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Herrmann S, Recht S, Boenn M, Feldhahn L, Angay O, Fleischmann F, Tarkka MT, Grams TEE, Buscot F. Endogenous rhythmic growth in oak trees is regulated by internal clocks rather than resource availability. J Exp Bot 2015; 66:7113-27. [PMID: 26320242 PMCID: PMC4765786 DOI: 10.1093/jxb/erv408] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Common oak trees display endogenous rhythmic growth with alternating shoot and root flushes. To explore the mechanisms involved, microcuttings of the Quercus robur L. clone DF159 were used for (13)C/(15)N labelling in combination with RNA sequencing (RNASeq) transcript profiling of shoots and roots. The effect of plant internal resource availability on the rhythmic growth of the cuttings was tested through inoculation with the ectomycorrhizal fungus Piloderma croceum. Shoot and root flushes were related to parallel shifts in above- and below-ground C and, to a lesser extent, N allocation. Increased plant internal resource availability by P. croceum inoculation with enhanced plant growth affected neither the rhythmic growth nor the associated resource allocation patterns. Two shifts in transcript abundance were identified during root and shoot growth cessation, and most concerned genes were down-regulated. Inoculation with P. croceum suppressed these transcript shifts in roots, but not in shoots. To identify core processes governing the rhythmic growth, functions [Gene Ontology (GO) terms] of the genes differentially expressed during the growth cessation in both leaves and roots of non-inoculated plants and leaves of P. croceum-inoculated plants were examined. Besides genes related to resource acquisition and cell development, which might reflect rather than trigger rhythmic growth, genes involved in signalling and/or regulated by the circadian clock were identified. The results indicate that rhythmic growth involves dramatic oscillations in plant metabolism and gene regulation between below- and above-ground parts. Ectomycorrhizal symbiosis may play a previously unsuspected role in smoothing these oscillations without modifying the rhythmic growth pattern.
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Affiliation(s)
- S Herrmann
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, D-06120 Halle/Saale, Germany Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research,Theodor-Lieser-Str. 4, D-06120 Halle/Saale, Germany German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103 Leipzig, Germany
| | - S Recht
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, D-06120 Halle/Saale, Germany
| | - M Boenn
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, D-06120 Halle/Saale, Germany
| | - L Feldhahn
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, D-06120 Halle/Saale, Germany
| | - O Angay
- Section Pathology of Woody Plants, Technische Universität München, Hans-Carl-von-Carlowitz-Platz 2, D-85354 Freising, Germany Ecophysiology of Plants, Technische Universität München, Hans-Carl-von-Carlowitz-Platz 2, D-85354 Freising, Germany
| | - F Fleischmann
- Section Pathology of Woody Plants, Technische Universität München, Hans-Carl-von-Carlowitz-Platz 2, D-85354 Freising, Germany
| | - M T Tarkka
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, D-06120 Halle/Saale, Germany German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103 Leipzig, Germany
| | - T E E Grams
- Ecophysiology of Plants, Technische Universität München, Hans-Carl-von-Carlowitz-Platz 2, D-85354 Freising, Germany
| | - F Buscot
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, D-06120 Halle/Saale, Germany German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103 Leipzig, Germany
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Angay O, Fleischmann F, Recht S, Herrmann S, Matyssek R, Oßwald W, Buscot F, Grams TEE. Sweets for the foe - effects of nonstructural carbohydrates on the susceptibility of Quercus robur against Phytophthora quercina. New Phytol 2014; 203:1282-1290. [PMID: 24902781 DOI: 10.1111/nph.12876] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [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: 03/18/2014] [Accepted: 04/30/2014] [Indexed: 05/10/2023]
Abstract
The root-rot pathogen Phytophthora quercina is a key determinant of oak decline in Europe. The susceptibility of pedunculate oak (Quercus robur) to this pathogen has been hypothesized to depend on the carbon availability in roots as an essential resource for defense. Microcuttings of Q. robur undergo an alternating rhythm of root and shoot growth. Inoculation of mycorrhizal (Piloderma croceum) and nonmycorrhizal oak roots with P. quercina was performed during both growth phases, that is, root flush (RF) and shoot flush (SF). Photosynthetic and morphological responses as well as concentrations of nonstructural carbohydrates (NSC) were analyzed. Infection success was quantified by the presence of pathogen DNA in roots. Concentrations of NSC in roots depended on the alternating root/shoot growth rhythm, being high and low during RF and SF, respectively. Infection success was high during RF and low during SF, resulting in a significantly positive correlation between pathogen DNA and NSC concentration in roots, contrary to the hypothesis. The alternating growth of roots and shoots plays a crucial role for the susceptibility of lateral roots to the pathogen. NSC availability in oak roots has to be considered as a benchmark for susceptibility rather than resistance against P. quercina.
