL acclimation appears to be less likely. Various candidate genes involved in retrograde control of nuclear gene expression emerged from the analyses of global gene expression.
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Affiliation(s)
- Jessica Schmitz
- Department of Botany II, Cologne Biocenter, University of Cologne, Zülpicher Straße 47b, D-50674 Cologne, Germany
- * Present address: Plant Molecular Physiology and Biotechnology, Heinrich-Heine-University, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Luisa Heinrichs
- Department of Botany II, Cologne Biocenter, University of Cologne, Zülpicher Straße 47b, D-50674 Cologne, Germany
| | - Federico Scossa
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam OT Golm, Germany
- Agriculture Research Council, Research Center for Vegetable Crops, Via Cavalleggeri 25, 84098 Pontecagnano (Salerno), Italy
| | - Alisdair R. Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam OT Golm, Germany
| | - Marie-Luise Oelze
- Biochemistry and Physiology of Plants, University of Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Karl-Josef Dietz
- Biochemistry and Physiology of Plants, University of Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Maxi Rothbart
- Institute of Biology, Plant Physiology, Humboldt-University Berlin, Philippstraße 13, D-10115 Berlin, Germany
| | - Bernhard Grimm
- Institute of Biology, Plant Physiology, Humboldt-University Berlin, Philippstraße 13, D-10115 Berlin, Germany
| | - Ulf-Ingo Flügge
- Department of Botany II, Cologne Biocenter, University of Cologne, Zülpicher Straße 47b, D-50674 Cologne, Germany
| | - Rainer E. Häusler
- Department of Botany II, Cologne Biocenter, University of Cologne, Zülpicher Straße 47b, D-50674 Cologne, Germany
- To whom correspondence should be addressed. E-mail:
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Díaz-Riquelme J, Martínez-Zapater JM, Carmona MJ. Transcriptional analysis of tendril and inflorescence development in grapevine (Vitis vinifera L.). PLoS One 2014; 9:e92339. [PMID: 24637773 PMCID: PMC3956920 DOI: 10.1371/journal.pone.0092339] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 02/21/2014] [Indexed: 11/19/2022] Open
Abstract
In grapevine (Vitis vinifera L.), the lateral meristem can give rise to either tendrils or inflorescences which are determined organs. To get insights into the processes of tendril and inflorescence development, we characterized the transcriptional variation taking place in both organs. The results of the global transcriptional analyses along tendril and inflorescence development suggested that these two homologous organs initially share a common transcriptional program related to cell proliferation and growth functions. In later developmental stages they showed organ specific gene expression programs related to the particular differentiation processes taking place in each organ. In this way, tendrils showed higher transcription of genes related to photosynthesis, hormone signaling and secondary metabolism than inflorescences, while inflorescences displayed higher transcriptional activity for genes encoding transcription factors, mainly those belonging to the MADS-box gene family. The expression profiles of selected transcription factors related with inflorescence and flower meristem identity and with flower organogenesis were generally conserved with respect to their homologs in model species. Regarding tendrils, it was interesting to find that genes related with reproductive development in other species were also recruited for grapevine tendril development. These results suggest a role for those genes in the regulation of basic cellular mechanisms common to both developmental processes.
