51
|
Naidoo S, Külheim C, Zwart L, Mangwanda R, Oates CN, Visser EA, Wilken FE, Mamni TB, Myburg AA. Uncovering the defence responses of Eucalyptus to pests and pathogens in the genomics age. TREE PHYSIOLOGY 2014; 34:931-43. [PMID: 25261123 DOI: 10.1093/treephys/tpu075] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Long-lived tree species are subject to attack by various pests and pathogens during their lifetime. This problem is exacerbated by climate change, which may increase the host range for pathogens and extend the period of infestation by pests. Plant defences may involve preformed barriers or induced resistance mechanisms based on recognition of the invader, complex signalling cascades, hormone signalling, activation of transcription factors and production of pathogenesis-related (PR) proteins with direct antimicrobial or anti-insect activity. Trees have evolved some unique defence mechanisms compared with well-studied model plants, which are mostly herbaceous annuals. The genome sequence of Eucalyptus grandis W. Hill ex Maiden has recently become available and provides a resource to extend our understanding of defence in large woody perennials. This review synthesizes existing knowledge of defence mechanisms in model plants and tree species and features mechanisms that may be important for defence in Eucalyptus, such as anatomical variants and the role of chemicals and proteins. Based on the E. grandis genome sequence, we have identified putative PR proteins based on sequence identity to the previously described plant PR proteins. Putative orthologues for PR-1, PR-2, PR-4, PR-5, PR-6, PR-7, PR-8, PR-9, PR-10, PR-12, PR-14, PR-15 and PR-17 have been identified and compared with their orthologues in Populus trichocarpa Torr. & A. Gray ex Hook and Arabidopsis thaliana (L.) Heynh. The survey of PR genes in Eucalyptus provides a first step in identifying defence gene targets that may be employed for protection of the species in future. Genomic resources available for Eucalyptus are discussed and approaches for improving resistance in these hardwood trees, earmarked as a bioenergy source in future, are considered.
Collapse
Affiliation(s)
- Sanushka Naidoo
- Department of Genetics, Genomics Research Institute (GRI), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria 0028, South Africa;
| | - Carsten Külheim
- Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
| | - Lizahn Zwart
- Department of Genetics, Genomics Research Institute (GRI), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| | - Ronishree Mangwanda
- Department of Genetics, Genomics Research Institute (GRI), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| | - Caryn N Oates
- Department of Genetics, Genomics Research Institute (GRI), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| | - Erik A Visser
- Department of Genetics, Genomics Research Institute (GRI), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| | - Febé E Wilken
- Department of Genetics, Genomics Research Institute (GRI), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| | - Thandekile B Mamni
- Department of Genetics, Genomics Research Institute (GRI), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| | - Alexander A Myburg
- Department of Genetics, Genomics Research Institute (GRI), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| |
Collapse
|
52
|
|
53
|
Lange O, Binder A, Lahaye T. From dead leaf, to new life:
TAL
effectors as tools for synthetic biology. THE PLANT JOURNAL 2014; 78:753-771. [PMID: 24602153 DOI: 10.1111/tpj.12431] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Affiliation(s)
- Orlando Lange
- Department of General Genetics Centre for Plant Molecular Biology Eberhard‐Karls‐University Tübingen Auf der Morgenstelle 32 72076 Tübingen Germany
| | - Andreas Binder
- Genetics Faculty of Biology I University of Munich Großhaderner Straße 2‐4 82152 Martinsried Germany
| | - Thomas Lahaye
- Department of General Genetics Centre for Plant Molecular Biology Eberhard‐Karls‐University Tübingen Auf der Morgenstelle 32 72076 Tübingen Germany
| |
Collapse
|
54
|
Bogdanove AJ. Principles and applications of TAL effectors for plant physiology and metabolism. CURRENT OPINION IN PLANT BIOLOGY 2014; 19:99-104. [PMID: 24907530 PMCID: PMC4086460 DOI: 10.1016/j.pbi.2014.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 05/08/2014] [Accepted: 05/08/2014] [Indexed: 05/27/2023]
Abstract
Recent advances in DNA targeting allow unprecedented control over gene function and expression. Targeting based on TAL effectors is arguably the most promising for systems biology and metabolic engineering. Multiple, orthogonal TAL-effector reagents of different types can be used in the same cell. Furthermore, variation in base preferences of the individual structural repeats that make up the TAL effector DNA recognition domain makes targeting stringency tunable. Realized applications range from genome editing to epigenome modification to targeted gene regulation to chromatin labeling and capture. The principles that govern TAL effector DNA recognition make TAL effectors well suited for applications relevant to plant physiology and metabolism. TAL effector targeting has merits that are distinct from those of the RNA-based DNA targeting CRISPR/Cas9 system.
