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Corredor-Moreno P, Minter F, Davey PE, Wegel E, Kular B, Brett P, Lewis CM, Morgan YML, Macías Pérez LA, Korolev AV, Hill L, Saunders DGO. The branched-chain amino acid aminotransferase TaBCAT1 modulates amino acid metabolism and positively regulates wheat rust susceptibility. Plant Cell 2021; 33:1728-1747. [PMID: 33565586 PMCID: PMC8254495 DOI: 10.1093/plcell/koab049] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 02/02/2021] [Indexed: 05/21/2023]
Abstract
Plant pathogens suppress defense responses to evade recognition and promote successful colonization. Although identifying the genes essential for pathogen ingress has traditionally relied on screening mutant populations, the post-genomic era provides an opportunity to develop novel approaches that accelerate identification. Here, RNA-seq analysis of 68 pathogen-infected bread wheat (Triticum aestivum) varieties, including three (Oakley, Solstice and Santiago) with variable levels of susceptibility, uncovered a branched-chain amino acid aminotransferase (termed TaBCAT1) as a positive regulator of wheat rust susceptibility. We show that TaBCAT1 is required for yellow and stem rust infection and likely functions in branched-chain amino acid (BCAA) metabolism, as TaBCAT1 disruption mutants had elevated BCAA levels. TaBCAT1 mutants also exhibited increased levels of salicylic acid (SA) and enhanced expression of associated defense genes, indicating that BCAA regulation, via TaBCAT1, has a key role in SA-dependent defense activation. We also identified an association between the levels of BCAAs and resistance to yellow rust infection in wheat. These findings provide insight into SA-mediated defense responses in wheat and highlight the role of BCAA metabolism in the defense response. Furthermore, TaBCAT1 could be manipulated to potentially provide resistance to two of the most economically damaging diseases of wheat worldwide.
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Affiliation(s)
| | | | | | - Eva Wegel
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Baldeep Kular
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Paul Brett
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Clare M Lewis
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Luis A Macías Pérez
- John Innes Centre, Norwich Research Park, Norwich, UK
- Aix Marseille Université, CNRS, IRD, College de France, CEREGE, Aix-en-Provence, France
| | | | - Lionel Hill
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Diane G O Saunders
- John Innes Centre, Norwich Research Park, Norwich, UK
- Author for correspondence: (D.G.O.S.)
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2
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Li Y, Leveau A, Zhao Q, Feng Q, Lu H, Miao J, Xue Z, Martin AC, Wegel E, Wang J, Orme A, Rey MD, Karafiátová M, Vrána J, Steuernagel B, Joynson R, Owen C, Reed J, Louveau T, Stephenson MJ, Zhang L, Huang X, Huang T, Fan D, Zhou C, Tian Q, Li W, Lu Y, Chen J, Zhao Y, Lu Y, Zhu C, Liu Z, Polturak G, Casson R, Hill L, Moore G, Melton R, Hall N, Wulff BBH, Doležel J, Langdon T, Han B, Osbourn A. Subtelomeric assembly of a multi-gene pathway for antimicrobial defense compounds in cereals. Nat Commun 2021; 12:2563. [PMID: 33963185 PMCID: PMC8105312 DOI: 10.1038/s41467-021-22920-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 04/07/2021] [Indexed: 02/06/2023] Open
Abstract
Non-random gene organization in eukaryotes plays a significant role in genome evolution. Here, we investigate the origin of a biosynthetic gene cluster for production of defence compounds in oat-the avenacin cluster. We elucidate the structure and organisation of this 12-gene cluster, characterise the last two missing pathway steps, and reconstitute the entire pathway in tobacco by transient expression. We show that the cluster has formed de novo since the divergence of oats in a subtelomeric region of the genome that lacks homology with other grasses, and that gene order is approximately colinear with the biosynthetic pathway. We speculate that the positioning of the late pathway genes furthest away from the telomere may mitigate against a 'self-poisoning' scenario in which toxic intermediates accumulate as a result of telomeric gene deletions. Our investigations reveal a striking example of adaptive evolution underpinned by remarkable genome plasticity.
