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Osorio S, Alba R, Damasceno CM, Lopez-Casado G, Lohse M, Zanor MI, Tohge T, Usadel B, Rose JK, Fei Z, Giovannoni JJ, Fernie AR. Systems biology of tomato fruit development: combined transcript, protein, and metabolite analysis of tomato transcription factor (nor, rin) and ethylene receptor (Nr) mutants reveals novel regulatory interactions. Plant Physiol 2011; 157:405-25. [PMID: 21795583 PMCID: PMC3165888 DOI: 10.1104/pp.111.175463] [Citation(s) in RCA: 212] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 07/24/2011] [Indexed: 05/18/2023]
Abstract
Tomato (Solanum lycopersicum) is an established model to study fleshy fruit development and ripening. Tomato ripening is regulated independently and cooperatively by ethylene and transcription factors, including nonripening (NOR) and ripening-inhibitor (RIN). Mutations of NOR, RIN, and the ethylene receptor Never-ripe (Nr), which block ethylene perception and inhibit ripening, have proven to be great tools for advancing our understanding of the developmental programs regulating ripening. In this study, we present systems analysis of nor, rin, and Nr at the transcriptomic, proteomic, and metabolomic levels during development and ripening. Metabolic profiling marked shifts in the abundance of metabolites of primary metabolism, which lead to decreases in metabolic activity during ripening. When combined with transcriptomic and proteomic data, several aspects of the regulation of metabolism during ripening were revealed. First, correlations between the expression levels of a transcript and the abundance of its corresponding protein were infrequently observed during early ripening, suggesting that posttranscriptional regulatory mechanisms play an important role in these stages; however, this correlation was much greater in later stages. Second, we observed very strong correlation between ripening-associated transcripts and specific metabolite groups, such as organic acids, sugars, and cell wall-related metabolites, underlining the importance of these metabolic pathways during fruit ripening. These results further revealed multiple ethylene-associated events during tomato ripening, providing new insights into the molecular biology of ethylene-mediated ripening regulatory networks.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany (S.O., M.L., M.I.Z., T.T., B.U., A.R.F.); Boyce Thompson Institute for Plant Research and United States Department of Agriculture-Agricultural Research Service Robert W. Holley Center (R.A., Z.F., J.J.G.) and Department of Plant Biology (C.M.B.D., G.L.-C., J.K.C.R.), Cornell University, Ithaca, New York 14853
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Zanor MI, Rambla JL, Chaïb J, Steppa A, Medina A, Granell A, Fernie AR, Causse M. Metabolic characterization of loci affecting sensory attributes in tomato allows an assessment of the influence of the levels of primary metabolites and volatile organic contents. J Exp Bot 2009; 60:2139-54. [PMID: 19346240 PMCID: PMC2682503 DOI: 10.1093/jxb/erp086] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2009] [Revised: 03/02/2009] [Accepted: 03/02/2009] [Indexed: 05/18/2023]
Abstract
Numerous studies have revealed the extent of genetic and phenotypic variation between both species and cultivars of tomato. Using a series of tomato lines resulting from crosses between a cherry tomato and three independent large fruit cultivar (Levovil, VilB, and VilD), extensive profiling of both central primary metabolism and volatile organic components of the fruit was performed. In this study, it was possible to define a number of quantitative trait loci (QTLs) which determined the levels of primary metabolites and/or volatile organic components and to evaluate their co-location with previously defined organoleptic QTLs. Correlation analyses between either the primary metabolites or the volatile organic compounds and organoleptic properties revealed a number of interesting associations, including pharmaceutical aroma-guaiacol and sourness-alanine, across the data set. Considerable correlation within the levels of primary metabolites or volatile organic compounds, respectively, were also observed. However, there was relatively little association between the levels of primary metabolites and volatile organic compounds, implying that they are not tightly linked to one another. A notable exception to this was the strong association between the levels of sucrose and those of a number of volatile organic compounds. The combined data presented here are thus discussed both with respect to those obtained recently from wide interspecific crosses of tomato and within the framework of current understanding of the chemical basis of fruit taste.