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Affiliation(s)
- José Díaz-Riquelme
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), Logroño, España
| | - José M. Martínez-Zapater
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), Logroño, España
| | - María J. Carmona
- Departamento de Biotecnología, Escuela Técnica Superior Ingenieros Agrónomos, Universidad Politécnica de Madrid, Madrid, España
- * E-mail:
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Pokhilko A, Flis A, Sulpice R, Stitt M, Ebenhöh O. Adjustment of carbon fluxes to light conditions regulates the daily turnover of starch in plants: a computational model. MOLECULAR BIOSYSTEMS 2014; 10:613-27. [PMID: 24413396 DOI: 10.1039/c3mb70459a] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the light, photosynthesis provides carbon for metabolism and growth. In the dark, plant growth depends on carbon reserves that were accumulated during previous light periods. Many plants accumulate part of their newly-fixed carbon as starch in their leaves in the day and remobilise it to support metabolism and growth at night. The daily rhythms of starch accumulation and degradation are dynamically adjusted to the changing light conditions such that starch is almost but not totally exhausted at dawn. This requires the allocation of a larger proportion of the newly fixed carbon to starch under low carbon conditions, and the use of information about the carbon status at the end of the light period and the length of the night to pace the rate of starch degradation. This regulation occurs in a circadian clock-dependent manner, through unknown mechanisms. We use mathematical modelling to explore possible diurnal mechanisms regulating the starch level. Our model combines the main reactions of carbon fixation, starch and sucrose synthesis, starch degradation and consumption of carbon by sink tissues. To describe the dynamic adjustment of starch to daily conditions, we introduce diurnal regulators of carbon fluxes, which modulate the activities of the key steps of starch metabolism. The sensing of the diurnal conditions is mediated in our model by the timer α and the "dark sensor"β, which integrate daily information about the light conditions and time of the day through the circadian clock. Our data identify the β subunit of SnRK1 kinase as a good candidate for the role of the dark-accumulated component β of our model. The developed novel approach for understanding starch kinetics through diurnal metabolic and circadian sensors allowed us to explain starch time-courses in plants and predict the kinetics of the proposed diurnal regulators under various genetic and environmental perturbations.
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Affiliation(s)
- Alexandra Pokhilko
- Institute for Complex Systems and Mathematical Biology, University of Aberdeen, UK
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Kutyniok M, Viehhauser A, Vogel MO, Dietz KJ, Müller C. Local and systemic transcriptional responses to crosstalk between above- and belowground herbivores in Arabidopsis thaliana. PLANT SIGNALING & BEHAVIOR 2014; 9:e976113. [PMID: 25482783 PMCID: PMC4623459 DOI: 10.4161/15592324.2014.976113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Accepted: 08/08/2014] [Indexed: 06/04/2023]
Abstract
Plants are often simultaneously infested by several herbivores at the shoots and roots. Recent results revealed that the model plant Arabidopsis thaliana shows highly challenge-specific local and systemic responses to individual and simultaneous attacks of shoot-infesting aphids and root-infesting nematodes at the metabolome level. (1) Here, we present the corresponding transcriptional changes in plants treated with Brevicoryne brassicae aphids and Heterodera schachtii nematodes individually and in combination. Overall, shoots were much less responsive than roots. Gene expression in shoots and roots was mainly altered by aphids. Nematode infestation alone had only little effect, but nematodes modified the transcript accumulation response to aphids particularly in the roots. The responding genes are involved in plant defense cascades, signaling, oxidation-reduction processes, as well as primary and secondary metabolism and degradation. These changes in transcription may become relevant for the herbivores when they are translated into changes in host plant quality.
