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Chiang BJ, Lin KY, Chen YF, Huang CY, Goh FJ, Huang LT, Chen LH, Wu CH. Development of a tightly regulated copper-inducible transient gene expression system in Nicotiana benthamiana incorporating a suicide exon and Cre recombinase. THE NEW PHYTOLOGIST 2024; 244:318-331. [PMID: 39081031 DOI: 10.1111/nph.20021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 07/15/2024] [Indexed: 09/17/2024]
Abstract
Chemical-inducible gene expression systems are commonly used to regulate gene expression for functional genomics in various plant species. However, a convenient system that can tightly regulate transgene expression in Nicotiana benthamiana is still lacking. In this study, we developed a tightly regulated copper-inducible system that can control transgene expression and conduct cell death assays in N. benthamiana. We tested several chemical-inducible systems using Agrobacterium-mediated transient expression and found that the copper-inducible system exhibited the least concerns regarding leakiness in N. benthamiana. Although the copper-inducible system can control the expression of some tested reporters, it is not sufficiently tight to regulate certain tested hypersensitive cell death responses. Using the MoClo-based synthetic biology approach, we incorporated the suicide exon HyP5SM/OsL5 and Cre/LoxP as additional regulatory elements to enhance the tightness of the regulation. This new design allowed us to tightly control the hypersensitive cell death induced by several tested leucine-rich repeat-containing proteins and their matching avirulence factors, and it can be easily applied to regulate the expression of other transgenes in transient expression assays. Our findings offer new approaches for both fundamental and translational studies in plant functional genomics.
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Affiliation(s)
- Bing-Jen Chiang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115 201, Taiwan
| | - Kuan-Yu Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115 201, Taiwan
| | - Yi-Feng Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115 201, Taiwan
| | - Ching-Yi Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115 201, Taiwan
| | - Foong-Jing Goh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115 201, Taiwan
| | - Lo-Ting Huang
- Department of Plant Pathology, National Chung Hsing University, Taichung, 402 202, Taiwan
| | - Li-Hung Chen
- Department of Plant Pathology, National Chung Hsing University, Taichung, 402 202, Taiwan
- Advanced Plant and Food Crop Biotechnology Center, National Chung Hsing University, Taichung, 402 202, Taiwan
| | - Chih-Hang Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115 201, Taiwan
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Yang Y, Tan L, Xu X, Tang Q, Wang J, Xing S, Wang R, Zou T, Wang S, Zhu J, Li S, Liang Y, Deng Q, Li P. Activation and Autoinhibition Mechanisms of NLR Immune Receptor Pi36 in Rice. Int J Mol Sci 2024; 25:7301. [PMID: 39000408 PMCID: PMC11242311 DOI: 10.3390/ijms25137301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 06/23/2024] [Accepted: 06/27/2024] [Indexed: 07/16/2024] Open
Abstract
Nucleotide-binding and leucine-rich repeat receptors (NLRs) are the most important and largest class of immune receptors in plants. The Pi36 gene encodes a canonical CC-NBS-LRR protein that confers resistance to rice blast fungal infections. Here, we show that the CC domain of Pi36 plays a role in cell death induction. Furthermore, self-association is required for the CC domain-mediated cell death, and the self-association ability is correlated with the cell death level. In addition, the NB-ARC domain may suppress the activity of the CC domain through intramolecular interaction. The mutations D440G next to the RNBS-D motif and D503V in the MHD motif autoactivated Pi36, but the mutation K212 in the P-loop motif inhibited this autoactivation, indicating that nucleotide binding of the NB-ARC domain is essential for Pi36 activation. We also found that the LRR domain is required for D503V- and D440G-mediated Pi36 autoactivation. Interestingly, several mutations in the CC domain compromised the CC domain-mediated cell death without affecting the D440G- or D503V-mediated Pi36 autoactivation. The autoactivate Pi36 variants exhibited stronger self-associations than the inactive variants. Taken together, we speculated that the CC domain of Pi36 executes cell death activities, whereas the NB-ARC domain suppressed CC-mediated cell death via intermolecular interaction. The NB-ARC domain releases its suppression of the CC domain and strengthens the self-association of Pi36 to support the CC domain, possibly through nucleotide exchange.
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Affiliation(s)
- Yang Yang
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.Y.); (L.T.); (X.X.); (S.X.); (S.W.); (J.Z.)
| | - Liu Tan
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.Y.); (L.T.); (X.X.); (S.X.); (S.W.); (J.Z.)
| | - Xingzhe Xu
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.Y.); (L.T.); (X.X.); (S.X.); (S.W.); (J.Z.)
| | - Qiaoyi Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Q.T.); (J.W.); (R.W.); (S.L.); (Y.L.)
| | - Ji Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Q.T.); (J.W.); (R.W.); (S.L.); (Y.L.)
| | - Shiyue Xing
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.Y.); (L.T.); (X.X.); (S.X.); (S.W.); (J.Z.)
| | - Rui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Q.T.); (J.W.); (R.W.); (S.L.); (Y.L.)
| | - Ting Zou
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.Y.); (L.T.); (X.X.); (S.X.); (S.W.); (J.Z.)
| | - Shiquan Wang
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.Y.); (L.T.); (X.X.); (S.X.); (S.W.); (J.Z.)
| | - Jun Zhu
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.Y.); (L.T.); (X.X.); (S.X.); (S.W.); (J.Z.)
| | - Shuangcheng Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Q.T.); (J.W.); (R.W.); (S.L.); (Y.L.)
| | - Yueyang Liang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Q.T.); (J.W.); (R.W.); (S.L.); (Y.L.)
| | - Qiming Deng
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.Y.); (L.T.); (X.X.); (S.X.); (S.W.); (J.Z.)
| | - Ping Li
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.Y.); (L.T.); (X.X.); (S.X.); (S.W.); (J.Z.)
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Fu R, Zhao L, Chen C, Wang J, Lu D. Conjunctive Analysis of BSA-Seq and SSR Markers Unveil the Candidate Genes for Resistance to Rice False Smut. Biomolecules 2024; 14:79. [PMID: 38254679 PMCID: PMC10813778 DOI: 10.3390/biom14010079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/23/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
Rice false smut (RFS) caused by the fungus Ustilaginoidea virens (Cook) leads to serious yield losses in rice. Identification of the gene or quantitative trait loci (QTLs) is crucial to resistance breeding and mitigation of RFS damage. In this study, we crossed a resistant variety, IR77298-14-1-2::IRGC117374-1, with a susceptible indica cultivar, 9311, and evaluated recombinant inbred lines in a greenhouse. The genetic analysis showed that the RFS resistance of IR77298-14-1-2::IRGC117374-1 was controlled by multiple recessive loci. We identified a novel QTL, qRFS12.01, for RFS resistance in IR77298-14-1-2::IRGC117374-1 by combining bulked segregant analysis with whole genome resequencing (BSA-seq) and simple sequence repeat (SSR) marker mapping approaches. The phenotypic effect of qRFS12.01 on RFS resistance reached 28.74%, suggesting that SSR markers linked to qRFS12.01 are valuable for marker-assisted breeding of RFS resistance in rice. The prediction of putative candidate genes within qRFS12.01 revealed five disease resistance proteins containing NB-ARC domains. In conclusion, our findings provide a new rice chromosome region carrying genes/QTLs for resistance to RFS.
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Affiliation(s)
- Rongtao Fu
- Institute of Plant Protection, Sichuan Academy of Agricultural Science, Chengdu 610066, China; (R.F.)
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu 610066, China
| | - Liyu Zhao
- Institute of Plant Protection, Sichuan Academy of Agricultural Science, Chengdu 610066, China; (R.F.)
| | - Cheng Chen
- Institute of Plant Protection, Sichuan Academy of Agricultural Science, Chengdu 610066, China; (R.F.)
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu 610066, China
| | - Jian Wang
- Institute of Plant Protection, Sichuan Academy of Agricultural Science, Chengdu 610066, China; (R.F.)
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu 610066, China
| | - Daihua Lu
- Institute of Plant Protection, Sichuan Academy of Agricultural Science, Chengdu 610066, China; (R.F.)
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu 610066, China
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Cui W, Fiore N, Figueroa F, Rubilar C, Pizarro L, Pinto M, Pérez S, Beltrán MF, Carreras C, Pimentel P, Zamorano A. Transcriptome Analysis of Sweet Cherry ( Prunus avium L.) Cultivar 'Lapins' upon Infection of Pseudomonas syringae pv. syringae. PLANTS (BASEL, SWITZERLAND) 2023; 12:3718. [PMID: 37960074 PMCID: PMC10647540 DOI: 10.3390/plants12213718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 11/15/2023]
Abstract
Bacterial canker caused by Pseudomonas syringae pv. syringae (Pss) is responsible for substantial loss to the production of sweet cherry in Chile. To date, the molecular mechanisms of the Pss-sweet cherry interaction and the disease-related genes in the plant are poorly understood. In order to gain insight into these aspects, a transcriptomic analysis of the sweet cherry cultivar 'Lapins' for differentially expressed genes (DEGs) in response to Pss inoculation was conducted. Three Pss strains, A1M3, A1M197, and 11116_b1, were inoculated in young twigs, and RNA was extracted from tissue samples at the inoculation site and distal sections. RNA sequencing and transcriptomic expression analysis revealed that the three strains induced different patterns of responses in local and distal tissues. In the local tissues, A1M3 triggered a much more extensive response than the other two strains, enriching DEGs especially involved in photosynthesis. In the distal tissues, the three strains triggered a comparable extent of responses, among which 11116_b1 induced a group of DEGs involved in defense responses. Furthermore, tissues from various inoculations exhibited an enrichment of DEGs related to carbohydrate metabolism, terpene metabolism, and cell wall biogenesis. This study opened doors to future research on the Pss-sweet cherry interaction, immunity responses, and disease control.
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Affiliation(s)
- Weier Cui
- Laboratorio de Fitovirología, Departamento de Sanidad Vegetal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago 8820808, Chile; (W.C.); (N.F.); (M.F.B.); (C.C.)
| | - Nicola Fiore
- Laboratorio de Fitovirología, Departamento de Sanidad Vegetal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago 8820808, Chile; (W.C.); (N.F.); (M.F.B.); (C.C.)
| | - Franco Figueroa
- Laboratorio de Inmunidad Vegetal, Instituto de Ciencias Agroalimentarias, Universidad de O’Higgins, San Fernando 3070000, Chile; (F.F.); (C.R.); (L.P.); (M.P.)
| | - Carlos Rubilar
- Laboratorio de Inmunidad Vegetal, Instituto de Ciencias Agroalimentarias, Universidad de O’Higgins, San Fernando 3070000, Chile; (F.F.); (C.R.); (L.P.); (M.P.)
| | - Lorena Pizarro
- Laboratorio de Inmunidad Vegetal, Instituto de Ciencias Agroalimentarias, Universidad de O’Higgins, San Fernando 3070000, Chile; (F.F.); (C.R.); (L.P.); (M.P.)
| | - Manuel Pinto
- Laboratorio de Inmunidad Vegetal, Instituto de Ciencias Agroalimentarias, Universidad de O’Higgins, San Fernando 3070000, Chile; (F.F.); (C.R.); (L.P.); (M.P.)
| | - Set Pérez
- Laboratorio de Patología Vegetal, Instituto de Ciencias Agroalimentarias, Animales y Ambientales, Universidad de O’Higgins, San Fernando 3070000, Chile;
| | - María Francisca Beltrán
- Laboratorio de Fitovirología, Departamento de Sanidad Vegetal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago 8820808, Chile; (W.C.); (N.F.); (M.F.B.); (C.C.)
| | - Claudia Carreras
- Laboratorio de Fitovirología, Departamento de Sanidad Vegetal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago 8820808, Chile; (W.C.); (N.F.); (M.F.B.); (C.C.)
| | - Paula Pimentel
- Laboratorio de Fisiología del Estrés, Centro de Estudios Avanzados en Fruticultura (CEAF), Camino Las Parcelas, 882, Rengo 2940000, Chile;
| | - Alan Zamorano
- Laboratorio de Fitovirología, Departamento de Sanidad Vegetal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago 8820808, Chile; (W.C.); (N.F.); (M.F.B.); (C.C.)
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Khan MA, Cowling WA, Banga SS, Barbetti MJ, Cantila AY, Amas JC, Thomas WJ, You MP, Tyagi V, Bharti B, Edwards D, Batley J. Genetic and molecular analysis of stem rot (Sclerotinia sclerotiorum) resistance in Brassica napus (canola type). Heliyon 2023; 9:e19237. [PMID: 37674843 PMCID: PMC10477455 DOI: 10.1016/j.heliyon.2023.e19237] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 08/16/2023] [Accepted: 08/16/2023] [Indexed: 09/08/2023] Open
Abstract
Identifying the molecular and genetic basis of resistance to Sclerotinia stem rot (Sclerotinia sclerotiorum) is critical for developing long-term and cost-effective management of this disease in rapeseed/canola (Brassica napus). Current cultural or chemical management options provide, at best, only partial and/or sporadic control. Towards this, a B. napus breeding population (Mystic x Rainbow), including the parents, F1, F2, BC1P1 and BC1P2, was utilized in a field study to determine the inheritance pattern of Sclerotinia stem rot resistance (based on stem lesion length, SLL). Broad sense heritability was 0.58 for SLL and 0.44 for days to flowering (DTF). There was a significant negative correlation between SLL and stem diameter (SD) (r = -0.39) and between SLL and DTF (r = -0.28), suggesting co-selection of SD and DTF traits, along with SLL, should assist in improving overall resistance. Non-additive genetic variance was evident for SLL, DTF, and SD. In a genome wide association study (GWAS), a significant quantitative trait locus (QTL) was identified for SLL. Several putative candidate marker trait associations (MTA) were located within this QTL region. Overall, this study has provided valuable new understanding of inheritance of resistance to S. sclerotiorum, and has identified QTL, MTAs and transgressive segregants with high-level resistances. Together, these will foster more rapid selection for multiple traits associated with Sclerotinia stem rot resistance, by enabling breeders to make critical choices towards selecting/developing cultivars with enhanced resistance to this devastating pathogen.