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Affiliation(s)
- Yan Li
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | | | - Qiang Zhao
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Qi Feng
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Hengyun Lu
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Jiashun Miao
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Zheyong Xue
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Eva Wegel
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Jing Wang
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | - Miroslava Karafiátová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | | | - Ryan Joynson
- Earlham Institute, Norwich Research Park, Norwich, UK
| | | | - James Reed
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | - Lei Zhang
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Xuehui Huang
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Tao Huang
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Danling Fan
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Congcong Zhou
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Qilin Tian
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Wenjun Li
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Yiqi Lu
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Jiaying Chen
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Yan Zhao
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Ying Lu
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Chuanrang Zhu
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Zhenhua Liu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Guy Polturak
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Lionel Hill
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Graham Moore
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Rachel Melton
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich, UK
| | | | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Tim Langdon
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EE, UK
| | - Bin Han
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China.
| | - Anne Osbourn
- John Innes Centre, Norwich Research Park, Norwich, UK.
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3
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Wegel E. Fluorescence In Situ Hybridization in Oat. Methods Mol Biol 2018; 1536:3-21. [PMID: 28132139 DOI: 10.1007/978-1-4939-6682-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
This chapter describes methods to detect gene loci or gene transcripts by fluorescence labeling. Fluorescence in situ hybridization (FISH) can be used to identify the positions of genes or BACs or the distribution of repetitive sequences on metaphase chromosomes as well as the identification of alien chromosomes. It enables the identification of gene loci and active transcription sites in interphase nuclei and also the localization of cellular transcripts. The protocols here deal with the production of DNA and RNA probes, the preparation of oat metaphase spreads and root tissue sections, the subsequent hybridization, post-hybridization washes, and detection by immunofluorescence.
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Affiliation(s)
- Eva Wegel
- Cell and Developmental Biology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK.
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4
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Wegel E, Göhler A, Lagerholm BC, Wainman A, Uphoff S, Kaufmann R, Dobbie IM. Imaging cellular structures in super-resolution with SIM, STED and Localisation Microscopy: A practical comparison. Sci Rep 2016; 6:27290. [PMID: 27264341 PMCID: PMC4893670 DOI: 10.1038/srep27290] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 05/18/2016] [Indexed: 12/19/2022] Open
Abstract
Many biological questions require fluorescence microscopy with a resolution beyond the diffraction limit of light. Super-resolution methods such as Structured Illumination Microscopy (SIM), STimulated Emission Depletion (STED) microscopy and Single Molecule Localisation Microscopy (SMLM) enable an increase in image resolution beyond the classical diffraction-limit. Here, we compare the individual strengths and weaknesses of each technique by imaging a variety of different subcellular structures in fixed cells. We chose examples ranging from well separated vesicles to densely packed three dimensional filaments. We used quantitative and correlative analyses to assess the performance of SIM, STED and SMLM with the aim of establishing a rough guideline regarding the suitability for typical applications and to highlight pitfalls associated with the different techniques.
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Affiliation(s)
- Eva Wegel
- Micron Oxford Advanced Imaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Antonia Göhler
- Micron Oxford Advanced Imaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - B Christoffer Lagerholm
- Wolfson Imaging Centre Oxford, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, United Kingdom
| | - Alan Wainman
- Micron Oxford Advanced Imaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.,Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - Stephan Uphoff
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Rainer Kaufmann
- Micron Oxford Advanced Imaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.,Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Ian M Dobbie
- Micron Oxford Advanced Imaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
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5
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Demmerle J, Wegel E, Schermelleh L, Dobbie IM. Assessing resolution in super-resolution imaging. Methods 2015; 88:3-10. [PMID: 26164701 DOI: 10.1016/j.ymeth.2015.07.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 07/06/2015] [Accepted: 07/07/2015] [Indexed: 01/10/2023] Open
Abstract
Resolution is a central concept in all imaging fields, and particularly in optical microscopy, but it can be easily misinterpreted. The mathematical definition of optical resolution was codified by Abbe, and practically defined by the Rayleigh Criterion in the late 19th century. The limit of conventional resolution was also achieved in this period, and it was thought that fundamental constraints of physics prevented further increases in resolution. With the recent development of a range of super-resolution techniques, it is necessary to revisit the concept of optical resolution. Fundamental differences in super-resolution modalities mean that resolution is not a directly transferrable metric between techniques. This article considers the issues in resolution raised by these new technologies, and presents approaches for comparing resolution between different super-resolution methods.