Collapse
Affiliation(s)
- Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology, 334 Plant Science, Cornell University, Ithaca, NY 14853, USA.
| |
Collapse
|
55
|
Li W, Cui X. Focus on rice: towards better understanding of the life cycle of crop plants. MOLECULAR PLANT 2014; 7:931-933. [PMID: 24891313 DOI: 10.1093/mp/ssu057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Affiliation(s)
- Wei Li
- Scientific Editor, Molecular Plant
| | | |
Collapse
|
56
|
Yuan M, Zhao J, Huang R, Li X, Xiao J, Wang S. Rice MtN3/saliva/SWEET gene family: Evolution, expression profiling, and sugar transport. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:559-70. [PMID: 24456138 DOI: 10.1111/jipb.12173] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 01/06/2014] [Indexed: 05/06/2023]
Abstract
The rice MtN3/saliva/SWEET gene family consists of 21 paralogs. However, their functions in physiological processes are largely unknown, although at least three of the 21 paralogs are used by pathogenic bacteria to infect rice. Here, we report the evolutionary features, transcriptional characteristics, and putative functions in sugar transport of this gene family. The wild rice accessions in this study included those with AA, BB, CC, BBCC, CCDD, EE, and GG genomes, which appeared approximately 0.58-14.6 million years ago. The structures, chromosomal locations, phylogenetic relationships, and homologous distribution among the accessions suggest that the number of rice MtN3/saliva/SWEET paralogs gradually increased as the Oryza genus evolved, and one third of the paralogs may have originated recently. These paralogs are differentially expressed in vegetative and reproductive tissues, in the leaf senescence process, and in signaling dependent on gibberellic acid, cytokinin, or 1-naphthalene acetic acid (an analog of auxin), suggesting that they may be associated with multiple physiological processes. Four paralogs could transport galactose in yeast, which suggests that they may have a similar function in rice. These results will help to elucidate their roles and biochemical functions in rice development, adaptation to environment, host-pathogen interaction, and so forth.
Collapse
Affiliation(s)
- Meng Yuan
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | | | | | | | | | | |
Collapse
|
57
|
Fichtner F, Urrea Castellanos R, Ülker B. Precision genetic modifications: a new era in molecular biology and crop improvement. PLANTA 2014; 239:921-39. [PMID: 24510124 DOI: 10.1007/s00425-014-2029-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 01/06/2014] [Indexed: 05/26/2023]
Abstract
Recently, the use of programmable DNA-binding proteins such as ZFP/ZFNs, TALE/TALENs and CRISPR/Cas has produced unprecedented advances in gene targeting and genome editing in prokaryotes and eukaryotes. These advances allow researchers to specifically alter genes, reprogram epigenetic marks, generate site-specific deletions and potentially cure diseases. Unlike previous methods, these precision genetic modification techniques (PGMs) are specific, efficient, easy to use and economical. Here we discuss the capabilities and pitfalls of PGMs and highlight the recent, exciting applications of PGMs in molecular biology and crop genetic engineering. Further improvement of the efficiency and precision of PGM techniques will enable researchers to precisely alter gene expression and biological/chemical pathways, probe gene function, modify epigenetic marks and improve crops by increasing yield, quality and tolerance to limiting biotic and abiotic stress conditions.