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Affiliation(s)
- Muhammad Azam Khan
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia 6009
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6009
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Wallace A. Cowling
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia 6009
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6009
| | - Surinder Singh Banga
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Martin J. Barbetti
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia 6009
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6009
| | - Aldrin Y. Cantila
- School of Biological Sciences, The University of Western Australia, Perth, WA, Australia 6009
| | - Junrey C. Amas
- School of Biological Sciences, The University of Western Australia, Perth, WA, Australia 6009
| | - William J.W. Thomas
- School of Biological Sciences, The University of Western Australia, Perth, WA, Australia 6009
| | - Ming Pei You
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia 6009
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6009
| | - Vikrant Tyagi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Baudh Bharti
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - David Edwards
- School of Biological Sciences, The University of Western Australia, Perth, WA, Australia 6009
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6009
| | - Jacqueline Batley
- School of Biological Sciences, The University of Western Australia, Perth, WA, Australia 6009
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6009
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Xu Y, Gan ES, Ito T. Misexpression Approaches for the Manipulation of Flower Development. Methods Mol Biol 2023; 2686:429-451. [PMID: 37540372 DOI: 10.1007/978-1-0716-3299-4_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
The generation of dominant gain-of-function mutants through activation tagging is a forward genetic approach that can be applied to study the mechanisms of flower development, complementing the screening of loss-of-function mutants. In addition, the functions of genes of interest can be further analyzed through reverse genetics. A commonly used method is gene overexpression, where ectopic expression can result in an opposite phenotype to that caused by a loss-of-function mutation. When overexpression is detrimental, the misexpression of a gene using tissue-specific promoters can be useful to study spatial-specific function. As flower development is a multistep process, it can be advantageous to control gene expression, or its protein product activity, in a temporal and/or spatial manner. This has been made possible through several inducible promoter systems as well as inducible proteins by constructing chimeric fusions between the ligand-binding domain of the glucocorticoid receptor (GR) and the protein of interest. The recently introduced CRISPR-Cas9-based platform provides a new way of bioengineering transcriptional regulators in plants. By fusing a catalytically inactive dCas9 with functional activation or repression domains, the CRISPR-Cas9 module can achieve transcriptional activation or repression of endogenous genes. All these methods allow us to genetically manipulate gene expression during flower development. In this chapter, we describe methods to produce the expression constructs, method of screening, and more general applications of the techniques.
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Affiliation(s)
- Yifeng Xu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China.
| | - Eng-Seng Gan
- Republic Polytechnic, School of Applied Science (SAS), Singapore, Singapore
| | - Toshiro Ito
- Nara Institute of Science and Technology, Biological Sciences, Plant Stem Cell Regulation and Floral Patterning Laboratory, Ikoma, Nara, Japan.
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Cantila AY, Thomas WJW, Bayer PE, Edwards D, Batley J. Predicting Cloned Disease Resistance Gene Homologs (CDRHs) in Radish, Underutilised Oilseeds, and Wild Brassicaceae Species. PLANTS (BASEL, SWITZERLAND) 2022; 11:3010. [PMID: 36432742 PMCID: PMC9693284 DOI: 10.3390/plants11223010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
Brassicaceae crops, including Brassica, Camelina and Raphanus species, are among the most economically important crops globally; however, their production is affected by several diseases. To predict cloned disease resistance (R) gene homologs (CDRHs), we used the protein sequences of 49 cloned R genes against fungal and bacterial diseases in Brassicaceae species. In this study, using 20 Brassicaceae genomes (17 wild and 3 domesticated species), 3172 resistance gene analogs (RGAs) (2062 nucleotide binding-site leucine-rich repeats (NLRs), 497 receptor-like protein kinases (RLKs) and 613 receptor-like proteins (RLPs)) were identified. CDRH clusters were also observed in Arabis alpina, Camelina sativa and Cardamine hirsuta with assigned chromosomes, consisting of 62 homogeneous (38 NLR, 17 RLK and 7 RLP clusters) and 10 heterogeneous RGA clusters. This study highlights the prevalence of CDRHs in the wild relatives of the Brassicaceae family, which may lay the foundation for rapid identification of functional genes and genomics-assisted breeding to develop improved disease-resistant Brassicaceae crop cultivars.
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Zhang L, Liu Y, Wang Q, Wang C, Lv S, Wang Y, Wang J, Wang Y, Yuan J, Zhang H, Kang Z, Ji W. An alternative splicing isoform of wheat TaYRG1 resistance protein activates immunity by interacting with dynamin-related proteins. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5474-5489. [PMID: 35652375 DOI: 10.1093/jxb/erac245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Wheat (Triticum aestivum) is a commercially important crop and its production is seriously threatened by the fungal pathogen Puccinia striiformis f. sp. tritici West (Pst). Resistance (R) genes are critical factors that facilitate plant immune responses. Here, we report a wheat R gene NB-ARC-LRR ortholog, TaYRG1, that is associated with distinct alternative splicing events in wheat infected by Pst. The native splice variant, TaYRG1.6, encodes internal-motif-deleted polypeptides with the same N- and C-termini as TaYRG1.1, resulting in gain of function. Transient expression of protein variants in Nicotiana benthamiana showed that the NB and ARC domains, and TaYRG1.6 (half LRR domain), stimulate robust elicitor-independent cell death based on a signal peptide, although the activity was negatively modulated by the CC and complete LRR domains. Furthermore, molecular genetic analyses indicated that TaYRG1.6 enhanced resistance to Pst in wheat. Moreover, we provide multiple lines of evidence that TaYRG1.6 interacts with a dynamin-related protein, TaDrp1. Proteome profiling suggested that the TaYRG1.6-TaDrp1-DNM complex in the membrane trafficking systems may trigger cell death by mobilizing lipid and kinase signaling in the endocytosis pathway. Our findings reveal a unique mechanism by which TaYRG1 activates cell death and enhances disease resistance by reconfiguring protein structure through alternative splicing.
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Affiliation(s)
- Lu Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuanming Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Qiaohui Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Chao Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Shikai Lv
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Yanzhen Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Jianfeng Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Yajuan Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Jing Yuan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
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He H, Guo R, Gao A, Chen Z, Liu R, Liu T, Kang X, Zhu S. Large-scale mutational analysis of wheat powdery mildew resistance gene Pm21. FRONTIERS IN PLANT SCIENCE 2022; 13:988641. [PMID: 36017260 PMCID: PMC9396339 DOI: 10.3389/fpls.2022.988641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
Wheat powdery mildew is a devastating disease leading to severe yield loss. The powdery mildew resistance gene Pm21, encoding a nucleotide-binding leucine-rich repeat receptor (NLR) protein, confers broad-spectrum resistance to powdery mildew and has great potential for controlling this disease. In this study, a large-scale mutagenesis was conducted on wheat cultivar (cv.) Yangmai 18 carrying Pm21. As a result, a total of 113 independent mutant lines susceptible to powdery mildew were obtained, among which, only one lost the whole Pm21 locus and the other 112 harbored one- (107) or two-base (5) mutations in the encoding region of Pm21. From the 107 susceptible mutants containing one-base change, we found that 25 resulted in premature stop codons leading to truncated proteins and 82 led to amino acid changes involving in 59 functional sites. We determined the mutations per one hundred amino acids (MPHA) indexes of different domains, motifs, and non-domain and non-motif regions of PM21 protein and found that the loss-of-function mutations occurred in a tendentious means. We also observed a new mutation hotspot that was closely linked to RNBS-D motif of the NB-ARC domain and relatively conserved in different NLRs of wheat crops. In addition, we crossed all the susceptible mutants with Yangmai 18 carrying wild-type Pm21, subsequently phenotyped their F1 plants and revealed that the variant E44K in the coiled-coil (CC) domain could lead to dominant-negative effect. This study revealed key functional sites of PM21 and their distribution characteristics, which would contribute to understanding the relationship of resistance and structure of Pm21-encoded NLR.
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Affiliation(s)
- Huagang He
- School of Life Sciences, Jiangsu University, Zhenjiang, China
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Rui Guo
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Anli Gao
- School of Life Sciences, Henan University, Kaifeng, China
| | - Zhaozhao Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Renkang Liu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Tianlei Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Xusen Kang
- School of Life Sciences, Henan University, Kaifeng, China
| | - Shanying Zhu
- School of Environment, Jiangsu University, Zhenjiang, China
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10
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Mining of Cloned Disease Resistance Gene Homologs (CDRHs) in Brassica Species and Arabidopsis thaliana. BIOLOGY 2022; 11:biology11060821. [PMID: 35741342 PMCID: PMC9220128 DOI: 10.3390/biology11060821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/15/2022] [Accepted: 05/24/2022] [Indexed: 01/23/2023]
Abstract
Simple Summary Developing cultivars with resistance genes (R genes) is an effective strategy to support high yield and quality in Brassica crops. The availability of clone R gene and genomic sequences in Brassica species and Arabidopsis thaliana provide the opportunity to compare genomic regions and survey R genes across genomic databases. In this paper, we aim to identify genes related to cloned genes through sequence identity, providing a repertoire of species-wide related R genes in Brassica crops. The comprehensive list of candidate R genes can be used as a reference for functional analysis. Abstract Various diseases severely affect Brassica crops, leading to significant global yield losses and a reduction in crop quality. In this study, we used the complete protein sequences of 49 cloned resistance genes (R genes) that confer resistance to fungal and bacterial diseases known to impact species in the Brassicaceae family. Homology searches were carried out across Brassica napus, B. rapa, B. oleracea, B. nigra, B. juncea, B. carinata and Arabidopsis thaliana genomes. In total, 660 cloned disease R gene homologs (CDRHs) were identified across the seven species, including 431 resistance gene analogs (RGAs) (248 nucleotide binding site-leucine rich repeats (NLRs), 150 receptor-like protein kinases (RLKs) and 33 receptor-like proteins (RLPs)) and 229 non-RGAs. Based on the position and distribution of specific homologs in each of the species, we observed a total of 87 CDRH clusters composed of 36 NLR, 16 RLK and 3 RLP homogeneous clusters and 32 heterogeneous clusters. The CDRHs detected consistently across the seven species are candidates that can be investigated for broad-spectrum resistance, potentially providing resistance to multiple pathogens. The R genes identified in this study provide a novel resource for the future functional analysis and gene cloning of Brassicaceae R genes towards crop improvement.
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11
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Ahmed EA, Farrag AA, Kheder AA, Shaaban A. Effect of Phytoplasma Associated with Sesame Phyllody on Ultrastructural Modification, Physio-Biochemical Traits, Productivity and Oil Quality. PLANTS 2022; 11:plants11040477. [PMID: 35214810 PMCID: PMC8879811 DOI: 10.3390/plants11040477] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/08/2022] [Accepted: 02/08/2022] [Indexed: 11/24/2022]
Abstract
Phytoplasmas are obligate cell-wall-less plant pathogenic bacteria that infect many economically important crops, causing considerable yield losses worldwide. Very little information is known about phytoplasma–host plant interaction mechanisms and their influence on sesame yield and oil quality. Therefore, our aim was to explore the ultrastructural and agro-physio-biochemical responses of sesame plants and their effects on sesame productivity and oil quality in response to phytoplasma infection. Sesame leaf samples exhibiting phyllody symptoms were collected from three experimental fields during the 2021 growing season. Phytoplasma was successfully detected by nested- polymerase chain reaction (PCR) assays using the universal primer pairs P1/P7 and R16F2n/R16R2, and the product of approximately 1200 bp was amplified. The amplified product of 16S rRNA was sequenced and compared with other available phytoplasma’s 16S rRNA in the GenBank database. Phylogenetic analysis revealed that our Egyptian isolate under accession number MW945416 is closely related to the 16SrII group and showed close (99.7%) identity with MH011394 and L33765.1, which were isolated from Egypt and the USA, respectively. The microscopic examination of phytoplasma-infected plants revealed an observable deterioration in tissue and cell ultrastructure. The primary and secondary metabolites considerably increased in infected plants compared with healthy ones. Moreover, phytoplasma-infected plants showed drastically reduced water content, chlorophyll content, growth, and yield components, resulting in 37.9% and 42.5% reductions in seed and oil yield, respectively. The peroxide value of the infected plant’s oil was 43.2% higher than that of healthy ones, suggesting a short shelf-life. Our findings will provide a better understanding of the phyllody disease pathosystem, helping us to develop effective strategies for overcoming such diseases.
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Affiliation(s)
- Eman A. Ahmed
- Virus and Phytoplasma Research Department, Plant Pathology Research Institute, Agricultural Research Center, Giza 12619, Egypt; (E.A.A.); (A.A.F.); (A.A.K.)
| | - Amro A. Farrag
- Virus and Phytoplasma Research Department, Plant Pathology Research Institute, Agricultural Research Center, Giza 12619, Egypt; (E.A.A.); (A.A.F.); (A.A.K.)
| | - Ahmed A. Kheder
- Virus and Phytoplasma Research Department, Plant Pathology Research Institute, Agricultural Research Center, Giza 12619, Egypt; (E.A.A.); (A.A.F.); (A.A.K.)
| | - Ahmed Shaaban
- Agronomy Department, Faculty of Agriculture, Fayoum University, Fayoum 63514, Egypt
- Correspondence:
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12
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Analysis of the miRNA expression profile involved in the tomato spotted wilt orthotospovirus–pepper interaction. Virus Res 2022; 312:198710. [DOI: 10.1016/j.virusres.2022.198710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 02/12/2022] [Accepted: 02/12/2022] [Indexed: 11/30/2022]
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13
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Jia H, Xue S, Lei L, Fan M, Peng S, Li T, Nagarajan R, Carver B, Ma Z, Deng J, Yan L. A semi-dominant NLR allele causes whole-seedling necrosis in wheat. PLANT PHYSIOLOGY 2021; 186:483-496. [PMID: 33576803 PMCID: PMC8154059 DOI: 10.1093/plphys/kiab058] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/26/2021] [Indexed: 05/26/2023]
Abstract
Programmed cell death (PCD) and apoptosis have key functions in development and disease resistance in diverse organisms; however, the induction of necrosis remains poorly understood. Here, we identified a semi-dominant mutant allele that causes the necrotic death of the entire seedling (DES) of wheat (Triticum aestivum L.) in the absence of any pathogen or external stimulus. Positional cloning of the lethal allele mDES1 revealed that this premature death via necrosis was caused by a point mutation from Asp to Asn at amino acid 441 in a nucleotide-binding leucine-rich repeat protein containing nucleotide-binding domain and leucine-rich repeats. The overexpression of mDES1 triggered necrosis and PCD in transgenic plants. However, transgenic wheat harboring truncated wild-type DES1 proteins produced through gene editing that exhibited no significant developmental defects. The point mutation in mDES1 did not cause changes in this protein in the oligomeric state, but mDES1 failed to interact with replication protein A leading to abnormal mitotic cell division. DES1 is an ortholog of Sr35, which recognizes a Puccinia graminis f. sp. tritici stem rust disease effector in wheat, but mDES1 gained function as a direct inducer of plant death. These findings shed light on the intersection of necrosis, apoptosis, and autoimmunity in plants.