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Affiliation(s)
- Maria Inés Zanor
- Max-Planck-Institute for Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - José-Luis Rambla
- Universidad Politecnica Valencia, CSIC, Instituto de Biología Molecular y Celular Plantas (IBMCP), Avda de los Naranjos s/n, Valencia 46022, Spain
| | - Jamila Chaïb
- INRA, UR1052, Unité de Génétique et Amélioration des Fruits et Légumes, Domaine Saint-Maurice, BP94, F-84143 Montfavet Cedex, France
| | - Agnes Steppa
- Max-Planck-Institute for Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Aurora Medina
- Universidad Politecnica Valencia, CSIC, Instituto de Biología Molecular y Celular Plantas (IBMCP), Avda de los Naranjos s/n, Valencia 46022, Spain
| | - Antonio Granell
- Universidad Politecnica Valencia, CSIC, Instituto de Biología Molecular y Celular Plantas (IBMCP), Avda de los Naranjos s/n, Valencia 46022, Spain
| | - Alisdair R. Fernie
- Max-Planck-Institute for Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
- To whom correspondence should be addressed. E-mail:
| | - Mathilde Causse
- INRA, UR1052, Unité de Génétique et Amélioration des Fruits et Légumes, Domaine Saint-Maurice, BP94, F-84143 Montfavet Cedex, France
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Falkenberg B, Witt I, Zanor MI, Steinhauser D, Mueller-Roeber B, Hesse H, Hoefgen R. Transcription factors relevant to auxin signalling coordinate broad-spectrum metabolic shifts including sulphur metabolism. J Exp Bot 2008; 59:2831-46. [PMID: 18596113 PMCID: PMC2486478 DOI: 10.1093/jxb/ern144] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Revised: 04/22/2008] [Accepted: 04/28/2008] [Indexed: 05/18/2023]
Abstract
A systems approach has previously been used to follow the response behaviour of Arabidopsis thaliana plants upon sulphur limitation. A response network was reconstructed from a time series of transcript and metabolite profiles, integrating complex metabolic and transcript data in order to investigate a potential causal relationship. The resulting scale-free network allowed potential transcriptional regulators of sulphur metabolism to be identified. Here, three sulphur-starvation responsive transcription factors, IAA13, IAA28, and ARF-2 (ARF1-Binding Protein), all of which are related to auxin signalling, were selected for further investigation. IAA28 overexpressing and knock-down lines showed no major morphological changes, whereas IAA13- and ARF1-BP-overexpressing plants grew more slowly than the wild type. Steady-state metabolite levels and expression of pathway-relevant genes were monitored under normal and sulphate-depleted conditions. For all lines, changes in transcript and metabolite levels were observed, yet none of these changes could exclusively be linked to sulphur stress. Instead, up- or down-regulation of the transcription factors caused metabolic changes which in turn affected sulphur metabolism. Auxin-relevant transcription factors are thus part of a complex response pattern to nutrient starvation that serve as coordinators of the metabolic shifts driving sulphur homeostasis rather then as direct effectors of the sulphate assimilation pathway. This study provides the first evidence ever presented that correlates auxin-related transcriptional regulators with primary plant metabolism.
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Affiliation(s)
- Bettina Falkenberg
- Max-Planck-Institut fuer Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, 14424 Potsdam, Germany
| | - Isabell Witt
- Max-Planck-Institut fuer Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, 14424 Potsdam, Germany
| | - Maria Inés Zanor
- Max-Planck-Institut fuer Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, 14424 Potsdam, Germany
| | - Dirk Steinhauser
- Max-Planck-Institut fuer Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, 14424 Potsdam, Germany
| | - Bernd Mueller-Roeber
- Universität Potsdam, Institut fuer Biochemie und Biologie, Karl-Liebknecht-Str. 24–25, Haus 20, 14476 Potsdam-Golm, Germany
| | - Holger Hesse
- Max-Planck-Institut fuer Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, 14424 Potsdam, Germany
- To whom correspondence should be addressed. E-mail:
| | - Rainer Hoefgen
- Max-Planck-Institut fuer Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, 14424 Potsdam, Germany
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Skirycz A, Jozefczuk S, Stobiecki M, Muth D, Zanor MI, Witt I, Mueller-Roeber B. Transcription factor AtDOF4;2 affects phenylpropanoid metabolism in Arabidopsis thaliana. New Phytol 2007; 175:425-438. [PMID: 17635218 DOI: 10.1111/j.1469-8137.2007.02129.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
In a phenotypic screen of plants constitutively overexpressing DOF (DNA-binding-with-one-finger) transcription factors under the control of the Cauliflower mosaic virus 35S promoter, AtDOF4;2 was identified as a gene inducing a bushy plant phenotype and potentially being involved in the regulation of phenylpropanoid metabolism in Arabidopsis. Further molecular and biochemical characterization was performed in parallel using transgenic plants with enhanced and reduced AtDOF4;2 expression. The expression pattern of AtDOF4;2 was determined by quantitative real-time polymerase chain reaction (Q-RTPCR) and through promoter-beta-glucuronidase (GUS) fusions, indicating preferential transcriptional activity in axillary buds of the flower stalk, the hypocotyls periderm and in tapetum cells. Constitutive overexpression and RNAi-mediated silencing of AtDOF4;2 caused reciprocal changes in the expression of flavonoid biosynthetic genes and the accumulation of flavonoids under cold and high-light conditions. Moreover, tapetum-specific overexpression of AtDOF4;2 led to pollen grains devoid of flavonols. In contrast to its negative influence on flavonoid biosynthesis and coincident with high expression in the periderm and tapetum, AtDOF4;2 positively influences the production of hydroxycinnamic acids in the hypocotyl and flower buds, implicating its possible importance for suberin and sporopollenin production. These data provide evidence that AtDOF4;2, influences phenylpropanoid metabolism in an environmental and tissue-specific manner.