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Affiliation(s)
- Magdalene Kutyniok
- Department of Chemical Ecology; Bielefeld University; Bielefeld, Germany
| | - Andrea Viehhauser
- Department of Plant Biochemistry and Physiology; Bielefeld University; Bielefeld, Germany
| | - Marc Oliver Vogel
- Department of Plant Biochemistry and Physiology; Bielefeld University; Bielefeld, Germany
- Proteome- and Metabolome Research; Bielefeld University; Bielefeld, Germany
| | - Karl-Josef Dietz
- Department of Plant Biochemistry and Physiology; Bielefeld University; Bielefeld, Germany
| | - Caroline Müller
- Department of Chemical Ecology; Bielefeld University; Bielefeld, Germany
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Defense responses in two ecotypes of Lotus japonicus against non-pathogenic Pseudomonas syringae. PLoS One 2013; 8:e83199. [PMID: 24349460 PMCID: PMC3859661 DOI: 10.1371/journal.pone.0083199] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 10/30/2013] [Indexed: 11/20/2022] Open
Abstract
Lotus japonicus is a model legume broadly used to study many important processes as nitrogen fixing nodule formation and adaptation to salt stress. However, no studies on the defense responses occurring in this species against invading microorganisms have been carried out at the present. Understanding how this model plant protects itself against pathogens will certainly help to develop more tolerant cultivars in economically important Lotus species as well as in other legumes. In order to uncover the most important defense mechanisms activated upon bacterial attack, we explored in this work the main responses occurring in the phenotypically contrasting ecotypes MG-20 and Gifu B-129 of L. japonicus after inoculation with Pseudomonas syringae DC3000 pv. tomato. Our analysis demonstrated that this bacterial strain is unable to cause disease in these accessions, even though the defense mechanisms triggered in these ecotypes might differ. Thus, disease tolerance in MG-20 was characterized by bacterial multiplication, chlorosis and desiccation at the infiltrated tissues. In turn, Gifu B-129 plants did not show any symptom at all and were completely successful in restricting bacterial growth. We performed a microarray based analysis of these responses and determined the regulation of several genes that could play important roles in plant defense. Interestingly, we were also able to identify a set of defense genes with a relative high expression in Gifu B-129 plants under non-stress conditions, what could explain its higher tolerance. The participation of these genes in plant defense is discussed. Our results position the L. japonicus-P. syringae interaction as a interesting model to study defense mechanisms in legume species.
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Oliveira E, Casado M, Faria M, Soares AMVM, Navas JM, Barata C, Piña B. Transcriptomic response of zebrafish embryos to polyaminoamine (PAMAM) dendrimers. Nanotoxicology 2013; 8 Suppl 1:92-9. [PMID: 24266889 DOI: 10.3109/17435390.2013.858376] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The progressive practical applications of engineered nanoparticles results in their ever-increasing release into the environment. Accurate assessment of their environmental and health risks requires the development of methods allowing their monitoring in different environmental compartments and the evaluation of their potential toxicity at different levels of organization. Toxic effects of third-generation (G3) and fourth-generation (G4) poly(amidoamine) dendrimers (ethylenediamine cored, imine-terminated) were assessed on zebrafish embryos during the first two days post-fertilization. Particle characterization by dynamic light scattering showed no tendency to form aggregates in the assay conditions. G3 particles showed somewhat a higher acute toxicity than G4 particles, with LC50 values of 1.8 and 2.3 mg/L, respectively. At sublethal concentrations, both particles affected the zebrafish transcriptome following similar patterns, suggesting a similar mode of action. About 700 transcripts were affected by at least one of the treatments, following a pattern with significant correlations to the effects of bacterial infection in zebrafish embryos. We concluded that the response to G3 and G4 dendrimers was consistent with the activation of the innate immune response, a still unreported potential effect of these particles. These data may contribute to the characterization of hazards of these nanomaterials for both human health and the environment.
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Lee YP, Giorgi FM, Lohse M, Kvederaviciute K, Klages S, Usadel B, Meskiene I, Reinhardt R, Hincha DK. Transcriptome sequencing and microarray design for functional genomics in the extremophile Arabidopsis relative Thellungiella salsuginea (Eutrema salsugineum). BMC Genomics 2013; 14:793. [PMID: 24228715 PMCID: PMC3832907 DOI: 10.1186/1471-2164-14-793] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 11/11/2013] [Indexed: 11/29/2022] Open
Abstract