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Affiliation(s)
- Haiyan Jia
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK 74078, USA
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Jiangsu, Nanjing 210095, China
| | - Shulin Xue
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK 74078, USA
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Jiangsu, Nanjing 210095, China
| | - Lei Lei
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK 74078, USA
| | - Min Fan
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK 74078, USA
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Jiangsu, Nanjing 210095, China
| | - Shuxia Peng
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Tian Li
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK 74078, USA
| | - Ragupathi Nagarajan
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK 74078, USA
| | - Brett Carver
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK 74078, USA
| | - Zhengqiang Ma
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Jiangsu, Nanjing 210095, China
| | - Junpeng Deng
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Liuling Yan
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK 74078, USA
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14
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Ngou BPM, Ahn HK, Ding P, Jones JDG. Mutual potentiation of plant immunity by cell-surface and intracellular receptors. Nature 2021; 592:110-115. [PMID: 33692545 DOI: 10.1101/2020.04.10.034173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 02/01/2021] [Indexed: 05/25/2023]
Abstract
The plant immune system involves cell-surface receptors that detect intercellular pathogen-derived molecules, and intracellular receptors that activate immunity upon detection of pathogen-secreted effector proteins that act inside the plant cell. Immunity mediated by surface receptors has been extensively studied1, but that mediated by intracellular receptors has rarely been investigated in the absence of surface-receptor-mediated immunity. Furthermore, interactions between these two immune pathways are poorly understood. Here, by activating intracellular receptors without inducing surface-receptor-mediated immunity, we analyse interactions between these two distinct immune systems in Arabidopsis. Pathogen recognition by surface receptors activates multiple protein kinases and NADPH oxidases, and we find that intracellular receptors primarily potentiate the activation of these proteins by increasing their abundance through several mechanisms. Likewise, the hypersensitive response that depends on intracellular receptors is strongly enhanced by the activation of surface receptors. Activation of either immune system alone is insufficient to provide effective resistance against the bacterial pathogen Pseudomonas syringae. Thus, immune pathways activated by cell-surface and intracellular receptors in plants mutually potentiate to activate strong defences against pathogens. These findings reshape our understanding of plant immunity and have broad implications for crop improvement.
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Affiliation(s)
| | - Hee-Kyung Ahn
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Pingtao Ding
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK.
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands.
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15
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Ngou BPM, Ahn HK, Ding P, Jones JDG. Mutual potentiation of plant immunity by cell-surface and intracellular receptors. Nature 2021; 592:110-115. [PMID: 33692545 DOI: 10.1038/s41586-021-03315-7] [Citation(s) in RCA: 468] [Impact Index Per Article: 156.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 02/01/2021] [Indexed: 02/03/2023]
Abstract
The plant immune system involves cell-surface receptors that detect intercellular pathogen-derived molecules, and intracellular receptors that activate immunity upon detection of pathogen-secreted effector proteins that act inside the plant cell. Immunity mediated by surface receptors has been extensively studied1, but that mediated by intracellular receptors has rarely been investigated in the absence of surface-receptor-mediated immunity. Furthermore, interactions between these two immune pathways are poorly understood. Here, by activating intracellular receptors without inducing surface-receptor-mediated immunity, we analyse interactions between these two distinct immune systems in Arabidopsis. Pathogen recognition by surface receptors activates multiple protein kinases and NADPH oxidases, and we find that intracellular receptors primarily potentiate the activation of these proteins by increasing their abundance through several mechanisms. Likewise, the hypersensitive response that depends on intracellular receptors is strongly enhanced by the activation of surface receptors. Activation of either immune system alone is insufficient to provide effective resistance against the bacterial pathogen Pseudomonas syringae. Thus, immune pathways activated by cell-surface and intracellular receptors in plants mutually potentiate to activate strong defences against pathogens. These findings reshape our understanding of plant immunity and have broad implications for crop improvement.
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Affiliation(s)
| | - Hee-Kyung Ahn
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Pingtao Ding
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK. .,Institute of Biology Leiden, Leiden University, Leiden, The Netherlands.
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16
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Liu C, Atanasov KE, Arafaty N, Murillo E, Tiburcio AF, Zeier J, Alcázar R. Putrescine elicits ROS-dependent activation of the salicylic acid pathway in Arabidopsis thaliana. PLANT, CELL & ENVIRONMENT 2020; 43:2755-2768. [PMID: 32839979 DOI: 10.1111/pce.13874] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/21/2020] [Accepted: 08/22/2020] [Indexed: 05/20/2023]
Abstract
Polyamines are small amines that accumulate during stress and contribute to disease resistance through as yet unknown signaling pathways. Using a comprehensive RNA-sequencing analysis, we show that early transcriptional responses triggered by each of the most abundant polyamines (putrescine, spermidine, spermine, thermospermine and cadaverine) exhibit specific quantitative differences, suggesting that polyamines (rather than downstream metabolites) elicit defense responses. Signaling by putrescine, which accumulates in response to bacteria that trigger effector triggered immunity (ETI) and systemic acquired resistance (SAR), is largely dependent on the accumulation of hydrogen peroxide, and is partly dependent on salicylic acid (SA), the expression of ENHANCED DISEASE SUSCEPTIBILITY (EDS1) and NONEXPRESSOR of PR GENES1 (NPR1). Putrescine elicits local SA accumulation as well as local and systemic transcriptional reprogramming that overlaps with SAR. Loss-of-function mutations in arginine decarboxylase 2 (ADC2), which is required for putrescine synthesis and copper amine oxidase (CuAO), which is involved in putrescine oxidation, compromise basal defenses, as well as putrescine and pathogen-triggered systemic resistance. These findings confirm that putrescine elicits ROS-dependent SA pathways in the activation of plant defenses.
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Affiliation(s)
- Changxin Liu
- Department of Biology, Healthcare and Environment, Section of Plant Physiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Kostadin E Atanasov
- Department of Biology, Healthcare and Environment, Section of Plant Physiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Nazanin Arafaty
- Department of Biology, Healthcare and Environment, Section of Plant Physiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Ester Murillo
- Department of Biology, Healthcare and Environment, Section of Plant Physiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Antonio F Tiburcio
- Department of Biology, Healthcare and Environment, Section of Plant Physiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Jürgen Zeier
- Department of Biology, Institute for Molecular Ecophysiology of Plants, Heinrich Heine University, Düsseldorf, Germany
| | - Rubén Alcázar
- Department of Biology, Healthcare and Environment, Section of Plant Physiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
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17
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Pottinger SE, Innes RW. RPS5-Mediated Disease Resistance: Fundamental Insights and Translational Applications. ANNUAL REVIEW OF PHYTOPATHOLOGY 2020; 58:139-160. [PMID: 32284014 DOI: 10.1146/annurev-phyto-010820-012733] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Focusing on the discovery and characterization of the Arabidopsis disease resistance protein RPS5 and its guardee PBS1, this review discusses work done in the Innes laboratory from the initial identification of the RPS5 gene in 1995 to the recent deployment of the PBS1 decoy system in crops. This is done through discussion of the structure, function, and signaling environment of RPS5 and PBS1, highlighting collaborations and influential ideas along the way. RPS5, a nucleotide-binding leucine-rich repeat (NLR) protein, is activated by the proteolytic cleavage of PBS1. We have shown that the cleavage site within PBS1 can be altered to contain cleavage sites for other proteases, enabling RPS5 activation by these proteases, thereby conferring resistance to different pathogens. This decoy approach has since been translated into crop species using endogenous PBS1 orthologs and holds strong potential for GMO-free development of new genetic resistance against important crop pathogens.
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Affiliation(s)
- Sarah E Pottinger
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA;
| | - Roger W Innes
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA;
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18
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Xanthopoulou A, Manioudaki M, Bazakos C, Kissoudis C, Farsakoglou AM, Karagiannis E, Michailidis M, Polychroniadou C, Zambounis A, Kazantzis K, Tsaftaris A, Madesis P, Aravanopoulos F, Molassiotis A, Ganopoulos I. Whole genome re-sequencing of sweet cherry ( Prunus avium L.) yields insights into genomic diversity of a fruit species. HORTICULTURE RESEARCH 2020; 7:60. [PMID: 32377351 PMCID: PMC7193578 DOI: 10.1038/s41438-020-0281-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/17/2020] [Accepted: 02/18/2020] [Indexed: 05/30/2023]
Abstract
Sweet cherries, Prunus avium L. (Rosaceae), are gaining importance due to their perenniallity and nutritional attributes beneficial for human health. Interestingly, sweet cherry cultivars exhibit a wide range of phenotypic diversity in important agronomic traits, such as flowering time and defense reactions against pathogens. In this study, whole-genome resequencing (WGRS) was employed to characterize genetic variation, population structure and allelic variants in a panel of 20 sweet cherry and one wild cherry genotypes, embodying the majority of cultivated Greek germplasm and a representative of a local wild cherry elite phenotype. The 21 genotypes were sequenced in an average depth of coverage of 33.91×. and effective mapping depth, to the genomic reference sequence of 'Satonishiki' cultivar, between 22.21× to 36.62×. Discriminant analysis of principal components (DAPC) with SNPs revealed two clusters of genotypes. There was a rapid linkage disequilibrium decay, as the majority of SNP pairs with r2 in near complete disequilibrium (>0.8) were found at physical distances less than 10 kb. Functional analysis of the variants showed that the genomic ratio of non-synonymous/synonymous (dN/dS) changes was 1.78. The higher dN frequency in the Greek cohort of sweet cherry could be the result of artificial selection pressure imposed by breeding, in combination with the vegetative propagation of domesticated cultivars through grafting. The majority of SNPs with high impact (e.g., stop codon gaining, frameshift), were identified in genes involved in flowering time, dormancy and defense reactions against pathogens, providing promising resources for future breeding programs. Our study has established the foundation for further large scale characterization of sweet cherry germplasm, enabling breeders to incorporate diverse germplasm and allelic variants to fine tune flowering and maturity time and disease resistance in sweet cherry cultivars.
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Affiliation(s)
- Aliki Xanthopoulou
- Laboratory of Pomology, Department of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Maria Manioudaki
- Laboratory of Pomology, Department of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Christos Bazakos
- Institute of Plant Breeding and Genetic Resources, ELGO-DEMETER. Thermi, Thessaloniki, 570001 Greece
| | | | - Anna-Maria Farsakoglou
- Laboratory of Forest Genetics & Tree Breeding, Faculty of Agriculture, Forestry & Environmental Science, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Evangelos Karagiannis
- Laboratory of Pomology, Department of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Michail Michailidis
- Laboratory of Pomology, Department of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Chrysanthi Polychroniadou
- Laboratory of Pomology, Department of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Antonios Zambounis
- Institute of Plant Breeding and Genetic Resources, ELGO-DEMETER. Department of Deciduous Fruit Growing, Naoussa, 59035 Greece
| | - Konstantinos Kazantzis
- Institute of Plant Breeding and Genetic Resources, ELGO-DEMETER. Department of Deciduous Fruit Growing, Naoussa, 59035 Greece
| | | | - Panagiotis Madesis
- Institute of Applied Biosciences, CERTH, Thermi, Thessaloniki, 570 01 Greece
| | - Filippos Aravanopoulos
- Laboratory of Forest Genetics & Tree Breeding, Faculty of Agriculture, Forestry & Environmental Science, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Athanassios Molassiotis
- Laboratory of Pomology, Department of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, ELGO-DEMETER. Thermi, Thessaloniki, 570001 Greece
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19
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Hernandez J, Del Blanco A, Filichkin T, Fisk S, Gallagher L, Helgerson L, Meints B, Mundt C, Steffenson B, Hayes P. A Genome-Wide Association Study of Resistance to Puccinia striiformis f. sp. hordei and P. graminis f. sp. tritici in Barley and Development of Resistant Germplasm. PHYTOPATHOLOGY 2020; 110:1082-1092. [PMID: 32023173 DOI: 10.1094/phyto-11-19-0415-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Stripe rust (incited by Puccinia striiformis f. sp. hordei) and stem rust (incited by P. graminis f. sp. tritici) are two of the most important diseases affecting barley. Building on prior work involving the introgression of the resistance genes rpg4/Rpg5 into diverse genetic backgrounds and the discovery of additional quantitative trait locus (QTLs) for stem rust resistance, we generated an array of germplasm in which we mapped resistance to stripe rust and stem rust. Stem rust races TTKSK and QCCJB were used for resistance mapping at the seedling and adult plant stages, respectively. Resistance to stripe rust, at the adult plant stage, was determined by QTLs on chromosomes 1H, 4H, and 5H that were previously reported in the literature. The rpg4/Rpg5 complex was validated as a source of resistance to stem rust at the seedling stage. Some parental germplasm, selected as potentially resistant to stem rust or susceptible but having other positive attributes, showed resistance at the seedling stage, which appears to be allelic to rpg4/Rpg5. The rpg4/Rpg5 complex, and this new allele, were not sufficient for adult plant resistance to stem rust in one environment. A QTL on 5H, distinct from Rpg5 and a previously reported resistance QTL, was required for resistance at the adult plant stage in all environments. This QTL is coincident with the QTL for stripe rust resistance. Germplasm with mapped genes/QTLs conferring resistance to stripe and stem rust was identified and is available as a resource to the research and breeding communities.