Collapse
Affiliation(s)
- Franziska Fichtner
- Plant Molecular Engineering Group, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | | | | |
Collapse
|
58
|
A TAL effector repeat architecture for frameshift binding. Nat Commun 2014; 5:3447. [PMID: 24614980 DOI: 10.1038/ncomms4447] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 02/13/2014] [Indexed: 11/08/2022] Open
Abstract
Transcription activator-like effectors (TALEs) are important Xanthomonas virulence factors that bind DNA via a unique tandem 34-amino-acid repeat domain to induce expression of plant genes. So far, TALE repeats are described to bind as a consecutive array to a consecutive DNA sequence, in which each repeat independently recognizes a single DNA base. This modular protein architecture enables the design of any desired DNA-binding specificity for biotechnology applications. Here we report that natural TALE repeats of unusual amino-acid sequence length break the strict one repeat-to-one base pair binding mode and introduce a local flexibility to TALE-DNA binding. This flexibility allows TALEs and TALE nucleases to recognize target sequence variants with single nucleotide deletions. The flexibility also allows TALEs to activate transcription at allelic promoters that otherwise confer resistance to the host plant.
Collapse
|
59
|
Chen LQ. SWEET sugar transporters for phloem transport and pathogen nutrition. THE NEW PHYTOLOGIST 2014; 201:1150-5. [PMID: 24649486 DOI: 10.1111/nph.12445] [Citation(s) in RCA: 209] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Many intercellular solute transport processes require an apoplasmic step, that is, efflux from one cell and subsequent uptake by an adjacent cell. Cellular uptake transporters have been identified for many solutes, including sucrose; however, efflux transporters have remained elusive for a long time. Cellular efflux of sugars plays essential roles in many processes, such as sugar efflux as the first step in phloem loading, sugar efflux for nectar secretion, and sugar efflux for supplying symbionts such as mycorrhiza, and maternal efflux for filial tissue development. Furthermore, sugar efflux systems can be hijacked by pathogens for access to nutrition from hosts. Mutations that block recruitment of the efflux mechanism by the pathogen thus cause pathogen resistance. Until recently, little was known regarding the underlying mechanism of sugar efflux. The identification of sugar efflux carriers, SWEETs (Sugars Will Eventually be Exported Transporters), has shed light on cellular sugar efflux. SWEETs appear to function as uniporters, facilitating diffusion of sugars across cell membranes. Indeed, SWEETs probably mediate sucrose efflux from putative phloem parenchyma into the phloem apoplasm, a key step proceeding phloem loading. Engineering of SWEET mutants using transcriptional activator-like effector nuclease (TALEN)-based genomic editing allowed the engineering of pathogen resistance. The widespread expression of the SWEET family promises to provide insights into many other cellular efflux mechanisms.
Collapse
|
60
|
Denancé N, Szurek B, Noël LD. Emerging functions of nodulin-like proteins in non-nodulating plant species. PLANT & CELL PHYSIOLOGY 2014; 55:469-74. [PMID: 24470637 DOI: 10.1093/pcp/pct198] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Plant genes whose expression is induced in legumes by Rhizobium bacteria upon nodulation were initially referred to as nodulins. Several of them play a key role in the establishment of symbiosis. Yet, nodulin-like proteins are also found in non-nodulating plant species such as Arabidopsis, rice, maize or poplar. For instance, 132 are predicted in the Arabidopsis thaliana Col-0 genome. Recent studies now highlight the importance of nodulin-like proteins for the transport of nutrients, solutes, amino acids or hormones and for major aspects of plant development. Interestingly, nodulin-like activities at the plant-microbe interface are also important for pathogens to enhance their fitness during host colonization. This work presents a genomic and functional overview of nodulin-like proteins in non-leguminous plant species, with a particular focus on Arabidopsis and rice.