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Affiliation(s)
- Oguzhan Angay
- Ecophysiology of Plants, Technische Universität München, Hans-Carl-von-Carlowitz-Platz 2, 85354, Freising, Germany
- Section Pathology of Woody Plants, Technische Universität München, Hans-Carl-von-Carlowitz-Platz 2, 85354, Freising, Germany
| | - Frank Fleischmann
- Section Pathology of Woody Plants, Technische Universität München, Hans-Carl-von-Carlowitz-Platz 2, 85354, Freising, Germany
| | - Sabine Recht
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Strasse 4, Halle, Germany
| | - Sylvie Herrmann
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Strasse 4, Halle, Germany
- Department of Community Ecology, UFZ - Helmholtz Centre for Enviromental Research, Theodor-Lieser-Str. 4, 06120, Halle/Saale, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Deutscher Platz 5e, 04103, Leipzig, Germany
| | - Rainer Matyssek
- Ecophysiology of Plants, Technische Universität München, Hans-Carl-von-Carlowitz-Platz 2, 85354, Freising, Germany
| | - Wolfgang Oßwald
- Section Pathology of Woody Plants, Technische Universität München, Hans-Carl-von-Carlowitz-Platz 2, 85354, Freising, Germany
| | - François Buscot
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Strasse 4, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Deutscher Platz 5e, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, Johannisallee 21-23, 04103, Leipzig, Germany
| | - Thorsten E E Grams
- Ecophysiology of Plants, Technische Universität München, Hans-Carl-von-Carlowitz-Platz 2, 85354, Freising, Germany
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Tarkka MT, Herrmann S, Wubet T, Feldhahn L, Recht S, Kurth F, Mailänder S, Bönn M, Neef M, Angay O, Bacht M, Graf M, Maboreke H, Fleischmann F, Grams TEE, Ruess L, Schädler M, Brandl R, Scheu S, Schrey SD, Grosse I, Buscot F. OakContigDF159.1, a reference library for studying differential gene expression in Quercus robur during controlled biotic interactions: use for quantitative transcriptomic profiling of oak roots in ectomycorrhizal symbiosis. New Phytol 2013; 199:529-540. [PMID: 23672230 DOI: 10.1111/nph.12317] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 04/02/2013] [Indexed: 05/09/2023]
Abstract
Oaks (Quercus spp.), which are major forest trees in the northern hemisphere, host many biotic interactions, but molecular investigation of these interactions is limited by fragmentary genome data. To date, only 75 oak expressed sequence tags (ESTs) have been characterized in ectomycorrhizal (EM) symbioses. We synthesized seven beneficial and detrimental biotic interactions between microorganisms and animals and a clone (DF159) of Quercus robur. Sixteen 454 and eight Illumina cDNA libraries from leaves and roots were prepared and merged to establish a reference for RNA-Seq transcriptomic analysis of oak EMs with Piloderma croceum. Using the Mimicking Intelligent Read Assembly (MIRA) and Trinity assembler, the OakContigDF159.1 hybrid assembly, containing 65 712 contigs with a mean length of 1003 bp, was constructed, giving broad coverage of metabolic pathways. This allowed us to identify 3018 oak contigs that were differentially expressed in EMs, with genes encoding proline-rich cell wall proteins and ethylene signalling-related transcription factors showing up-regulation while auxin and defence-related genes were down-regulated. In addition to the first report of remorin expression in EMs, the extensive coverage provided by the study permitted detection of differential regulation within large gene families (nitrogen, phosphorus and sugar transporters, aquaporins). This might indicate specific mechanisms of genome regulation in oak EMs compared with other trees.