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Affiliation(s)
- Javier Hernandez
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Alicia Del Blanco
- Department of Plant Sciences, University of California-Davis, Davis, CA 95616
| | - Tanya Filichkin
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Scott Fisk
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Lynn Gallagher
- Department of Plant Sciences, University of California-Davis, Davis, CA 95616
| | - Laura Helgerson
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Brigid Meints
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Chris Mundt
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Brian Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Patrick Hayes
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
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20
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Ngou BPM, Ahn HK, Ding P, Redkar A, Brown H, Ma Y, Youles M, Tomlinson L, Jones JDG. Estradiol-inducible AvrRps4 expression reveals distinct properties of TIR-NLR-mediated effector-triggered immunity. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2186-2197. [PMID: 32050020 PMCID: PMC7242080 DOI: 10.1093/jxb/erz571] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 01/14/2020] [Indexed: 05/18/2023]
Abstract
Plant nucleotide-binding domain, leucine-rich repeat receptor (NLR) proteins play important roles in recognition of pathogen-derived effectors. However, the mechanism by which plant NLRs activate immunity is still largely unknown. The paired Arabidopsis NLRs RRS1-R and RPS4, that confer recognition of bacterial effectors AvrRps4 and PopP2, are well studied, but how the RRS1/RPS4 complex activates early immediate downstream responses upon effector detection is still poorly understood. To study RRS1/RPS4 responses without the influence of cell surface receptor immune pathways, we generated an Arabidopsis line with inducible expression of the effector AvrRps4. Induction does not lead to hypersensitive cell death response (HR) but can induce electrolyte leakage, which often correlates with plant cell death. Activation of RRS1 and RPS4 without pathogens cannot activate mitogen-associated protein kinase cascades, but still activates up-regulation of defence genes, and therefore resistance against bacteria.
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Affiliation(s)
- Bruno Pok Man Ngou
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Hee-Kyung Ahn
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Pingtao Ding
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Amey Redkar
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Department of Genetics, University of Córdoba, Córdoba, Spain
| | - Hannah Brown
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Yan Ma
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Mark Youles
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Laurence Tomlinson
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
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21
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Halder J, Zhang J, Ali S, Sidhu JS, Gill HS, Talukder SK, Kleinjan J, Turnipseed B, Sehgal SK. Mining and genomic characterization of resistance to tan spot, Stagonospora nodorum blotch (SNB), and Fusarium head blight in Watkins core collection of wheat landraces. BMC PLANT BIOLOGY 2019; 19:480. [PMID: 31703626 PMCID: PMC6839225 DOI: 10.1186/s12870-019-2093-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 10/21/2019] [Indexed: 05/26/2023]
Abstract
BACKGROUND In the late 1920s, A. E. Watkins collected about 7000 landrace cultivars (LCs) of bread wheat (Triticum aestivum L.) from 32 different countries around the world. Among which 826 LCs remain viable and could be a valuable source of superior/favorable alleles to enhance disease resistance in wheat. In the present study, a core set of 121 LCs, which captures the majority of the genetic diversity of Watkins collection, was evaluated for identifying novel sources of resistance against tan spot, Stagonospora nodorum blotch (SNB), and Fusarium Head Blight (FHB). RESULTS A diverse response was observed in 121 LCs for all three diseases. The majority of LCs were moderately susceptible to susceptible to tan spot Ptr race 1 (84%) and FHB (96%) whereas a large number of LCs were resistant or moderately resistant against tan spot Ptr race 5 (95%) and SNB (54%). Thirteen LCs were identified in this study could be a valuable source for multiple resistance to tan spot Ptr races 1 and 5, and SNB, and another five LCs could be a potential source for FHB resistance. GWAS analysis was carried out using disease phenotyping score and 8807 SNPs data of 118 LCs, which identified 30 significant marker-trait associations (MTAs) with -log10 (p-value) > 3.0. Ten, five, and five genomic regions were found to be associated with resistance to tan spot Ptr race 1, race 5, and SNB, respectively in this study. In addition to Tsn1, several novel genomic regions Q.Ts1.sdsu-4BS and Q.Ts1.sdsu-5BS (tan spot Ptr race 1) and Q.Ts5.sdsu-1BL, Q.Ts5.sdsu-2DL, Q.Ts5.sdsu-3AL, and Q.Ts5.sdsu-6BL (tan spot Ptr race 5) were also identified. Our results indicate that these putative genomic regions contain several genes that play an important role in plant defense mechanisms. CONCLUSION Our results suggest the existence of valuable resistant alleles against leaf spot diseases in Watkins LCs. The single-nucleotide polymorphism (SNP) markers linked to the quantitative trait loci (QTLs) for tan spot and SNB resistance along with LCs harboring multiple disease resistance could be useful for future wheat breeding.
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Affiliation(s)
- Jyotirmoy Halder
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Jinfeng Zhang
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Shaukat Ali
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Jagdeep S Sidhu
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Harsimardeep S Gill
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Shyamal K Talukder
- California Cooperative Rice Research Foundation, Inc., Rice Experiment Station, Biggs, CA, 95917, USA
| | - Jonathan Kleinjan
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Brent Turnipseed
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Sunish K Sehgal
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA.
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Yan J, Liu Y, Huang X, Li L, Hu Z, Zhang J, Qin Q, Yan L, He K, Wang Y, Hou S. An unreported NB-LRR protein SUT1 is required for the autoimmune response mediated by type one protein phosphatase 4 mutation (topp4-1) in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:357-373. [PMID: 31257685 DOI: 10.1111/tpj.14447] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 06/08/2019] [Accepted: 06/13/2019] [Indexed: 06/09/2023]
Abstract
Our previous study indicates that protein phosphatase 1 (PP1) is involved in plant immunity. To elucidate the underlying molecular mechanism, a genetic screening assay was carried out to identify suppressors of type one protein phosphatase 4 mutation (topp4-1) (sut). Molecular and genetic approaches were used to investigate the mechanism of activation of autoimmune response in topp4-1. We performed a map-based cloning assay to identify the SUT1 gene, which encodes a coiled-coil nucleotide-binding leucine-rich-repeat (NB-LRR) protein (CNL). SUT1 physically interacts with TYPE ONE PROTEIN PHOSPHATASE 4 (TOPP4) and topp4-1. The mutated topp4-1 protein activates the autoimmune response in the cytoplasm and promotes the accumulation of SUT1 at both the transcription and the protein levels. Furthermore, our genetic and physical interactions confirm that the topp4-1-induced autoimmune responses are probably mediated by HEAT SHOCK PROTEIN 90 (HSP90) and REQUIRED FOR MLA12 RESISTANCE 1 (RAR1). This study reveals that TOPP4 phosphatase is likely guarded by SUT1 in plant immunity.
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Affiliation(s)
- Jia Yan
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yaqiong Liu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lang Li
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Zhihong Hu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Jing Zhang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Qianqian Qin
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Longfeng Yan
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Kai He
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Suiwen Hou
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
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23
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Li TG, Wang BL, Yin CM, Zhang DD, Wang D, Song J, Zhou L, Kong ZQ, Klosterman SJ, Li JJ, Adamu S, Liu TL, Subbarao KV, Chen JY, Dai XF. The Gossypium hirsutum TIR-NBS-LRR gene GhDSC1 mediates resistance against Verticillium wilt. MOLECULAR PLANT PATHOLOGY 2019; 20:857-876. [PMID: 30957942 DOI: 10.5897/ajmr11.781] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Improving genetic resistance is a preferred method to manage Verticillium wilt of cotton and other hosts. Identifying host resistance is difficult because of the dearth of resistance genes against this pathogen. Previously, a novel candidate gene involved in Verticillium wilt resistance was identified by a genome-wide association study using a panel of Gossypium hirsutum accessions. In this study, we cloned the candidate resistance gene from cotton that encodes a protein sharing homology with the TIR-NBS-LRR receptor-like defence protein DSC1 in Arabidopsis thaliana (hereafter named GhDSC1). GhDSC1 expressed at higher levels in response to Verticillium wilt and jasmonic acid (JA) treatment in resistant cotton cultivars as compared to susceptible cultivars and its product was localized to nucleus. The transfer of GhDSC1 to Arabidopsis conferred Verticillium resistance in an A. thaliana dsc1 mutant. This resistance response was associated with reactive oxygen species (ROS) accumulation and increased expression of JA-signalling-related genes. Furthermore, the expression of GhDSC1 in response to Verticillium wilt and JA signalling in A. thaliana displayed expression patterns similar to GhCAMTA3 in cotton under identical conditions, suggesting a coordinated DSC1 and CAMTA3 response in A. thaliana to Verticillium wilt. Analyses of GhDSC1 sequence polymorphism revealed a single nucleotide polymorphism (SNP) difference between resistant and susceptible cotton accessions, within the P-loop motif encoded by GhDSC1. This SNP difference causes ineffective activation of defence response in susceptible cultivars. These results demonstrated that GhDSC1 confers Verticillium resistance in the model plant system of A. thaliana, and therefore represents a suitable candidate for the genetic engineering of Verticillium wilt resistance in cotton.
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Affiliation(s)
- Ting-Gang Li
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Bao-Li Wang
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Chun-Mei Yin
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Dan-Dan Zhang
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, 100193, China
| | - Dan Wang
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jian Song
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lei Zhou
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, 100193, China
| | - Zhi-Qiang Kong
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Steven J Klosterman
- United States Department of Agriculture, Agricultural Research Service, Salinas, California, USA
| | - Jun-Jiao Li
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Sabiu Adamu
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ting-Li Liu
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, 210014, China
| | - Krishna V Subbarao
- Department of Plant Pathology, University of California, Davis, c/o United States Agricultural Research Station, Salinas, California, USA
| | - Jie-Yin Chen
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, 100193, China
| | - Xiao-Feng Dai
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, 100193, China
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24
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Li T, Wang B, Yin C, Zhang D, Wang D, Song J, Zhou L, Kong Z, Klosterman SJ, Li J, Adamu S, Liu T, Subbarao KV, Chen J, Dai X. The Gossypium hirsutum TIR-NBS-LRR gene GhDSC1 mediates resistance against Verticillium wilt. MOLECULAR PLANT PATHOLOGY 2019; 20:857-876. [PMID: 30957942 PMCID: PMC6637886 DOI: 10.1111/mpp.12797] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Improving genetic resistance is a preferred method to manage Verticillium wilt of cotton and other hosts. Identifying host resistance is difficult because of the dearth of resistance genes against this pathogen. Previously, a novel candidate gene involved in Verticillium wilt resistance was identified by a genome-wide association study using a panel of Gossypium hirsutum accessions. In this study, we cloned the candidate resistance gene from cotton that encodes a protein sharing homology with the TIR-NBS-LRR receptor-like defence protein DSC1 in Arabidopsis thaliana (hereafter named GhDSC1). GhDSC1 expressed at higher levels in response to Verticillium wilt and jasmonic acid (JA) treatment in resistant cotton cultivars as compared to susceptible cultivars and its product was localized to nucleus. The transfer of GhDSC1 to Arabidopsis conferred Verticillium resistance in an A. thaliana dsc1 mutant. This resistance response was associated with reactive oxygen species (ROS) accumulation and increased expression of JA-signalling-related genes. Furthermore, the expression of GhDSC1 in response to Verticillium wilt and JA signalling in A. thaliana displayed expression patterns similar to GhCAMTA3 in cotton under identical conditions, suggesting a coordinated DSC1 and CAMTA3 response in A. thaliana to Verticillium wilt. Analyses of GhDSC1 sequence polymorphism revealed a single nucleotide polymorphism (SNP) difference between resistant and susceptible cotton accessions, within the P-loop motif encoded by GhDSC1. This SNP difference causes ineffective activation of defence response in susceptible cultivars. These results demonstrated that GhDSC1 confers Verticillium resistance in the model plant system of A. thaliana, and therefore represents a suitable candidate for the genetic engineering of Verticillium wilt resistance in cotton.