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Affiliation(s)
- Justin Demmerle
- Micron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3PT, United Kingdom
| | - Eva Wegel
- Micron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3PT, United Kingdom
| | - Lothar Schermelleh
- Micron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3PT, United Kingdom
| | - Ian M Dobbie
- Micron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3PT, United Kingdom.
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6
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Affiliation(s)
- Anne Osbourn
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom.
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7
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Abstract
Gene clusters for the synthesis of secondary metabolites are a common feature of microbial genomes. Well-known examples include clusters for the synthesis of antibiotics in actinomycetes, and also for the synthesis of antibiotics and toxins in filamentous fungi. Until recently it was thought that genes for plant metabolic pathways were not clustered, and this is certainly true in many cases; however, five plant secondary metabolic gene clusters have now been discovered, all of them implicated in synthesis of defence compounds. An obvious assumption might be that these eukaryotic gene clusters have arisen by horizontal gene transfer from microbes, but there is compelling evidence to indicate that this is not the case. This raises intriguing questions about how widespread such clusters are, what the significance of clustering is, why genes for some metabolic pathways are clustered and those for others are not, and how these clusters form. In answering these questions we may hope to learn more about mechanisms of genome plasticity and adaptive evolution in plants. It is noteworthy that for the five plant secondary metabolic gene clusters reported so far, the enzymes for the first committed steps all appear to have been recruited directly or indirectly from primary metabolic pathways involved in hormone synthesis. This may or may not turn out to be a common feature of plant secondary metabolic gene clusters as new clusters emerge.
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Affiliation(s)
- Hoi Yee Chu
- Department of Metabolic Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
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8
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Wegel E, Koumproglou R, Shaw P, Osbourn A. Cell type-specific chromatin decondensation of a metabolic gene cluster in oats. Plant Cell 2009; 21:3926-36. [PMID: 20040536 PMCID: PMC2814510 DOI: 10.1105/tpc.109.072124] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Revised: 11/29/2009] [Accepted: 12/04/2009] [Indexed: 05/18/2023]
Abstract
Transcription-related chromatin decondensation has been studied in mammals for clusters of structurally and/or functionally related genes that are coordinately regulated (e.g., the homeobox locus in mice and the major histocompatability complex locus in humans). Plant genes have generally been considered to be randomly distributed throughout the genome, although several examples of metabolic gene clusters for synthesis of plant defense compounds have recently been discovered. Clustering provides for genetic linkage of genes that together confer a selective advantage and may also facilitate coordinate regulation of gene expression by enabling localized changes in chromatin structure. Here, we use cytological methods to investigate components of a metabolic gene cluster for synthesis of developmentally regulated defense compounds (avenacins) in diploid oat (Avena strigosa). Our experiments reveal that expression of the avenacin gene cluster is associated with cell type-specific chromatin decondensation, providing new insights into regulation of gene clusters in plants. Importantly, chromatin decondensation could be visualized not only at the large-scale level but down to the single gene level. We further show that the avenacin and sterol pathways are likely to be inversely regulated at the level of transcription.