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Affiliation(s)
- Aleksandra Skirycz
- Max-Planck Institute of Molecular Plant Physiology, Cooperative Research Group, Am Mühlenberg 1, D-14476 Potsdam, Germany
- University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Szymon Jozefczuk
- Max-Planck Institute of Molecular Plant Physiology, Cooperative Research Group, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | - Maciej Stobiecki
- Institute of Bioorganic Chemistry PAS, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Dorota Muth
- Institute of Bioorganic Chemistry PAS, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Maria Inés Zanor
- Max-Planck Institute of Molecular Plant Physiology, Cooperative Research Group, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | - Isabell Witt
- Max-Planck Institute of Molecular Plant Physiology, Cooperative Research Group, Am Mühlenberg 1, D-14476 Potsdam, Germany
- University of Cologne Zülpicher Straße 47 D-50674 Cologne, Germany
| | - Bernd Mueller-Roeber
- Max-Planck Institute of Molecular Plant Physiology, Cooperative Research Group, Am Mühlenberg 1, D-14476 Potsdam, Germany
- University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
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Kersten B, Feilner T, Kramer A, Wehrmeyer S, Possling A, Witt I, Zanor MI, Stracke R, Lueking A, Kreutzberger J, Lehrach H, Cahilll DJ. Generation of Arabidopsis protein chips for antibody and serum screening. Plant Mol Biol 2003; 52:999-1010. [PMID: 14558660 DOI: 10.1023/a:1025424814739] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Protein array technology has emerged as a new tool to enable ordered screening of proteins for expression and molecular interactions in high throughput. Besides classical solid-phase substrates, such as micro-titre plates and membrane filters, protein arrays have recently been devised with chip-sized supports. Several applications on protein chips have been described, but to our knowledge no studies using plant protein chips were published so far. The aim of this study was to generate Arabidopsis protein chips and to demonstrate the feasibility of the protein chip technology for the investigation of antigen-antibody interactions. Therefore, Arabidopsis cDNAs encoding 95 different proteins were cloned into a GATEWAY-compatible Escherichia coli expression vector. RGS-His6-tagged recombinant proteins were purified in high throughput and robotically arrayed onto glass slides coated either with a nitrocellulose based polymer (FAST slides) or polyacrylamide (PAA slides). Using an anti-RGS-His6 antibody all proteins were detected on the chips. The detection limit was ca. 2-3.6 fmol per spot on FAST slides or 0.1-1.8 fmol per spot on PAA slides. The Arabidopsis protein chips were used for the characterisation of monoclonal antibodies or polyclonal sera. We were able to show that a monoclonal anti-TCP1 antibody and anti-MYB6 and anti-DOF11 sera bound specifically to their respective antigens and did not cross-react with the other 94 proteins including other DOF and MYB transcription factors on the chips. To enable screening of antibodies or other interacting molecules against thousands of Arabidopsis proteins in future, we generated an ordered cDNA expression library and started with high-throughput cloning of full-length cDNAs with GATEWAY technology.
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Affiliation(s)
- B Kersten
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany.
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Abstract
A beta-1,3-glucanase gene from Hordeum vulgare was isolated by a PCR strategy, cloned and subsequently sequenced. The amplified sequence contained the entire coding region of the isoenzyme II, which is interrupted by a 165 bp intron at 73 bp downstream the starting codon. This intron contains all the elements required for the processing mechanism in monocots: a high A + U content, the appropriate splice sites in the 5' and 3' ends and four typical YUNAN consensus sequences. Transient transformation of wheat protoplasts with the complete beta-1,3-glucanase gene under the control of maize polyubiquitin promoter revealed that the intron sequence was spliced out. The gene was also expressed at high levels, probably due to an enhancer-like sequence found near the 3' end of the intron.
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MESH Headings
- Base Sequence
- Blotting, Northern
- DNA, Plant/chemistry
- DNA, Plant/genetics
- DNA, Plant/isolation & purification
- Exons
- Gene Expression Regulation, Enzymologic
- Gene Expression Regulation, Plant
- Genes, Plant/genetics
- Glucan 1,3-beta-Glucosidase
- Hordeum/enzymology
- Hordeum/genetics
- Introns
- Isoenzymes/genetics
- Molecular Sequence Data
- Promoter Regions, Genetic/genetics
- Protoplasts/enzymology
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Sequence Analysis, DNA
- Triticum
- Ubiquitins/genetics
- Zea mays
- beta-Glucosidase/genetics
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Affiliation(s)
- M I Zanor
- Centro de Estudíos Fotosintéticos y Bioquímicos, Instituto de Biología Molecular y Celular de Rosario, CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, UNR, Argentina
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