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Affiliation(s)
- Ting‐Gang Li
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Bao‐Li Wang
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Chun‐Mei Yin
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Dan‐Dan Zhang
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
- Key Laboratory of Agro‐products Quality and Safety Control in Storage and Transport Process, Ministry of AgricultureBeijing100193China
| | - Dan Wang
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Jian Song
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Lei Zhou
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
- Key Laboratory of Agro‐products Quality and Safety Control in Storage and Transport Process, Ministry of AgricultureBeijing100193China
| | - Zhi‐Qiang Kong
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Steven J. Klosterman
- United States Department of AgricultureAgricultural Research ServiceSalinasCaliforniaUSA
| | - Jun‐Jiao Li
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Sabiu Adamu
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Ting‐Li Liu
- Provincial Key Laboratory of AgrobiologyJiangsu Academy of Agricultural SciencesNanjingJiangsu210014China
| | - Krishna V. Subbarao
- Department of Plant PathologyUniversity of California, Davis, c/o United States Agricultural Research StationSalinasCaliforniaUSA
| | - Jie‐Yin Chen
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
- Key Laboratory of Agro‐products Quality and Safety Control in Storage and Transport Process, Ministry of AgricultureBeijing100193China
| | - Xiao‐Feng Dai
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
- Key Laboratory of Agro‐products Quality and Safety Control in Storage and Transport Process, Ministry of AgricultureBeijing100193China
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25
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Dracatos PM, Bartoš J, Elmansour H, Singh D, Karafiátová M, Zhang P, Steuernagel B, Svačina R, Cobbin JCA, Clark B, Hoxha S, Khatkar MS, Doležel J, Wulff BB, Park RF. The Coiled-Coil NLR Rph1, Confers Leaf Rust Resistance in Barley Cultivar Sudan. PLANT PHYSIOLOGY 2019; 179:1362-1372. [PMID: 30593453 PMCID: PMC6446784 DOI: 10.1104/pp.18.01052] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 12/18/2018] [Indexed: 05/18/2023]
Abstract
Unraveling and exploiting mechanisms of disease resistance in cereal crops is currently limited by their large repeat-rich genomes and the lack of genetic recombination or cultivar (cv)-specific sequence information. We cloned the first leaf rust resistance gene Rph1 (Rph1 a) from cultivated barley (Hordeum vulgare) using "MutChromSeq," a recently developed molecular genomics tool for the rapid cloning of genes in plants. Marker-trait association in the CI 9214/Stirling doubled haploid population mapped Rph1 to the short arm of chromosome 2H in a physical region of 1.3 megabases relative to the barley cv Morex reference assembly. A sodium azide mutant population in cv Sudan was generated and 10 mutants were confirmed by progeny-testing. Flow-sorted 2H chromosomes from Sudan (wild type) and six of the mutants were sequenced and compared to identify candidate genes for the Rph1 locus. MutChromSeq identified a single gene candidate encoding a coiled-coil nucleotide binding site Leucine-rich repeat (NLR) receptor protein that was altered in three different mutants. Further Sanger sequencing confirmed all three mutations and identified an additional two independent mutations within the same candidate gene. Phylogenetic analysis determined that Rph1 clustered separately from all previously cloned NLRs from the Triticeae and displayed highest sequence similarity (89%) with a homolog of the Arabidopsis (Arabidopsis thaliana) disease resistance protein 1 protein in Triticum urartu In this study we determined the molecular basis for Rph1-mediated resistance in cultivated barley enabling varietal improvement through diagnostic marker design, gene editing, and gene stacking technologies.
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Affiliation(s)
- Peter Michael Dracatos
- Sydney Institute of Agriculture, Plant Breeding Institute, The University of Sydney, Narellan, NSW 2567, Australia
| | - Jan Bartoš
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc CZ-78371, Czech Republic
| | - Huda Elmansour
- Sydney Institute of Agriculture, Plant Breeding Institute, The University of Sydney, Narellan, NSW 2567, Australia
| | - Davinder Singh
- Sydney Institute of Agriculture, Plant Breeding Institute, The University of Sydney, Narellan, NSW 2567, Australia
| | - Miroslava Karafiátová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc CZ-78371, Czech Republic
| | - Peng Zhang
- Sydney Institute of Agriculture, Plant Breeding Institute, The University of Sydney, Narellan, NSW 2567, Australia
| | | | - Radim Svačina
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc CZ-78371, Czech Republic
| | - Joanna C A Cobbin
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Bethany Clark
- Sydney Institute of Agriculture, Plant Breeding Institute, The University of Sydney, Narellan, NSW 2567, Australia
| | - Sami Hoxha
- Sydney Institute of Agriculture, Plant Breeding Institute, The University of Sydney, Narellan, NSW 2567, Australia
| | - Mehar S Khatkar
- Faculty of Veterinary Science, The University of Sydney, Camden, NSW 2570, Australia
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc CZ-78371, Czech Republic
| | | | - Robert F Park
- Sydney Institute of Agriculture, Plant Breeding Institute, The University of Sydney, Narellan, NSW 2567, Australia
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Chakraborty J, Priya P, Dastidar SG, Das S. Physical interaction between nuclear accumulated CC-NB-ARC-LRR protein and WRKY64 promotes EDS1 dependent Fusarium wilt resistance in chickpea. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 276:111-133. [PMID: 30348309 DOI: 10.1016/j.plantsci.2018.08.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/30/2018] [Accepted: 08/17/2018] [Indexed: 06/08/2023]
Abstract
Fusarium wilt is one of the most serious diseases affecting chickpea (Cicer arietinum L.). Here, we identified a putative Resistance Gene Analog (CaRGA) from chickpea, encoding a coiled-coil (CC) nucleotide-binding oligomerization domain (NB-ARC) containing leucine-rich repeat (LRR) protein (CC-NLR protein) that confers resistance against Fusarium oxysporum f. sp. ciceri race1 (Foc1). Over-expression and silencing of CaRGA in chickpea resulted in enhanced resistance and hyper-susceptibility, respectively against Foc1. Furthermore, defense response to Foc1 depends on CC-NLR interaction with WRKY64 transcription factor. CaRGA mediated wilt resistance largely compromised when WRKY64 was silenced. We also determined in planta intramolecular interactions and self-association of chickpea CC-NLR protein. The study shows CC domain suppressing auto-activation of the full-length CC-NLR protein in the absence of pathogen through self-inhibitory intramolecular interaction with NB-ARC domain, which is attenuated by self-interactions to LRR domain. Chickpea CC-NLR protein forms homocomplexes and then interacts with WRKY64. CC-NLR protein further phosphorylates WRKY64 thereby, ubiquitination and proteasome mediated degradation are protected. Phosphorylated WRKY64 with increased stability binds to EDS1 promoter and stimulates its transcription that induces in planta ectopic cell-death. The detailed analysis of CC-NLR and WRKY interactions provide a better understanding of the immune regulation by NLR proteins under biotic stresses.
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Affiliation(s)
- Joydeep Chakraborty
- Division of Plant Biology, Bose Institute, Centenary Campus, P-1/12, CIT Scheme-VIIM, Kankurgachi, Kolkata 700054, West Bengal, India.
| | - Prerna Priya
- Centre of Excellence in Bioinformatics, Bose Institute, Centenary Campus, P-1/12, CIT Scheme-VIIM, Kankurgachi, Kolkata 700054, West Bengal, India.
| | - Shubhra Ghosh Dastidar
- Centre of Excellence in Bioinformatics, Bose Institute, Centenary Campus, P-1/12, CIT Scheme-VIIM, Kankurgachi, Kolkata 700054, West Bengal, India.
| | - Sampa Das
- Division of Plant Biology, Bose Institute, Centenary Campus, P-1/12, CIT Scheme-VIIM, Kankurgachi, Kolkata 700054, West Bengal, India.
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27
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Deng Y, Chen H, Zhang C, Cai T, Zhang B, Zhou S, Fountain JC, Pan RL, Guo B, Zhuang WJ. Evolution and characterisation of the AhRAF4 NB-ARC gene family induced by Aspergillus flavus inoculation and abiotic stresses in peanut. PLANT BIOLOGY (STUTTGART, GERMANY) 2018; 20:737-750. [PMID: 29603544 DOI: 10.1111/plb.12726] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 03/23/2018] [Indexed: 06/08/2023]
Abstract
Aflatoxin contamination in peanut is a serious food safety issue to human health around the world. Finding disease resistance genes is a key strategy for genetic improvement in breeding to deal with this issue. We identified an Aspergillus flavus-induced NBS-LRR gene, AhRAF4, using a microarray-based approach. By comparison of 23 sequences from three species using phytogenetics, protein secondary structure and three-dimensional structural analyses, AhRAF4 was revealed to be derived from Arachis duranensis by recombination, and has newly evolved into a family of several members, characterised by duplications and point mutations. However, the members of the family descended from A. ipaensis were lost following tetraploidisation. AhRAF4 was slightly up-regulated by low temperature, drought, salicylic acid and ethylene, but down-regulated by methyl jasmonate. The distinct responses upon As. flavus inoculation and the differential reactions between resistant and susceptible varieties indicate that AhRAF4 might play a role in defence responses. Temporal and spatial expression and the phenotype of transformed protoplasts suggest that AhRAF4 may also be associated with pericarp development. Because tetraploid cultivated peanuts are vulnerable to many pathogens, an exploration of R-genes may provide an effective method for genetic improvement of peanut cultivars.
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Affiliation(s)
- Y Deng
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - H Chen
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - C Zhang
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - T Cai
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - B Zhang
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - S Zhou
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - J C Fountain
- Department of Plant Pathology, University of Georgia, Tifton, GA, USA
| | - R-L Pan
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, Hsin Chu, Taiwan, China
| | - B Guo
- Department of Plant Pathology, University of Georgia, Tifton, GA, USA
- Crop Protection and Management Research Unit, US Department of Agriculture, Agricultural Research Service, Tifton, GA, USA
| | - W-J Zhuang
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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28
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Borrelli GM, Mazzucotelli E, Marone D, Crosatti C, Michelotti V, Valè G, Mastrangelo AM. Regulation and Evolution of NLR Genes: A Close Interconnection for Plant Immunity. Int J Mol Sci 2018; 19:E1662. [PMID: 29867062 PMCID: PMC6032283 DOI: 10.3390/ijms19061662] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/01/2018] [Accepted: 06/02/2018] [Indexed: 12/12/2022] Open
Abstract
NLR (NOD-like receptor) genes belong to one of the largest gene families in plants. Their role in plants' resistance to pathogens has been clearly described for many members of this gene family, and dysregulation or overexpression of some of these genes has been shown to induce an autoimmunity state that strongly affects plant growth and yield. For this reason, these genes have to be tightly regulated in their expression and activity, and several regulatory mechanisms are described here that tune their gene expression and protein levels. This gene family is subjected to rapid evolution, and to maintain diversity at NLRs, a plethora of genetic mechanisms have been identified as sources of variation. Interestingly, regulation of gene expression and evolution of this gene family are two strictly interconnected aspects. Indeed, some examples have been reported in which mechanisms of gene expression regulation have roles in promotion of the evolution of this gene family. Moreover, co-evolution of the NLR gene family and other gene families devoted to their control has been recently demonstrated, as in the case of miRNAs.
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Affiliation(s)
- Grazia M Borrelli
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 673, km 25.2, 71122 Foggia, Italy.
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Daniela Marone
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 673, km 25.2, 71122 Foggia, Italy.
| | - Cristina Crosatti
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Vania Michelotti
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Giampiero Valè
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100 Vercelli, Italy.
| | - Anna M Mastrangelo
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, via Stezzano 24, 24126 Bergamo, Italy.
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Choudhury S, Hu H, Larkin P, Meinke H, Shabala S, Ahmed I, Zhou M. Agronomical, biochemical and histological response of resistant and susceptible wheat and barley under BYDV stress. PeerJ 2018; 6:e4833. [PMID: 29868264 PMCID: PMC5978399 DOI: 10.7717/peerj.4833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 05/03/2018] [Indexed: 11/20/2022] Open
Abstract
Barley yellow dwarf virus-PAV (BYDV-PAV) is one of the major viruses causing a widespread and serious viral disease affecting cereal crops. To gain a better understanding of plant defence mechanisms of BYDV resistance genes (Bdv2 and RYd2) against BYDV-PAV infection, the differences in agronomical, biochemical and histological changes between susceptible and resistant wheat and barley cultivars were investigated. We found that root growth and total dry matter of susceptible cultivars showed greater reduction than that of resistant ones after infection. BYDV infected leaves in susceptible wheat and barley cultivars showed a significant reduction in photosynthetic pigments, an increase in the concentration of reducing sugar. The protein levels were also low in infected leaves. There was a significant increase in total phenol contents in resistant cultivars, which might reflect a protective mechanism of plants against virus infection. In phloem tissue, sieve elements (SE) and companion cells (CC) were severely damaged in susceptible cultivars after infection. It is suggested that restriction of viral movement in the phloem tissue and increased production of phenolic compounds may play a role in the resistance and defensive mechanisms of both Bdv2 and RYd2 against virus infection.
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Affiliation(s)
- Shormin Choudhury
- Tasmanian Institute of Agriculture, University of Tasmania, Prospect, Tasmania, Australia
- Department of Horticulture, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Sher-e-Bangla Nagar, Dhaka, Bangladesh
| | - Hongliang Hu
- Tasmanian Institute of Agriculture, University of Tasmania, Prospect, Tasmania, Australia
| | | | - Holger Meinke
- Tasmanian Institute of Agriculture, University of Tasmania, Prospect, Tasmania, Australia
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Ibrahim Ahmed
- Tasmanian Institute of Agriculture, University of Tasmania, Prospect, Tasmania, Australia
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Prospect, Tasmania, Australia
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Li NY, Zhou L, Zhang DD, Klosterman SJ, Li TG, Gui YJ, Kong ZQ, Ma XF, Short DPG, Zhang WQ, Li JJ, Subbarao KV, Chen JY, Dai XF. Heterologous Expression of the Cotton NBS-LRR Gene GbaNA1 Enhances Verticillium Wilt Resistance in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2018; 9:119. [PMID: 29467784 PMCID: PMC5808209 DOI: 10.3389/fpls.2018.00119] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 01/22/2018] [Indexed: 05/06/2023]
Abstract
Verticillium wilt caused by Verticillium dahliae results in severe losses in cotton, and is economically the most destructive disease of this crop. Improving genetic resistance is the cleanest and least expensive option to manage Verticillium wilt. Previously, we identified the island cotton NBS-LRR-encoding gene GbaNA1 that confers resistance to the highly virulent V. dahliae isolate Vd991. In this study, we expressed cotton GbaNA1 in the heterologous system of Arabidopsis thaliana and investigated the defense response mediated by GbaNA1 following inoculations with V. dahliae. Heterologous expression of GbaNA1 conferred Verticillium wilt resistance in A. thaliana. Moreover, overexpression of GbaNA1 enabled recovery of the resistance phenotype of A. thaliana mutants that had lost the function of GbaNA1 ortholog gene. Investigations of the defense response in A. thaliana showed that the reactive oxygen species (ROS) production and the expression of genes associated with the ethylene signaling pathway were enhanced significantly following overexpression of GbaNA1. Intriguingly, overexpression of the GbaNA1 ortholog from Gossypium hirsutum (GhNA1) in A. thaliana did not induce the defense response of ROS production due to the premature termination of GhNA1, which lacks the encoded NB-ARC and LRR motifs. GbaNA1 therefore confers Verticillium wilt resistance in A. thaliana by the activation of ROS production and ethylene signaling. These results demonstrate the functional conservation of the NBS-LRR-encoding GbaNA1 in a heterologous system, and the mechanism of this resistance, both of which may prove valuable in incorporating GbaNA1-mediated resistance into other plant species.