Background Most molecular studies of plant stress tolerance have been performed with Arabidopsis thaliana, although it is not particularly stress tolerant and may lack protective mechanisms required to survive extreme environmental conditions. Thellungiella salsuginea has attracted interest as an alternative plant model species with high tolerance of various abiotic stresses. While the T. salsuginea genome has recently been sequenced, its annotation is still incomplete and transcriptomic information is scarce. In addition, functional genomics investigations in this species are severely hampered by a lack of affordable tools for genome-wide gene expression studies. Results Here, we report the results of Thellungiella de novo transcriptome assembly and annotation based on 454 pyrosequencing and development and validation of a T. salsuginea microarray. ESTs were generated from a non-normalized and a normalized library synthesized from RNA pooled from samples covering different tissues and abiotic stress conditions. Both libraries yielded partially unique sequences, indicating their necessity to obtain comprehensive transcriptome coverage. More than 1 million sequence reads were assembled into 42,810 unigenes, approximately 50% of which could be functionally annotated. These unigenes were compared to all available Thellungiella genome sequence information. In addition, the groups of Late Embryogenesis Abundant (LEA) proteins, Mitogen Activated Protein (MAP) kinases and protein phosphatases were annotated in detail. We also predicted the target genes for 384 putative miRNAs. From the sequence information, we constructed a 44 k Agilent oligonucleotide microarray. Comparison of same-species and cross-species hybridization results showed superior performance of the newly designed array for T. salsuginea samples. The developed microarrays were used to investigate transcriptional responses of T. salsuginea and Arabidopsis during cold acclimation using the MapMan software. Conclusions This study provides the first comprehensive transcriptome information for the extremophile Arabidopsis relative T. salsuginea. The data constitute a more than three-fold increase in the number of publicly available unigene sequences and will greatly facilitate genome annotation. In addition, we have designed and validated the first genome-wide microarray for T. salsuginea, which will be commercially available. Together with the publicly available MapMan software this will become an important tool for functional genomics of plant stress tolerance.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Dirk K Hincha
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam, Germany.
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Blancquaert D, Van Daele J, Storozhenko S, Stove C, Lambert W, Van Der Straeten D. Rice folate enhancement through metabolic engineering has an impact on rice seed metabolism, but does not affect the expression of the endogenous folate biosynthesis genes. PLANT MOLECULAR BIOLOGY 2013; 83:329-49. [PMID: 23771598 DOI: 10.1007/s11103-013-0091-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 06/09/2013] [Indexed: 05/24/2023]
Abstract
Folates are key-players in one-carbon metabolism in all organisms. However, only micro-organisms and plants are able to synthesize folates de novo and humans rely entirely on their diet as a sole folate source. As a consequence, folate deficiency is a global problem. Although different strategies are currently implemented to fight folate deficiency, up until now, all of them have their own drawbacks. As an alternative and complementary means to those classical strategies, folate biofortification of rice by metabolic engineering was successfully achieved a couple of years ago. To gain more insight into folate biosynthesis regulation and the effect of folate enhancement on general rice seed metabolism, a transcriptomic study was conducted in developing transgenic rice seeds, overexpressing 2 genes of the folate biosynthetic pathway. Upon folate enhancement, the expression of 235 genes was significantly altered. Here, we show that rice folate biofortification has an important effect on folate dependent, seed developmental and plant stress response/defense processes, but does not affect the expression of the endogenous folate biosynthesis genes.
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Affiliation(s)
- Dieter Blancquaert
- Laboratory of Functional Plant Biology, Department of Physiology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
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Oliveira E, Casado M, Raldúa D, Soares A, Barata C, Piña B. Retinoic acid receptors' expression and function during zebrafish early development. J Steroid Biochem Mol Biol 2013; 138:143-51. [PMID: 23619336 DOI: 10.1016/j.jsbmb.2013.03.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 03/26/2013] [Accepted: 03/31/2013] [Indexed: 11/19/2022]
Abstract
Retinoic acid (RA) regulates many developmental processes through its binding to two types of nuclear receptors, the retinoic acid receptor (RAR), and the retinoid-X receptor (RXR), which preferentially binds to the 9-cis isomer. Here we analyzed the RAR/RXR regulatory system during the first 5 days of development of zebrafish. Analysis of the relative transcript abundances for the four RAR and the six RXR zebrafish genes present in the zebrafish genome indicates a transition from maternal to embryonic transcripts during the first 24h post fertilization. These changes did not affect the response to exogenous RA of the known RAR-responsive genes cyp26a1, dhrs3a, hoxb1b, hoxb5a, and hoxb5b. At the transcriptomic level, RA treatment elicited a negative feedback of genes involved in the endogenous RA synthesis and reduced levels of transcripts related to organ and anatomic development. These effects occurred at concentrations at which no morphological changes were observed. Data analysis suggests that exposure to exogenous RA results in an advance of the developing program, activating genes that should remain silent until later developmental stages and inhibiting expression of development-related genes. We conclude that zebrafish embryos are particularly sensitive to potential disruptors of the RAR/RXR regulatory system.