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Affiliation(s)
- Eva Wegel
- Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Rachil Koumproglou
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Peter Shaw
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Anne Osbourn
- Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
- Address correspondence to
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9
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Mugford ST, Qi X, Bakht S, Hill L, Wegel E, Hughes RK, Papadopoulou K, Melton R, Philo M, Sainsbury F, Lomonossoff GP, Roy AD, Goss RJM, Osbourn A. A serine carboxypeptidase-like acyltransferase is required for synthesis of antimicrobial compounds and disease resistance in oats. Plant Cell 2009; 21:2473-84. [PMID: 19684243 PMCID: PMC2751944 DOI: 10.1105/tpc.109.065870] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Revised: 07/07/2009] [Accepted: 07/29/2009] [Indexed: 05/18/2023]
Abstract
Serine carboxypeptidase-like (SCPL) proteins have recently emerged as a new group of plant acyltransferases. These enzymes share homology with peptidases but lack protease activity and instead are able to acylate natural products. Several SCPL acyltransferases have been characterized to date from dicots, including an enzyme required for the synthesis of glucose polyesters that may contribute to insect resistance in wild tomato (Solanum pennellii) and enzymes required for the synthesis of sinapate esters associated with UV protection in Arabidopsis thaliana. In our earlier genetic analysis, we identified the Saponin-deficient 7 (Sad7) locus as being required for the synthesis of antimicrobial triterpene glycosides (avenacins) and for broad-spectrum disease resistance in diploid oat (Avena strigosa). Here, we report on the cloning of Sad7 and show that this gene encodes a functional SCPL acyltransferase, SCPL1, that is able to catalyze the synthesis of both N-methyl anthraniloyl- and benzoyl-derivatized forms of avenacin. Sad7 forms part of an operon-like gene cluster for avenacin synthesis. Oat SCPL1 (SAD7) is the founder member of a subfamily of monocot-specific SCPL proteins that includes predicted proteins from rice (Oryza sativa) and other grasses with potential roles in secondary metabolism and plant defense.
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10
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Santos AP, Wegel E, Allen GC, Thompson WF, Stoger E, Shaw P, Abranches R. In situ methods to localize transgenes and transcripts in interphase nuclei: a tool for transgenic plant research. Plant Methods 2006; 2:18. [PMID: 17081287 PMCID: PMC1635696 DOI: 10.1186/1746-4811-2-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2006] [Accepted: 11/02/2006] [Indexed: 05/08/2023]
Abstract
Genetic engineering of commercially important crops has become routine in many laboratories. However, the inability to predict where a transgene will integrate and to efficiently select plants with stable levels of transgenic expression remains a limitation of this technology. Fluorescence in situ hybridization (FISH) is a powerful technique that can be used to visualize transgene integration sites and provide a better understanding of transgene behavior. Studies using FISH to characterize transgene integration have focused primarily on metaphase chromosomes, because the number and position of integration sites on the chromosomes are more easily determined at this stage. However gene (and transgene) expression occurs mainly during interphase. In order to accurately predict the activity of a transgene, it is critical to understand its location and dynamics in the three-dimensional interphase nucleus. We and others have developed in situ methods to visualize transgenes (including single copy genes) and their transcripts during interphase from different tissues and plant species. These techniques reduce the time necessary for characterization of transgene integration by eliminating the need for time-consuming segregation analysis, and extend characterization to the interphase nucleus, thus increasing the likelihood of accurate prediction of transgene activity. Furthermore, this approach is useful for studying nuclear organization and the dynamics of genes and chromatin.