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Affiliation(s)
- Nan-Yang Li
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
| | - Lei Zhou
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
| | - Dan-Dan Zhang
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
| | - Steven J. Klosterman
- Crop Improvement and Protection Research Unit, United States Department of Agriculture, Agricultural Research Service, Salinas, CA, United States
| | - Ting-Gang Li
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
| | - Yue-Jing Gui
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
| | - Zhi-Qiang Kong
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
| | - Xue-Feng Ma
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
| | - Dylan P. G. Short
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Wen-Qi Zhang
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
| | - Jun-Jiao Li
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
| | - Krishna V. Subbarao
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
- *Correspondence: Xiao-Feng Dai, Jie-Yin Chen, Krishna V. Subbarao,
| | - Jie-Yin Chen
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
- *Correspondence: Xiao-Feng Dai, Jie-Yin Chen, Krishna V. Subbarao,
| | - Xiao-Feng Dai
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
- *Correspondence: Xiao-Feng Dai, Jie-Yin Chen, Krishna V. Subbarao,
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Jacob P, Avni A, Bendahmane A. Translational Research: Exploring and Creating Genetic Diversity. TRENDS IN PLANT SCIENCE 2018; 23:42-52. [PMID: 29126790 DOI: 10.1016/j.tplants.2017.10.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/10/2017] [Accepted: 10/18/2017] [Indexed: 05/21/2023]
Abstract
The crop selection process has created a genetic bottleneck ultimately restricting breeding output. Wild relatives of major crops as well as the so-called 'neglected plant' species represent a reservoir of genetic diversity that remains underutilized. These species could be used as a tool to discover new alleles of agronomic interest or could be the target of breeding programs. Targeted induced local lesions in the genome (TILLING) can be used to translate in neglected crops what has been discovered in major crops and reciprocally. However, random mutagenesis, used in TILLING approaches, provides only a limited density of mutational events at a defined target locus. Alternatively, clustered regularly interspaced short palindromic repeats (CRISPR) associated 9 (Cas9) fused to a cytidine deaminase could serve as a localized mutagenic agent to produce high-density mutant populations. Artificial evolution is at hand.
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Affiliation(s)
- Pierre Jacob
- Institute of Plant Science - Paris-Saclay, INRA, 91190 Gif-sur-Yvette, France
| | - Adi Avni
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
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Hameed S, Akhtar KP, Hameed A, Gulzar T, Kiran S, Yousaf S, Abbas G, Asghar MJ, Sarwar N. Biochemical changes in the leaves of mungbean (Vigna radiata) plants infected by phytoplasma. ACTA ACUST UNITED AC 2017. [DOI: 10.1515/tjb-2016-0304] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractObjective:Phyllody disease caused by phytoplasma is an emerging problem in mungbean worldwide. However, the alterations in the host physiology and its associated biochemical components induced by the infection with phytoplasma in mungbean plant remain unknown. Hence the present study was performed with the diseased plants in order to determine the patho-physiological changes that take place.Methods:Under present study, the changes in total phenolic compounds, total soluble proteins, peroxidase (POD), catalase (CAT), polyphenol oxidase (PPO), Chlorophyll a, Chlorophyll b, and total chlorophyll were studied in leaves of phytoplasma-infected and healthy plants of six mungbean genotypes.Results:Total phenols were decreased significantly in four but increased in one genotype. Protein contents were increased significantly in two genotypes, POD in four, PPO in one and PAL in two genotypes. However, activity of CAT and amount ofConclusion:These results suggest that phytoplasma can interfere with host metabolism and photosynthesis to induce disease. In conclusion, this study provides new insights into the mungbean response to phytoplasma infection.
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Tran PT, Widyasari K, Park JY, Kim KH. Engineering an auto-activated R protein that is in vivo activated by a viral protease. Virology 2017; 510:242-247. [PMID: 28753465 DOI: 10.1016/j.virol.2017.07.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 07/13/2017] [Accepted: 07/19/2017] [Indexed: 01/09/2023]
Abstract
Autonomous hypersensitive responses (self-HRs) are caused by constitutively active R proteins. In this study, we identified an auto-activated form of the R gene Pvr9 (autoPvr9); the auto-activation results from an amino acid substitution between its NBS and LRR domains. Self-HR was strongly reduced or completely inhibited by fusion of an extra peptide to the autoPvr9 N-terminal or C-terminal, respectively. When an NIa recognition site was placed between autoPvr9 and the extra peptide, the fusion construct could trigger an NIa-dependent HR. Several C-terminal fusions were tested, but only those that maintained detectable protein expression were capable of an NIa-dependent HR. Our results suggest the potential for transforming malfunctioning and auto-activated R proteins into a new construct targeting potyviral NIa proteases.
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Affiliation(s)
- Phu-Tri Tran
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea; Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Kristin Widyasari
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jee Yoon Park
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Kook-Hyung Kim
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea; Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea; Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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34
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El Kasmi F, Chung EH, Anderson RG, Li J, Wan L, Eitas TK, Gao Z, Dangl JL. Signaling from the plasma-membrane localized plant immune receptor RPM1 requires self-association of the full-length protein. Proc Natl Acad Sci U S A 2017; 114:E7385-E7394. [PMID: 28808003 PMCID: PMC5584451 DOI: 10.1073/pnas.1708288114] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Plants evolved intracellular immune receptors that belong to the NOD-like receptor (NLR) family to recognize the presence of pathogen-derived effector proteins. NLRs possess an N-terminal Toll-like/IL-1 receptor (TIR) or a non-TIR domain [some of which contain coiled coils (CCs)], a central nucleotide-binding (NB-ARC) domain, and a C-terminal leucine-rich repeat (LRR). Activation of NLR proteins results in a rapid and high-amplitude immune response, eventually leading to host cell death at the infection site, the so-called hypersensitive response. Despite their important contribution to immunity, the exact mechanisms of NLR activation and signaling remain unknown and are likely heterogenous. We undertook a detailed structure-function analysis of the plasma membrane (PM)-localized CC NLR Resistance to Pseudomonas syringae pv. maculicola 1 (RPM1) using both stable transgenic Arabidopsis and transient expression in Nicotiana benthamiana We report that immune signaling is induced only by activated full-length PM-localized RPM1. Our interaction analyses demonstrate the importance of a functional P-loop for in planta interaction of RPM1 with the small host protein RPM1-interacting protein 4 (RIN4), for constitutive preactivation and postactivation self-association of RPM1 and for proper PM localization. Our results reveal an additive effect of hydrophobic conserved residues in the CC domain for RPM1 function and RPM1 self-association and their necessity for RPM1-RIN4 interaction. Thus, our findings considerably extend our understanding of the mechanisms regulating NLR activation at, and signaling from, the PM.
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Affiliation(s)
- Farid El Kasmi
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
| | - Eui-Hwan Chung
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
| | - Ryan G Anderson
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
| | - Jinyue Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei Province, P. R. China 430072
| | - Li Wan
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
| | - Timothy K Eitas
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
| | - Zhiyong Gao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei Province, P. R. China 430072;
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280;
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
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35
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Xing P, Zhang X, Bao Y, Wang Y, Wang H, Li X. Comparative Transcriptome Analyses of Resistant and Susceptible Near-Isogenic Wheat Lines following Inoculation with Blumeria graminis f. sp. tritici. Int J Genomics 2017; 2017:7305684. [PMID: 28553643 PMCID: PMC5434243 DOI: 10.1155/2017/7305684] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 02/08/2017] [Accepted: 03/06/2017] [Indexed: 12/02/2022] Open
Abstract
Powdery mildew is one of the most important diseases of wheat. In this study, the leaf RNA samples of wheat NILs carrying powdery mildew resistant and susceptible Pm2 alleles (L031 and Chancellor) and its F1 hybrid at two time points (16 h and 96 h postinoculation) were used for RNA-seq analysis. We carry comparison between similar materials at different times and between different materials at same times. The overlapping DEGs between the dominant phenotypes (L031 and F1 hybrid) and the recessive phenotype (Chancellor) were 1028 and 2214 DEGs, which were clearly lower than those between the dominant and recessive parents and thus could provide relatively accurate and valuable information. GO and KEGG enrichment analysis of DEGs revealed that other than the expected defense-related genes, differential up- and downregulation of genes from many other signaling networks were also involved. Comparative transcriptome analysis also revealed that early-stage postinoculation is important and suitable time points to study expression profiles and signaling pathways of resistance-related genes following fungal inoculation. qRT-PCR analyses showed highly consistent expression patterns of genes with RNA-seq data. The results will aid in the identification of genes and signaling pathways involved in powdery mildew response in wheat.
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Affiliation(s)
- Piyi Xing
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong, China
- Agronomy College, Shandong Agricultural University, Taian, Shandong, China
| | - Xueying Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong, China
- Agronomy College, Shandong Agricultural University, Taian, Shandong, China
| | - Yinguang Bao
- Agronomy College, Shandong Agricultural University, Taian, Shandong, China
| | - Yuhai Wang
- College of Life Science, Zaozhuang University, Zaozhuang, Shandong, China
| | - Honggang Wang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong, China
- Agronomy College, Shandong Agricultural University, Taian, Shandong, China
| | - Xingfeng Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong, China
- Agronomy College, Shandong Agricultural University, Taian, Shandong, China
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Lolle S, Greeff C, Petersen K, Roux M, Jensen MK, Bressendorff S, Rodriguez E, Sømark K, Mundy J, Petersen M. Matching NLR Immune Receptors to Autoimmunity in camta3 Mutants Using Antimorphic NLR Alleles. Cell Host Microbe 2017; 21:518-529.e4. [DOI: 10.1016/j.chom.2017.03.005] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 11/16/2016] [Accepted: 03/09/2017] [Indexed: 11/29/2022]
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Bentham A, Burdett H, Anderson PA, Williams SJ, Kobe B. Animal NLRs provide structural insights into plant NLR function. ANNALS OF BOTANY 2017; 119:827-702. [PMID: 27562749 PMCID: PMC5378188 DOI: 10.1093/aob/mcw171] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 05/26/2016] [Accepted: 06/07/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND The plant immune system employs intracellular NLRs (nucleotide binding [NB], leucine-rich repeat [LRR]/nucleotide-binding oligomerization domain [NOD]-like receptors) to detect effector proteins secreted into the plant cell by potential pathogens. Activated plant NLRs trigger a range of immune responses, collectively known as the hypersensitive response (HR), which culminates in death of the infected cell. Plant NLRs show structural and functional resemblance to animal NLRs involved in inflammatory and innate immune responses. Therefore, knowledge of the activation and regulation of animal NLRs can help us understand the mechanism of action of plant NLRs, and vice versa. SCOPE This review provides an overview of the innate immune pathways in plants and animals, focusing on the available structural and biochemical information available for both plant and animal NLRs. We highlight the gap in knowledge between the animal and plant systems, in particular the lack of structural information for plant NLRs, with crystal structures only available for the N-terminal domains of plant NLRs and an integrated decoy domain, in contrast to the more complete structures available for animal NLRs. We assess the similarities and differences between plant and animal NLRs, and use the structural information on the animal NLR pair NAIP/NLRC4 to derive a plausible model for plant NLR activation. CONCLUSIONS Signalling by cooperative assembly formation (SCAF) appears to operate in most innate immunity pathways, including plant and animal NLRs. Our proposed model of plant NLR activation includes three key steps: (1) initially, the NLR exists in an inactive auto-inhibited state; (2) a combination of binding by activating elicitor and ATP leads to a structural rearrangement of the NLR; and (3) signalling occurs through cooperative assembly of the resistosome. Further studies, structural and biochemical in particular, will be required to provide additional evidence for the different features of this model and shed light on the many existing variations, e.g. helper NLRs and NLRs containing integrated decoys.
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Affiliation(s)
- Adam Bentham
- School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Hayden Burdett
- School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia
| | - Peter A. Anderson
- School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia
| | - Simon J. Williams
- School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra 2601, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
- For correspondence. E-mail
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Siligato R, Wang X, Yadav SR, Lehesranta S, Ma G, Ursache R, Sevilem I, Zhang J, Gorte M, Prasad K, Wrzaczek M, Heidstra R, Murphy A, Scheres B, Mähönen AP. MultiSite Gateway-Compatible Cell Type-Specific Gene-Inducible System for Plants. PLANT PHYSIOLOGY 2016; 170:627-41. [PMID: 26644504 PMCID: PMC4734558 DOI: 10.1104/pp.15.01246] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 12/07/2015] [Indexed: 05/02/2023]
Abstract
A powerful method to study gene function is expression or overexpression in an inducible, cell type-specific system followed by observation of consequent phenotypic changes and visualization of linked reporters in the target tissue. Multiple inducible gene overexpression systems have been developed for plants, but very few of these combine plant selection markers, control of expression domains, access to multiple promoters and protein fusion reporters, chemical induction, and high-throughput cloning capabilities. Here, we introduce a MultiSite Gateway-compatible inducible system for Arabidopsis (Arabidopsis thaliana) plants that provides the capability to generate such constructs in a single cloning step. The system is based on the tightly controlled, estrogen-inducible XVE system. We demonstrate that the transformants generated with this system exhibit the expected cell type-specific expression, similar to what is observed with constitutively expressed native promoters. With this new system, cloning of inducible constructs is no longer limited to a few special cases but can be used as a standard approach when gene function is studied. In addition, we present a set of entry clones consisting of histochemical and fluorescent reporter variants designed for gene and promoter expression studies.