Collapse
Affiliation(s)
- Nicolas Denancé
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR 441, F-31326 Castanet-Tolosan, France
| | | | | |
Collapse
|
61
|
Liu W, Liu J, Triplett L, Leach JE, Wang GL. Novel insights into rice innate immunity against bacterial and fungal pathogens. ANNUAL REVIEW OF PHYTOPATHOLOGY 2014; 52:213-41. [PMID: 24906128 DOI: 10.1146/annurev-phyto-102313-045926] [Citation(s) in RCA: 235] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Rice feeds more than half of the world's population. Rice blast, caused by the fungal pathogen Magnaporthe oryzae, and bacterial blight, caused by the bacterial pathogen Xanthomonas oryzae pv. oryzae, are major constraints to rice production worldwide. Genome sequencing and extensive molecular analysis has led to the identification of many new pathogen-associated molecular patterns (PAMPs) and avirulence and virulence effectors in both pathogens, as well as effector targets and receptors in the rice host. Characterization of these effectors, host targets, and resistance genes has provided new insight into innate immunity in plants. Some of the new findings, such as the binding activity of X. oryzae transcriptional activator-like (TAL) effectors to specific rice genomic sequences, are being used for the development of effective disease control methods and genome modification tools. This review summarizes the recent progress toward understanding the recognition and signaling events that govern rice innate immunity.
Collapse
Affiliation(s)
- Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | | | | | | | | |
Collapse
|
62
|
Streubel J, Pesce C, Hutin M, Koebnik R, Boch J, Szurek B. Five phylogenetically close rice SWEET genes confer TAL effector-mediated susceptibility to Xanthomonas oryzae pv. oryzae. THE NEW PHYTOLOGIST 2013; 200:808-819. [PMID: 23879865 DOI: 10.1111/nph.12411] [Citation(s) in RCA: 229] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 06/03/2013] [Indexed: 05/03/2023]
Abstract
Bacterial plant-pathogenic Xanthomonas strains translocate transcription activator-like (TAL) effectors into plant cells to function as specific transcription factors. Only a few plant target genes of TAL effectors have been identified, so far. Three plant SWEET genes encoding putative sugar transporters are known to be induced by TAL effectors from rice-pathogenic Xanthomonas oryzae pv. oryzae (Xoo). We predict and validate that expression of OsSWEET14 is induced by a novel TAL effector, Tal5, from an African Xoo strain. Artificial TAL effectors (ArtTALs) were constructed to individually target 20 SWEET orthologs in rice. They were used as designer virulence factors to study which rice SWEET genes can support Xoo virulence. The Tal5 target box differs from those of the already known TAL effectors TalC, AvrXa7 and PthXo3, which also induce expression of OsSWEET14, suggesting evolutionary convergence on key targets. ArtTALs efficiently complemented an Xoo talC mutant, demonstrating that specific induction of OsSWEET14 is the key target of TalC. ArtTALs that specifically target individual members of the rice SWEET family revealed three known and two novel SWEET genes to support bacterial virulence. Our results demonstrate that five phylogenetically close SWEET proteins, which presumably act as sucrose transporters, can support Xoo virulence.