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Affiliation(s)
- Eva Oliveira
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Jordi Girona 18, 08034 Barcelona, Spain; CESAM & Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
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Rosenwasser S, Fluhr R, Joshi JR, Leviatan N, Sela N, Hetzroni A, Friedman H. ROSMETER: a bioinformatic tool for the identification of transcriptomic imprints related to reactive oxygen species type and origin provides new insights into stress responses. PLANT PHYSIOLOGY 2013; 163:1071-83. [PMID: 23922270 PMCID: PMC3793026 DOI: 10.1104/pp.113.218206] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Accepted: 07/31/2013] [Indexed: 05/19/2023]
Abstract
The chemical identity of the reactive oxygen species (ROS) and its subcellular origin will leave a specific imprint on the transcriptome response. In order to facilitate the appreciation of ROS signaling, we developed a tool that is tuned to qualify this imprint. Transcriptome data from experiments in Arabidopsis (Arabidopsis thaliana) for which the ROS type and organelle origin are known were compiled into indices and made accessible by a Web-based interface called ROSMETER. The ROSMETER algorithm uses a vector-based algorithm to portray the ROS signature for a given transcriptome. The ROSMETER platform was applied to identify the ROS signatures profiles in transcriptomes of senescing plants and of those exposed to abiotic and biotic stresses. An unexpected highly significant ROS transcriptome signature of mitochondrial stress was detected during the early presymptomatic stages of leaf senescence, which was accompanied by the specific oxidation of mitochondria-targeted redox-sensitive green fluorescent protein probe. The ROSMETER analysis of diverse stresses revealed both commonalties and prominent differences between various abiotic stress conditions, such as salt, cold, ultraviolet light, drought, heat, and pathogens. Interestingly, early responses to the various abiotic stresses clustered together, independent of later responses, and exhibited negative correlations to several ROS indices. In general, the ROS transcriptome signature of abiotic stresses showed limited correlation to a few indices, while biotic stresses showed broad correlation with multiple indices. The ROSMETER platform can assist in formulating hypotheses to delineate the role of ROS in plant acclimation to environmental stress conditions and to elucidate the molecular mechanisms of the oxidative stress response in plants.
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Shao N, Duan GY, Bock R. A mediator of singlet oxygen responses in Chlamydomonas reinhardtii and Arabidopsis identified by a luciferase-based genetic screen in algal cells. THE PLANT CELL 2013; 25:4209-26. [PMID: 24151292 PMCID: PMC3877789 DOI: 10.1105/tpc.113.117390] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
All cells produce reactive oxygen species (ROS) as by-products of their metabolism. In addition to being cytotoxic, ROS act as regulators of a wide range of developmental and physiological processes. Little is known about the molecular mechanisms underlying the perception of ROS and initiation of cellular responses in eukaryotes. Using the unicellular green alga Chlamydomonas reinhardtii, we developed a genetic screen for early components of singlet oxygen signaling. Here, we report the identification of a small zinc finger protein, methylene blue sensitivity (MBS), that is required for induction of singlet oxygen-dependent gene expression and, upon oxidative stress, accumulates in distinct granules in the cytosol. Loss-of-function mbs mutants produce singlet oxygen but are unable to fully respond to it at the level of gene expression. Knockout or knockdown of the homologous genes in the higher plant model Arabidopsis thaliana results in mutants that are hypersensitive to photooxidative stress, whereas overexpression produces plants with elevated stress tolerance. Together, our data indicate an important and evolutionarily conserved role of the MBS protein in ROS signaling and provide a strategy for engineering stress-tolerant plants.
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