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Affiliation(s)
- Riccardo Siligato
- Institute of Biotechnology (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., A.P.M.) and Department of Biosciences, Viikki Plant Science Centre (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., M.W., A.P.M.), University of Helsinki, Helsinki 00014, Finland;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (A.M., G.M.);Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands (M.G., R.H., B.S.);School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695016, Kerala, India (K.P.);Plant Developmental Biology, Wageningen University, Wageningen 6708 PB, The Netherlands (R.H., B.S.); andDepartment of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742 (A.M.)
| | - Xin Wang
- Institute of Biotechnology (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., A.P.M.) and Department of Biosciences, Viikki Plant Science Centre (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., M.W., A.P.M.), University of Helsinki, Helsinki 00014, Finland;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (A.M., G.M.);Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands (M.G., R.H., B.S.);School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695016, Kerala, India (K.P.);Plant Developmental Biology, Wageningen University, Wageningen 6708 PB, The Netherlands (R.H., B.S.); andDepartment of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742 (A.M.)
| | - Shri Ram Yadav
- Institute of Biotechnology (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., A.P.M.) and Department of Biosciences, Viikki Plant Science Centre (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., M.W., A.P.M.), University of Helsinki, Helsinki 00014, Finland;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (A.M., G.M.);Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands (M.G., R.H., B.S.);School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695016, Kerala, India (K.P.);Plant Developmental Biology, Wageningen University, Wageningen 6708 PB, The Netherlands (R.H., B.S.); andDepartment of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742 (A.M.)
| | - Satu Lehesranta
- Institute of Biotechnology (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., A.P.M.) and Department of Biosciences, Viikki Plant Science Centre (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., M.W., A.P.M.), University of Helsinki, Helsinki 00014, Finland;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (A.M., G.M.);Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands (M.G., R.H., B.S.);School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695016, Kerala, India (K.P.);Plant Developmental Biology, Wageningen University, Wageningen 6708 PB, The Netherlands (R.H., B.S.); andDepartment of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742 (A.M.)
| | - Guojie Ma
- Institute of Biotechnology (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., A.P.M.) and Department of Biosciences, Viikki Plant Science Centre (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., M.W., A.P.M.), University of Helsinki, Helsinki 00014, Finland;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (A.M., G.M.);Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands (M.G., R.H., B.S.);School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695016, Kerala, India (K.P.);Plant Developmental Biology, Wageningen University, Wageningen 6708 PB, The Netherlands (R.H., B.S.); andDepartment of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742 (A.M.)
| | - Robertas Ursache
- Institute of Biotechnology (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., A.P.M.) and Department of Biosciences, Viikki Plant Science Centre (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., M.W., A.P.M.), University of Helsinki, Helsinki 00014, Finland;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (A.M., G.M.);Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands (M.G., R.H., B.S.);School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695016, Kerala, India (K.P.);Plant Developmental Biology, Wageningen University, Wageningen 6708 PB, The Netherlands (R.H., B.S.); andDepartment of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742 (A.M.)
| | - Iris Sevilem
- Institute of Biotechnology (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., A.P.M.) and Department of Biosciences, Viikki Plant Science Centre (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., M.W., A.P.M.), University of Helsinki, Helsinki 00014, Finland;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (A.M., G.M.);Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands (M.G., R.H., B.S.);School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695016, Kerala, India (K.P.);Plant Developmental Biology, Wageningen University, Wageningen 6708 PB, The Netherlands (R.H., B.S.); andDepartment of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742 (A.M.)
| | - Jing Zhang
- Institute of Biotechnology (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., A.P.M.) and Department of Biosciences, Viikki Plant Science Centre (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., M.W., A.P.M.), University of Helsinki, Helsinki 00014, Finland;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (A.M., G.M.);Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands (M.G., R.H., B.S.);School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695016, Kerala, India (K.P.);Plant Developmental Biology, Wageningen University, Wageningen 6708 PB, The Netherlands (R.H., B.S.); andDepartment of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742 (A.M.)
| | - Maartje Gorte
- Institute of Biotechnology (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., A.P.M.) and Department of Biosciences, Viikki Plant Science Centre (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., M.W., A.P.M.), University of Helsinki, Helsinki 00014, Finland;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (A.M., G.M.);Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands (M.G., R.H., B.S.);School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695016, Kerala, India (K.P.);Plant Developmental Biology, Wageningen University, Wageningen 6708 PB, The Netherlands (R.H., B.S.); andDepartment of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742 (A.M.)
| | - Kalika Prasad
- Institute of Biotechnology (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., A.P.M.) and Department of Biosciences, Viikki Plant Science Centre (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., M.W., A.P.M.), University of Helsinki, Helsinki 00014, Finland;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (A.M., G.M.);Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands (M.G., R.H., B.S.);School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695016, Kerala, India (K.P.);Plant Developmental Biology, Wageningen University, Wageningen 6708 PB, The Netherlands (R.H., B.S.); andDepartment of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742 (A.M.)
| | - Michael Wrzaczek
- Institute of Biotechnology (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., A.P.M.) and Department of Biosciences, Viikki Plant Science Centre (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., M.W., A.P.M.), University of Helsinki, Helsinki 00014, Finland;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (A.M., G.M.);Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands (M.G., R.H., B.S.);School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695016, Kerala, India (K.P.);Plant Developmental Biology, Wageningen University, Wageningen 6708 PB, The Netherlands (R.H., B.S.); andDepartment of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742 (A.M.)
| | - Renze Heidstra
- Institute of Biotechnology (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., A.P.M.) and Department of Biosciences, Viikki Plant Science Centre (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., M.W., A.P.M.), University of Helsinki, Helsinki 00014, Finland;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (A.M., G.M.);Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands (M.G., R.H., B.S.);School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695016, Kerala, India (K.P.);Plant Developmental Biology, Wageningen University, Wageningen 6708 PB, The Netherlands (R.H., B.S.); andDepartment of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742 (A.M.)
| | - Angus Murphy
- Institute of Biotechnology (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., A.P.M.) and Department of Biosciences, Viikki Plant Science Centre (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., M.W., A.P.M.), University of Helsinki, Helsinki 00014, Finland;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (A.M., G.M.);Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands (M.G., R.H., B.S.);School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695016, Kerala, India (K.P.);Plant Developmental Biology, Wageningen University, Wageningen 6708 PB, The Netherlands (R.H., B.S.); andDepartment of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742 (A.M.)
| | - Ben Scheres
- Institute of Biotechnology (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., A.P.M.) and Department of Biosciences, Viikki Plant Science Centre (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., M.W., A.P.M.), University of Helsinki, Helsinki 00014, Finland;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (A.M., G.M.);Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands (M.G., R.H., B.S.);School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695016, Kerala, India (K.P.);Plant Developmental Biology, Wageningen University, Wageningen 6708 PB, The Netherlands (R.H., B.S.); andDepartment of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742 (A.M.)
| | - Ari Pekka Mähönen
- Institute of Biotechnology (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., A.P.M.) and Department of Biosciences, Viikki Plant Science Centre (R.S., X.W., S.R.Y., S.L., R.U., I.S., J.Z., M.W., A.P.M.), University of Helsinki, Helsinki 00014, Finland;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907 (A.M., G.M.);Molecular Genetics, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands (M.G., R.H., B.S.);School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695016, Kerala, India (K.P.);Plant Developmental Biology, Wageningen University, Wageningen 6708 PB, The Netherlands (R.H., B.S.); andDepartment of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742 (A.M.)
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Yang J, Zhang F, Li J, Chen JP, Zhang HM. Integrative Analysis of the microRNAome and Transcriptome Illuminates the Response of Susceptible Rice Plants to Rice Stripe Virus. PLoS One 2016; 11:e0146946. [PMID: 26799317 PMCID: PMC4723043 DOI: 10.1371/journal.pone.0146946] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 12/22/2015] [Indexed: 11/19/2022] Open
Abstract
Rice stripe virus (RSV) is one of the most serious rice viruses in East Asia. To investigate how rice responds to RSV infection, we integrated miRNA expression with parallel mRNA transcription profiling by deep sequencing. A total of 570 miRNAs were identified of which 69 miRNAs (56 up-regulated and 13 down-regulated) were significantly modified by RSV infection. Digital gene expression (DGE) analysis showed that 1274 mRNAs (431 up-regulated and 843 down-regulated genes) were differentially expressed as a result of RSV infection. The differential expression of selected miRNAs and mRNAs was confirmed by qRT-PCR. Gene ontology (GO) and pathway enrichment analysis showed that a complex set of miRNA and mRNA networks were selectively regulated by RSV infection. In particular, 63 differentially expressed miRNAs were found to be significantly and negatively correlated with 160 target mRNAs. Interestingly, 22 up-regulated miRNAs were negatively correlated with 24 down-regulated mRNAs encoding disease resistance-related proteins, indicating that the host defense responses were selectively suppressed by RSV infection. The suppression of both osa-miR1423-5p- and osa-miR1870-5p-mediated resistance pathways was further confirmed by qRT-PCR. Chloroplast functions were also targeted by RSV, especially the zeaxanthin cycle, which would affect the stability of thylakoid membranes and the biosynthesis of ABA. All these modifications may contribute to viral symptom development and provide new insights into the pathogenicity mechanisms of RSV.
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Affiliation(s)
- Jian Yang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Biotechnology in Plant Protection of MOA and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Fen Zhang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Biotechnology in Plant Protection of MOA and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, 321004, China
| | - Jing Li
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Biotechnology in Plant Protection of MOA and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jian-Ping Chen
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Biotechnology in Plant Protection of MOA and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
- * E-mail: (HZ); (JC)
| | - Heng-Mu Zhang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Biotechnology in Plant Protection of MOA and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
- * E-mail: (HZ); (JC)
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Kong LA, Wu DQ, Huang WK, Peng H, Wang GF, Cui JK, Liu SM, Li ZG, Yang J, Peng DL. Large-scale identification of wheat genes resistant to cereal cyst nematode Heterodera avenae using comparative transcriptomic analysis. BMC Genomics 2015; 16:801. [PMID: 26475271 PMCID: PMC4609135 DOI: 10.1186/s12864-015-2037-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 10/08/2015] [Indexed: 11/10/2022] Open
Abstract
Background Cereal cyst nematode Heterodera avenae, an important soil-borne pathogen in wheat, causes numerous annual yield losses worldwide, and use of resistant cultivars is the best strategy for control. However, target genes are not readily available for breeding resistant cultivars. Therefore, comparative transcriptomic analyses were performed to identify more applicable resistance genes for cultivar breeding. Methods The developing nematodes within roots were stained with acid fuchsin solution. Transcriptome assemblies and redundancy filteration were obtained by Trinity, TGI Clustering Tool and BLASTN, respectively. Gene Ontology annotation was yielded by Blast2GO program, and metabolic pathways of transcripts were analyzed by Path_finder. The ROS levels were determined by luminol-chemiluminescence assay. The transcriptional gene expression profiles were obtained by quantitative RT-PCR. Results The RNA-sequencing was performed using an incompatible wheat cultivar VP1620 and a compatible control cultivar WEN19 infected with H. avenae at 24 h, 3 d and 8 d. Infection assays showed that VP1620 failed to block penetration of H. avenae but disturbed the transition of developmental stages, leading to a significant reduction in cyst formation. Two types of expression profiles were established to predict candidate resistance genes after developing a novel strategy to generate clean RNA-seq data by removing the transcripts of H. avenae within the raw data before assembly. Using the uncoordinated expression profiles with transcript abundance as a standard, 424 candidate resistance genes were identified, including 302 overlapping genes and 122 VP1620-specific genes. Genes with similar expression patterns were further classified according to the scales of changed transcript abundances, and 182 genes were rescued as supplementary candidate resistance genes. Functional characterizations revealed that diverse defense-related pathways were responsible for wheat resistance against H. avenae. Moreover, phospholipase was involved in many defense-related pathways and localized in the connection position. Furthermore, strong bursts of reactive oxygen species (ROS) within VP1620 roots infected with H. avenae were induced at 24 h and 3 d, and eight ROS-producing genes were significantly upregulated, including three class III peroxidase and five lipoxygenase genes. Conclusions Large-scale identification of wheat resistance genes were processed by comparative transcriptomic analysis. Functional characterization showed that phospholipases associated with ROS production played vital roles in early defense responses to H. avenae via involvement in diverse defense-related pathways as a hub switch. This study is the first to investigate the early defense responses of wheat against H. avenae, not only provides applicable candidate resistance genes for breeding novel wheat cultivars, but also enables a better understanding of the defense mechanisms of wheat against H. avenae. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2037-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ling-An Kong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Du-Qing Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Wen-Kun Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Huan Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Gao-Feng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Jiang-Kuan Cui
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Shi-Ming Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Zhi-Gang Li
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing, 100193, China.
| | - Jun Yang
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing, 100193, China.
| | - De-Liang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Sueldo DJ, Shimels M, Spiridon LN, Caldararu O, Petrescu AJ, Joosten MHAJ, Tameling WIL. Random mutagenesis of the nucleotide-binding domain of NRC1 (NB-LRR Required for Hypersensitive Response-Associated Cell Death-1), a downstream signalling nucleotide-binding, leucine-rich repeat (NB-LRR) protein, identifies gain-of-function mutations in the nucleotide-binding pocket. THE NEW PHYTOLOGIST 2015; 208:210-23. [PMID: 26009937 DOI: 10.1111/nph.13459] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 03/25/2015] [Indexed: 05/26/2023]
Abstract
Plant nucleotide-binding, leucine-rich repeat (NB-LRR) proteins confer immunity to pathogens possessing the corresponding avirulence proteins. Activation of NB-LRR proteins is often associated with induction of the hypersensitive response (HR), a form of programmed cell death. NRC1 (NB-LRR Required for HR-Associated Cell Death-1) is a tomato (Solanum lycopersicum) NB-LRR protein that participates in the signalling cascade leading to resistance to the pathogens Cladosporium fulvum and Verticillium dahliae. To identify mutations in NRC1 that cause increased signalling activity, we generated a random library of NRC1 variants mutated in their nucleotide-binding domain and screened them for the ability to induce an elicitor-independent HR in Nicotiana tabacum. Screening of 1920 clones retrieved 11 gain-of-function mutants, with 10 of them caused by a single amino acid substitution. All substitutions are located in or very close to highly conserved motifs within the nucleotide-binding domain, suggesting modulation of the signalling activity of NRC1. Three-dimensional modelling of the nucleotide-binding domain of NRC1 revealed that the targeted residues are centred around the bound nucleotide. Our mutational approach has generated a wide set of novel gain-of-function mutations in NRC1 and provides insight into how the activity of this NB-LRR is regulated.