Collapse
Affiliation(s)
- Jana Streubel
- Department of Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, D-06120, Halle (Saale), Germany
| | - Céline Pesce
- UMR 186 IRD-UM2-Cirad 'Résistance des Plantes aux Bioagresseurs', BP 64501, 34394, Montpellier Cedex 5, France
- Earth and Life Institute, Applied Microbiology Phytopathology, Université Catholique de Louvain, 1348, Louvain-la-Neuve, Belgium
| | - Mathilde Hutin
- UMR 186 IRD-UM2-Cirad 'Résistance des Plantes aux Bioagresseurs', BP 64501, 34394, Montpellier Cedex 5, France
| | - Ralf Koebnik
- UMR 186 IRD-UM2-Cirad 'Résistance des Plantes aux Bioagresseurs', BP 64501, 34394, Montpellier Cedex 5, France
| | - Jens Boch
- Department of Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, D-06120, Halle (Saale), Germany
| | - Boris Szurek
- UMR 186 IRD-UM2-Cirad 'Résistance des Plantes aux Bioagresseurs', BP 64501, 34394, Montpellier Cedex 5, France
| |
Collapse
|
63
|
Kushalappa AC, Gunnaiah R. Metabolo-proteomics to discover plant biotic stress resistance genes. TRENDS IN PLANT SCIENCE 2013; 18:522-31. [PMID: 23790252 DOI: 10.1016/j.tplants.2013.05.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 04/26/2013] [Accepted: 05/17/2013] [Indexed: 05/23/2023]
Abstract
Plants continuously encounter various environmental stresses and use qualitative and quantitative measures to resist pathogen attack. Qualitative stress responses, based on monogenic inheritance, have been elucidated and successfully used in plant improvement. By contrast, quantitative stress responses remain largely unexplored in plant breeding, due to complex polygenic inheritance, although hundreds of quantitative trait loci for resistance have been identified. Recent advances in metabolomic and proteomic technologies now offer opportunities to overcome the hurdle of polygenic inheritance and identify candidate genes for use in plant breeding, thus improving the global food security. In this review, we describe a conceptual background to the plant-pathogen relationship and propose ten heuristic steps streamlining the application of metabolo-proteomics to improve plant resistance to biotic stress.
Collapse
Affiliation(s)
- Ajjamada C Kushalappa
- Plant Science Department, McGill University, Sainte-Anne-de-Bellevue, Quebec, H9X 3V9, Canada.
| | | |
Collapse
|
64
|
Pérez-Quintero AL, Rodriguez-R LM, Dereeper A, López C, Koebnik R, Szurek B, Cunnac S. An improved method for TAL effectors DNA-binding sites prediction reveals functional convergence in TAL repertoires of Xanthomonas oryzae strains. PLoS One 2013; 8:e68464. [PMID: 23869221 PMCID: PMC3711819 DOI: 10.1371/journal.pone.0068464] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 05/30/2013] [Indexed: 11/19/2022] Open
Abstract
Transcription Activators-Like Effectors (TALEs) belong to a family of virulence proteins from the Xanthomonas genus of bacterial plant pathogens that are translocated into the plant cell. In the nucleus, TALEs act as transcription factors inducing the expression of susceptibility genes. A code for TALE-DNA binding specificity and high-resolution three-dimensional structures of TALE-DNA complexes were recently reported. Accurate prediction of TAL Effector Binding Elements (EBEs) is essential to elucidate the biological functions of the many sequenced TALEs as well as for robust design of artificial TALE DNA-binding domains in biotechnological applications. In this work a program with improved EBE prediction performances was developed using an updated specificity matrix and a position weight correction function to account for the matching pattern observed in a validation set of TALE-DNA interactions. To gain a systems perspective on the large TALE repertoires from X. oryzae strains, this program was used to predict rice gene targets for 99 sequenced family members. Integrating predictions and available expression data in a TALE-gene network revealed multiple candidate transcriptional targets for many TALEs as well as several possible instances of functional convergence among TALEs.
Collapse
Affiliation(s)
- Alvaro L. Pérez-Quintero
- UMR 186 Résistance des Plantes aux Bioagresseurs, Institut de Recherche pour le Développement, Montpellier, France
- Biology Department, Universidad Nacional de Colombia, Bogotá D.C., Colombia
| | - Luis M. Rodriguez-R
- UMR 186 Résistance des Plantes aux Bioagresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Alexis Dereeper
- UMR 186 Résistance des Plantes aux Bioagresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Camilo López
- Biology Department, Universidad Nacional de Colombia, Bogotá D.C., Colombia
| | - Ralf Koebnik
- UMR 186 Résistance des Plantes aux Bioagresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Boris Szurek
- UMR 186 Résistance des Plantes aux Bioagresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Sebastien Cunnac
- UMR 186 Résistance des Plantes aux Bioagresseurs, Institut de Recherche pour le Développement, Montpellier, France
- * E-mail: .
| |
Collapse
|