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Affiliation(s)
- Ana Paula Santos
- Plant Genetic Engineering Laboratory, Instituto de Tecnologia Química e Biológica, UNL, Av. República, 2781-901 Oeiras, Portugal
| | - Eva Wegel
- Department of Cell and Developmental Biology, John Innes Centre, Colney, Norwich NR4 7UH, UK
| | - George C Allen
- Plant Transformation Laboratory (PTL), Departments of Crop Science and Horticultural Science, Campus Box 7550, North Carolina State University, Raleigh, NC 27695, USA
| | - William F Thompson
- Plant Gene Expression Laboratory, Campus Box 7550, North Carolina State University Raleigh, NC 27695, USA
| | - Eva Stoger
- Institute for Molecular Biotechnology, RWTH Aachen, 52074 Aachen, Germany
| | - Peter Shaw
- Department of Cell and Developmental Biology, John Innes Centre, Colney, Norwich NR4 7UH, UK
| | - Rita Abranches
- Plant Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica, UNL, Av. República, 2781-901 Oeiras, Portugal
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Abstract
We have analysed the chromosome organization in endosperm and embryo of bread wheat (Triticum aestivum L.), in order to compare these tissues with developing anthers, in which the centromeres associate, and the developing root xylem vessel cells, in which the chromosomes endoreduplicate to become polytene and associate via their centromeres. Both endosperm and embryo showed a typical Rabl configuration and a degree of non-homologous centromere association and the endosperm also showed extensive telomere association. Wheat endosperm is initially triploid and during its development a percentage of the nuclei increase their DNA content to 6C and 12C. 6C nuclei showed twice as many centromeres as 3C nuclei and the centromere number increased further in 12C nuclei. The higher the C-content of a nucleus the more the telomeres associated in endosperm. The vast majority of 12C nuclei showed six rye chromosome arms, although a few showed three associated groups of rye chromosome arms. This means that during endosperm development wheat nuclei show both polyploidization and polytenization.
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Affiliation(s)
- E Wegel
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK
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12
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Abstract
We have developed methods, based on confocal microscopy and three-dimensional (3D) modelling, for the analysis of complex tissues and individual nuclei. These methods were used to study the development of early wheat (Triticum aestivum) endosperm as a whole and of endosperm nuclei undergoing polyploidization. Fixed sections of immature caryopses were either stained with SYTOX Green or used for fluorescence in situ hybridization (FISH) to visualize centromeres, telomeres and a rye chromosome arm substitution. Each section was imaged as a confocal image stack. By using Amira 3.0 for computer image processing, rendered models were produced of the whole endosperm and of individual nuclei. We followed endosperm development up to the formation of a complete syncytium, which develops via a dorsal and a ventral plate of nuclei in the central cell. Modelling of nuclei showed that wheat chromosomes are not anchored to the nuclear membrane and become more randomly positioned in endoreduplicated nuclei. This analysis produced a precise description of the positioning of nuclei throughout the developing endosperm and of chromosomal domains in single nuclei.
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Affiliation(s)
- Eva Wegel
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
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13
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Wegel E, Shaw P. Gene activation and deactivation related changes in the three-dimensional structure of chromatin. Chromosoma 2005; 114:331-7. [PMID: 16075283 DOI: 10.1007/s00412-005-0015-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2005] [Revised: 06/30/2005] [Accepted: 06/30/2005] [Indexed: 12/12/2022]
Abstract
Chromatin in the interphase nucleus is dynamic, decondensing where genes are activated and condensing where they are silenced. Local chromatin remodelling to a more open structure during gene activation is followed by changes in nucleosome distribution through the action of the transcriptional machinery. This leads to chromatin expansion and looping out of whole genomic regions. Such chromatin loops can extend beyond the chromosome territory. As several studies point to the location of transcription sites inside chromosome territories as well as at their periphery, extraterritorial loops cannot simply be a mechanism for making transcribed genes accessible to the transcriptional machinery and must occur for other reasons. The level of decondensation within an activated region varies greatly and probably depends on the density of activated genes and the number of engaged RNA polymerases. Genes that are silenced during development form a more closed chromatin structure. Specific histone modifications are correlated with gene activation and silencing, and silenced genes may become associated with heterochromatin protein 1 homologues or with polycomb group complexes. Several levels of chromatin packaging are found in the nucleus relating to the different functions of and performed by active genes; euchromatic and heterochromatic regions and the models explaining higher-order chromatin structure are still disputed.