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Affiliation(s)
- Mika T Tarkka
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle/Saale, Germany
| | - Sylvie Herrmann
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle/Saale, Germany
- Department of Community Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle/Saale, Germany
| | - Tesfaye Wubet
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle/Saale, Germany
| | - Lasse Feldhahn
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle/Saale, Germany
- Institute of Computer Science, Martin-Luther University, Von-Seckendorff-Platz 1, 06120, Halle/Saale, Germany
| | - Sabine Recht
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle/Saale, Germany
| | - Florence Kurth
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle/Saale, Germany
| | - Sarah Mailänder
- IMIT-Physiological Ecology of Plants, Auf der Morgenstelle 1, 72076, Tübingen, Germany
| | - Markus Bönn
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle/Saale, Germany
- Institute of Computer Science, Martin-Luther University, Von-Seckendorff-Platz 1, 06120, Halle/Saale, Germany
| | - Maren Neef
- IMIT-Physiological Ecology of Plants, Auf der Morgenstelle 1, 72076, Tübingen, Germany
| | - Oguzhan Angay
- Section Pathology of Woody Plants, Technische Universität München, Hans-Carl-von-Carlowitz-Platz 2, 85354, Freising, Germany
- TEEG: Ecophysiology of Plants, Technische Universität München, Hans-Carl-von-Carlowitz-Platz 2, 85354, Freising, Germany
| | - Michael Bacht
- Animal Ecology, Department of Ecology, Faculty of Biology, Philipps-Universität Marburg, Karl-von-Frisch Str. 8, 35032, Marburg, Germany
| | - Marcel Graf
- J.F. Blumenbach Institute of Zoology and Anthropology, Georg August University Göttingen, Berliner Str. 28, 37073, Göttingen, Germany
| | - Hazel Maboreke
- Ecology Group, Institute of Biology, Humboldt-Universität zu Berlin, Philippstr. 13, 10115, Berlin, Germany
| | - Frank Fleischmann
- Section Pathology of Woody Plants, Technische Universität München, Hans-Carl-von-Carlowitz-Platz 2, 85354, Freising, Germany
| | - Thorsten E E Grams
- TEEG: Ecophysiology of Plants, Technische Universität München, Hans-Carl-von-Carlowitz-Platz 2, 85354, Freising, Germany
| | - Liliane Ruess
- Ecology Group, Institute of Biology, Humboldt-Universität zu Berlin, Philippstr. 13, 10115, Berlin, Germany
| | - Martin Schädler
- Department of Community Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle/Saale, Germany
- Animal Ecology, Department of Ecology, Faculty of Biology, Philipps-Universität Marburg, Karl-von-Frisch Str. 8, 35032, Marburg, Germany
| | - Roland Brandl
- Animal Ecology, Department of Ecology, Faculty of Biology, Philipps-Universität Marburg, Karl-von-Frisch Str. 8, 35032, Marburg, Germany
| | - Stefan Scheu
- J.F. Blumenbach Institute of Zoology and Anthropology, Georg August University Göttingen, Berliner Str. 28, 37073, Göttingen, Germany
| | - Silvia D Schrey
- IMIT-Physiological Ecology of Plants, Auf der Morgenstelle 1, 72076, Tübingen, Germany
| | - Ivo Grosse
- Institute of Computer Science, Martin-Luther University, Von-Seckendorff-Platz 1, 06120, Halle/Saale, Germany
| | - François Buscot
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle/Saale, Germany
- Institute of Biology, Leipzig University, Johannisallee 21-23, 04103, Leipzig, Germany
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Römer P, Recht S, Strauß T, Elsaesser J, Schornack S, Boch J, Wang S, Lahaye T. Promoter elements of rice susceptibility genes are bound and activated by specific TAL effectors from the bacterial blight pathogen, Xanthomonas oryzae pv. oryzae. New Phytol 2010; 187:1048-1057. [PMID: 20345643 DOI: 10.1111/j.1469-8137.2010.03217.x] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
*Plant pathogenic bacteria of the genus Xanthomonas inject transcription activator-like effector (TALe) proteins that bind to and activate host promoters, thereby promoting disease or inducing plant defense. TALes bind to corresponding UPT (up-regulated by TALe) promoter boxes via tandemly arranged 34/35-amino acid repeats. Recent studies uncovered the TALe code in which two amino acid residues of each repeat define specific pairing to UPT boxes. *Here we employed the TALe code to predict potential UPT boxes in TALe-induced host promoters and analyzed these via beta-glucuronidase (GUS) reporter and electrophoretic mobility shift assays (EMSA). *We demonstrate that the Xa13, OsTFX1 and Os11N3 promoters from rice are induced directly by the Xanthomonas oryzae pv. oryzae TALes PthXo1, PthXo6 and AvrXa7, respectively. We identified and functionally validated a UPT box in the corresponding rice target promoter for each TALe and show that box mutations suppress TALe-mediated promoter activation. Finally, EMSA demonstrate that code-predicted UPT boxes interact specifically with corresponding TALes. *Our findings show that variations in the UPT boxes of different rice accessions correlate with susceptibility or resistance of these accessions to the bacterial blight pathogen.
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Affiliation(s)
- Patrick Römer
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, 06099 Halle (Saale), Germany
- Present address: Institute of Genetics, University of Munich (LMU), Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Sabine Recht
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, 06099 Halle (Saale), Germany
- Present address: Institute of Genetics, University of Munich (LMU), Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Tina Strauß
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, 06099 Halle (Saale), Germany
- Present address: Institute of Genetics, University of Munich (LMU), Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Janett Elsaesser
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, 06099 Halle (Saale), Germany
- Present address: Institute of Genetics, University of Munich (LMU), Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Sebastian Schornack
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, 06099 Halle (Saale), Germany
- The Sainsbury Laboratory, Norwich, NR4 7UH, UK
| | - Jens Boch
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, 06099 Halle (Saale), Germany
| | - Shiping Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, PR China
| | - Thomas Lahaye
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, 06099 Halle (Saale), Germany
- Present address: Institute of Genetics, University of Munich (LMU), Großhaderner Straße 2, 82152 Martinsried, Germany
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