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Affiliation(s)
- Eva Wegel
- The Sainsbury Laboratory, John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
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Wegel E, Vallejos RH, Christou P, Stöger E, Shaw P. Large-scale chromatin decondensation induced in a developmentally activated transgene locus. J Cell Sci 2005; 118:1021-31. [PMID: 15713746 DOI: 10.1242/jcs.01685] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The high molecular weight (HMW) glutenin-encoding genes in wheat are developmentally activated in the endosperm at about 8 days after anthesis. We have investigated the physical changes that occur in these genes in two transgenic lines containing about 20 and 50 copies each of the HMW glutenin genes together with their promoters. Using fluorescence in-situ hybridisation (FISH) and confocal imaging, we demonstrate that, in non-expressing tissue, each transgene locus consists of one or two highly condensed sites, which decondense into many foci upon activation of transcription in endosperm nuclei. Initiation of transcription can precede decondensation but not vice versa. We show that, in one of the lines, cytoplasmic transcript levels are high after onset of transcription but disappear by 14 days after anthesis, whereas small interfering RNAs, which indicate post-transcriptional gene silencing (PTGS), are detected at this stage. However, the transcript levels remain high at the transcription sites, most of the transgene copies are transcriptionally active and transcriptional activity in the nucleus ceases only with cell death at the end of endosperm development.
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MESH Headings
- Cell Nucleus/metabolism
- Chromatin/chemistry
- Chromatin/metabolism
- Chromatin/ultrastructure
- Cytoplasm/metabolism
- DNA/metabolism
- DNA Methylation
- DNA Primers/chemistry
- Flow Cytometry
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Plant
- Gene Silencing
- Genes, Plant
- Glutens/genetics
- Image Processing, Computer-Assisted
- In Situ Hybridization
- In Situ Hybridization, Fluorescence
- Metaphase
- Microscopy, Confocal
- Plant Physiological Phenomena
- Plant Roots/metabolism
- Plants, Genetically Modified
- Plasmids/metabolism
- Promoter Regions, Genetic
- Protein Structure, Tertiary
- RNA/metabolism
- RNA, Messenger/metabolism
- RNA, Small Interfering/metabolism
- Seeds/metabolism
- Time Factors
- Transcription, Genetic
- Transformation, Genetic
- Transgenes
- Triticum/genetics
- Triticum/metabolism
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Affiliation(s)
- Eva Wegel
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
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15
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Abstract
It has been appreciated for many years that the structure of a transgene locus can have a major influence on the level and stability of transgene expression. Until recently, however, it has been common practice to discard plant lines with poor or unstable expression levels in favor of those with practical uses. In the last few years, an increasing number of experiments have been carried out with the primary aim of characterizing transgene loci and studying the fundamental links between locus structure and expression. Cereals have been at the forefront of this research because molecular, genetic and cytogenetic analysis can be carried out in parallel to examine transgene loci in detail. This review discusses what is known about the structure and organization of transgene loci in cereals, both at the molecular and cytogenetic levels. In the latter case, important links are beginning to be revealed between higher order locus organization, nuclear architecture, chromatin structure and transgene expression.
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Affiliation(s)
- Ajay Kohli
- Rexagen Corporation, Genome Centre, Norwich Bio-Incubator, Colney Lane, Norwich, NR4 7UH, United Kingdom.
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Shaw PJ, Abranches R, Paula Santos A, Beven AF, Stoger E, Wegel E, González-Melendi P. The architecture of interphase chromosomes and nucleolar transcription sites in plants. J Struct Biol 2002; 140:31-8. [PMID: 12490151 DOI: 10.1016/s1047-8477(02)00537-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Fluorescence in situ hybridization (FISH) coupled with confocal microscopy has been used to reveal the interphase chromosome organization in plants. In wheat and several other related species, we have shown that the interphase chromosomes are in a very well-defined organization, with centromeres and telomeres located at opposite sides of the nuclear envelope-a classic Rabl configuration. In transgenic wheat lines, FISH analysis of metaphase chromosomes has shown that multiple transgene copies can be integrated along a single chromosome, with large regions of intervening genomic sequence. These multiple copies are often colocalized in interphase, suggesting either an ectopic association or a highly reproducible interphase chromatin configuration. Bromo-uridine (BrU) incorporation has been used to label transcription sites in the nucleolus. Using pea root tissue, we have combined BrU incorporation with preembedding 1-nm gold detection to image the nucleolar transcription sites by electron microscopy. This has revealed many distinct elongated clusters of silver-gold particles. These clusters are 200-300 nm in length and are thicker at one end than the other. We suggest that each cluster corresponds to a single transcribed gene. Serial sectioning of several entire nucleoli has enabled the reconstruction of all the nucleolar transcription sites, and we have estimated that there are 200-300 transcribed genes per nucleolus.
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Affiliation(s)
- Peter J Shaw
- Department of Cell Biology, The John Innes Centre, Norwich Research Park, Colney Lane, Norwich, UK.
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Abranches R, Santos AP, Wegel E, Williams S, Castilho A, Christou P, Shaw P, Stoger E. Widely separated multiple transgene integration sites in wheat chromosomes are brought together at interphase. Plant J 2000; 24:713-723. [PMID: 11135106 DOI: 10.1046/j.1365-313x.2000.00908.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We have investigated the organization of transgenes delivered by particle bombardment into the wheat genome, combining conventional molecular analysis with fluorescence in situ hybridization (FISH) and three-dimensional confocal microscopy. We selected a representative population of transformed wheat lines and carried out molecular and expression analysis. FISH on metaphase chromosomes showed that transgene integration sites were often separated by considerable lengths of genomic DNA (>1 Mbp), or could even be on opposite chromosome arms. Plants showing multiple integration sites on a single chromosome were selected for three-dimensional confocal analysis of interphase nuclei in root and embryo tissue sections. Confocal microscopy revealed that these sites lay in close physical proximity in the interphase nuclei. Our results clearly show that multiple transgenes physically separated by large intervening regions of endogenous DNA at metaphase can be brought together at interphase. This may reflect the original physical organization of the endogenous DNA at the moment of transformation, with DNA strand breaks introduced into several co-localized DNA loops by the intruding gold particles. Alternatively, the transgenes may be brought together after transformation, either by an ectopic homologous pairing mechanism, or by recruitment to a common transcription site.
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Affiliation(s)
- R Abranches
- John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
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Gouni-Berthold I, Baumeister B, Wegel E, Berthold HK, Vetter H, Schmidt C. Neutrophil-elastase in chronic inflammatory bowel disease: a marker of disease activity? Hepatogastroenterology 1999; 46:2315-20. [PMID: 10521989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
BACKGROUND/AIMS Neutrophil elastase is a proteinase which exists in granulocytes and plays an important role in the pathogenesis of inflammatory disorders. In inflammatory bowel disease there is a leukocyte infiltration of the bowel mucosa. The purpose of this study was to examine whether plasma elastase represents a reliable laboratory marker for establishing the activity of chronic inflammatory bowel disease. METHODOLOGY We measured plasma elastase concentrations in 61 patients suffering from either Crohn's disease or ulcerative colitis and compared these data with other clinical and laboratory findings and with elastase concentrations in 40 healthy controls. The sensitivity and specificity of the elastase values in chronic IBD were calculated with the use of concomitant measurements of CRP and ESR. RESULTS Plasma levels were found to be significantly higher in patients (49 micrograms/l) compared with healthy controls (23 micrograms/l). Patients with active disease had higher plasma levels than patients in remission. In general, the sensitivity of elastase to detect active inflammatory bowel disease was about 60%; the specificity was 65%. For patients in remission, the sensitivity was higher than 80%. However, there was a wide range of overlapping values between chronic inactive patients and those with moderately active disease. CONCLUSIONS We conclude that plasma elastase is a useful independent marker of disease activity in inflammatory bowel disease. Especially for identifying patients in remission, the measurements of elastase seem to be more suitable than other parameters of inflammation, like CRP or ESR.
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