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Affiliation(s)
- Daniela J Sueldo
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Mahdere Shimels
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Laurentiu N Spiridon
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, 060036, Bucharest, Romania
| | - Octav Caldararu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, 060036, Bucharest, Romania
| | - Andrei-Jose Petrescu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, 060036, Bucharest, Romania
| | - Matthieu H A J Joosten
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Wladimir I L Tameling
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
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Chen M, Cao Z. Genome-wide expression profiling of microRNAs in poplar upon infection with the foliar rust fungus Melampsora larici-populina. BMC Genomics 2015; 16:696. [PMID: 26370267 PMCID: PMC4570220 DOI: 10.1186/s12864-015-1891-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 09/01/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are small non-coding RNAs that regulate the gene expression of target mRNAs involved in plant growth, development, and abiotic stress and pathogen responses. Previous studies have reported miRNAs in Populus that respond to abiotic stresses, such as cold, heat, drought, flooding, high salt and mechanical stress. However, little is known about the regulatory roles of these molecules in the Populus response to the stress of foliar rust fungal infection. Here, we identified the miRNA profiles of Populus after inoculation with Melampsora larici-populina using high-throughput sequencing and bioinformatics analysis. Quantitative real-time PCR (qRT-PCR) was used to validate the expression levels of 10 miRNAs. RESULTS A total of 90 known miRNAs belonging to 42 families and 378 novel miRNAs were identified from three small-RNA libraries of Populus szechuanica infected with M. larici-populina isolates Sb052 and Th053 and a control. Comparative analysis revealed that the expression of 38 known miRNAs and 92 novel miRNAs in P. szechuanica after infection with different rust fungus isolates showed significant differences, and more miRNAs were suppressed during rust infection. Among the differentially expressed miRNAs, 7 known and 20 novel miRNAs were relevant to the rust fungus infection, and according to KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathway analysis, these miRNAs primarily regulate genes encoding disease-resistance proteins, serine/threonine protein kinases, transcription factors, and related proteins. QRT-PCR analysis indicated that most miRNAs were up-regulated in the Sb052 library and down-regulated in the Th053 library at 48 h post-inoculation (hpi). CONCLUSIONS These results demonstrate that the expression of miRNAs was altered in poplar under stress associated with M. larici-populina infection, and different temporal dynamics were observed in incompatible and compatible libraries. These findings suggest important roles for miRNA regulation in Populus upon infection with foliar rust fungus.
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Affiliation(s)
- Min Chen
- College of Forestry, Northwest A & F University, Yangling, Shaanxi, 712100, People's Republic of China.
| | - Zhimin Cao
- College of Forestry, Northwest A & F University, Yangling, Shaanxi, 712100, People's Republic of China.
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Gonzalez TL, Liang Y, Nguyen BN, Staskawicz BJ, Loqué D, Hammond MC. Tight regulation of plant immune responses by combining promoter and suicide exon elements. Nucleic Acids Res 2015; 43:7152-61. [PMID: 26138488 PMCID: PMC4538838 DOI: 10.1093/nar/gkv655] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 06/12/2015] [Accepted: 06/16/2015] [Indexed: 11/20/2022] Open
Abstract
Effector-triggered immunity (ETI) is activated when plant disease resistance (R) proteins recognize the presence of pathogen effector proteins delivered into host cells. The ETI response generally encompasses a defensive 'hypersensitive response' (HR) that involves programmed cell death at the site of pathogen recognition. While many R protein and effector protein pairs are known to trigger HR, other components of the ETI signaling pathway remain elusive. Effector genes regulated by inducible promoters cause background HR due to leaky protein expression, preventing the generation of relevant transgenic plant lines. By employing the HyP5SM suicide exon, we have developed a strategy to tightly regulate effector proteins such that HR is chemically inducible and non-leaky. This alternative splicing-based gene regulation system was shown to successfully control Bs2/AvrBs2-dependent and RPP1/ATR1Δ51-dependent HR in Nicotiana benthamiana and Nicotiana tabacum, respectively. It was also used to generate viable and healthy transgenic Arabidopsis thaliana plants that inducibly initiate HR. Beyond enabling studies on the ETI pathway, our regulatory strategy is generally applicable to reduce or eliminate undesired background expression of transgenes.
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Affiliation(s)
- Tania L Gonzalez
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Yan Liang
- Joint BioEnergy Institute, 5885 Hollis St, Emeryville, CA 94608, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Bao N Nguyen
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Brian J Staskawicz
- Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Dominique Loqué
- Joint BioEnergy Institute, 5885 Hollis St, Emeryville, CA 94608, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ming C Hammond
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA Department of Chemistry, University of California, Berkeley, CA 94720, USA
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Pardo-Diaz C, Salazar C, Jiggins CD. Towards the identification of the loci of adaptive evolution. Methods Ecol Evol 2015; 6:445-464. [PMID: 25937885 PMCID: PMC4409029 DOI: 10.1111/2041-210x.12324] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 11/28/2014] [Indexed: 12/17/2022]
Abstract
1. Establishing the genetic and molecular basis underlying adaptive traits is one of the major goals of evolutionary geneticists in order to understand the connection between genotype and phenotype and elucidate the mechanisms of evolutionary change. Despite considerable effort to address this question, there remain relatively few systems in which the genes shaping adaptations have been identified. 2. Here, we review the experimental tools that have been applied to document the molecular basis underlying evolution in several natural systems, in order to highlight their benefits, limitations and suitability. In most cases, a combination of DNA, RNA and functional methodologies with field experiments will be needed to uncover the genes and mechanisms shaping adaptation in nature.
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Affiliation(s)
- Carolina Pardo-Diaz
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del RosarioCarrera 24 No 63C-69, Bogotá 111221, Colombia
| | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del RosarioCarrera 24 No 63C-69, Bogotá 111221, Colombia
| | - Chris D Jiggins
- Department of Zoology, University of CambridgeDowning Street, Cambridge, CB2 3EJ, UK
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Wang GF, Ji J, EI-Kasmi F, Dangl JL, Johal G, Balint-Kurti PJ. Molecular and functional analyses of a maize autoactive NB-LRR protein identify precise structural requirements for activity. PLoS Pathog 2015; 11:e1004674. [PMID: 25719542 PMCID: PMC4342346 DOI: 10.1371/journal.ppat.1004674] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 01/09/2015] [Indexed: 12/22/2022] Open
Abstract
Plant disease resistance is often mediated by nucleotide binding-leucine rich repeat (NLR) proteins which remain auto-inhibited until recognition of specific pathogen-derived molecules causes their activation, triggering a rapid, localized cell death called a hypersensitive response (HR). Three domains are recognized in one of the major classes of NLR proteins: a coiled-coil (CC), a nucleotide binding (NB-ARC) and a leucine rich repeat (LRR) domains. The maize NLR gene Rp1-D21 derives from an intergenic recombination event between two NLR genes, Rp1-D and Rp1-dp2 and confers an autoactive HR. We report systematic structural and functional analyses of Rp1 proteins in maize and N. benthamiana to characterize the molecular mechanism of NLR activation/auto-inhibition. We derive a model comprising the following three main features: Rp1 proteins appear to self-associate to become competent for activity. The CC domain is signaling-competent and is sufficient to induce HR. This can be suppressed by the NB-ARC domain through direct interaction. In autoactive proteins, the interaction of the LRR domain with the NB-ARC domain causes de-repression and thus disrupts the inhibition of HR. Further, we identify specific amino acids and combinations thereof that are important for the auto-inhibition/activity of Rp1 proteins. We also provide evidence for the function of MHD2, a previously uncharacterized, though widely conserved NLR motif. This work reports several novel insights into the precise structural requirement for NLR function and informs efforts towards utilizing these proteins for engineering disease resistance.
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Affiliation(s)
- Guan-Feng Wang
- Department of Plant Pathology, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail: (GFW); (PJBK)
| | - Jiabing Ji
- Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, United States of America
| | - Farid EI-Kasmi
- Department of Biology, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jeffery L. Dangl
- Department of Biology and Howard Hughes Medical Institute, Curriculum in Genetics and Molecular Biology, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Guri Johal
- Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, United States of America
| | - Peter J. Balint-Kurti
- Department of Plant Pathology, North Carolina State University, Raleigh, North Carolina, United States of America
- USDA-ARS Plant Science Research Unit, Raleigh, North Carolina, United States of America
- * E-mail: (GFW); (PJBK)
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Stirnweis D, Milani SD, Jordan T, Keller B, Brunner S. Substitutions of two amino acids in the nucleotide-binding site domain of a resistance protein enhance the hypersensitive response and enlarge the PM3F resistance spectrum in wheat. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:265-76. [PMID: 24329172 DOI: 10.1094/mpmi-10-13-0297-fi] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Proteins with nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains are major components of the plant immune system. They usually mediate resistance against a subgroup of races of a specific pathogen. For the allelic series of the wheat powdery mildew resistance gene Pm3, alleles with a broad and a narrow resistance spectrum have been described. Here, we show that a broad Pm3 spectrum range correlates with a fast and intense hypersensitive response (HR) in a Nicotiana transient-expression system and this activity can be attributed to two particular amino acids in the ARC2 subdomain of the NBS. The combined substitution of these amino acids in narrow-spectrum PM3 proteins enhances their capacity to induce an HR in Nicotiana benthamiana, and we demonstrate that these substitutions also enlarge the resistance spectrum of the Pm3f allele in wheat. Finally, using Bph14, we show that the region carrying the relevant amino acids also plays a role in the HR regulation of another coiled-coil NBS-LRR resistance protein. These results highlight the importance of an optimized NBS-'molecular switch' for the conversion of initial pathogen perception by the LRR into resistance-protein activation, and we describe a possible approach to extend the effectiveness of resistance genes via minimal targeted modifications in the NBS domain.
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Jin M, Lee SS, Ke L, Kim JS, Seo MS, Sohn SH, Park BS, Bonnema G. Identification and mapping of a novel dominant resistance gene, TuRB07 to Turnip mosaic virus in Brassica rapa. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:509-19. [PMID: 24346479 DOI: 10.1007/s00122-013-2237-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 11/19/2013] [Indexed: 05/12/2023]
Abstract
A novel dominant resistance gene, TuRB07, was found to confer resistance to an isolate of TuMV strain C4 in B. rapa line VC1 and mapped on the top of chromosome A06. The inheritance of resistance to Turnip mosaic virus in Brassica rapa was investigated by crossing the resistant line, VC1 with the susceptible line, SR5, and genotyping and phenotyping diverse progenies derived from this cross. Both a doubled haploid population, VCS3M-DH, an F2 and two BC1 (F1 × VC1 and F1 × SR5) populations were created. Population tests revealed that the resistance to the TuMV C4 isolate in B. rapa is controlled by a single dominant gene. This resistance gene, TuRB07 was positioned on the top of linkage group A06 of the B. rapa genome through bulk segregation analysis and fine mapping recombinants in three doubled haploid- and one backcross population using microsatellite markers developed from BAC end sequences. Within the region between the two closely linked markers flanking TuRB07, H132A24-s1, and KS10960, in the Chiifu reference genome, two genes encoding nucleotide-binding site and leucine-rich repeat proteins with a coiled-coil motif (CC-NBS-LRR), Bra018862 and Bra018863 were identified as candidate resistance genes. The gene Bra018862 is truncated, but the gene Bra018863 has all the domains to function. Furthermore, the analysis of structural variation using resequencing data of VC1 and SR5 revealed that Bra018863 might be a functional gene because the gene has no structural variation in the resistant line VC1 when compared with Chiifu, whereas at the other NBS-LRR genes large deletions were identified in the resistant line. Allelic differences of Bra018863 were found between VC1 and SR5, supporting the notion that this gene is a putative candidate gene for the virus resistance.
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Affiliation(s)
- Mina Jin
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro, Gwonseon-gu, Suwon, 441-707, Korea,
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Yu J, Tehrim S, Zhang F, Tong C, Huang J, Cheng X, Dong C, Zhou Y, Qin R, Hua W, Liu S. Genome-wide comparative analysis of NBS-encoding genes between Brassica species and Arabidopsis thaliana. BMC Genomics 2014; 15:3. [PMID: 24383931 PMCID: PMC4008172 DOI: 10.1186/1471-2164-15-3] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Accepted: 12/30/2013] [Indexed: 02/07/2023] Open
Abstract
Background Plant disease resistance (R) genes with the nucleotide binding site (NBS) play an important role in offering resistance to pathogens. The availability of complete genome sequences of Brassica oleracea and Brassica rapa provides an important opportunity for researchers to identify and characterize NBS-encoding R genes in Brassica species and to compare with analogues in Arabidopsis thaliana based on a comparative genomics approach. However, little is known about the evolutionary fate of NBS-encoding genes in the Brassica lineage after split from A. thaliana. Results Here we present genome-wide analysis of NBS-encoding genes in B. oleracea, B. rapa and A. thaliana. Through the employment of HMM search and manual curation, we identified 157, 206 and 167 NBS-encoding genes in B. oleracea, B. rapa and A. thaliana genomes, respectively. Phylogenetic analysis among 3 species classified NBS-encoding genes into 6 subgroups. Tandem duplication and whole genome triplication (WGT) analyses revealed that after WGT of the Brassica ancestor, NBS-encoding homologous gene pairs on triplicated regions in Brassica ancestor were deleted or lost quickly, but NBS-encoding genes in Brassica species experienced species-specific gene amplification by tandem duplication after divergence of B. rapa and B. oleracea. Expression profiling of NBS-encoding orthologous gene pairs indicated the differential expression pattern of retained orthologous gene copies in B. oleracea and B. rapa. Furthermore, evolutionary analysis of CNL type NBS-encoding orthologous gene pairs among 3 species suggested that orthologous genes in B. rapa species have undergone stronger negative selection than those in B .oleracea species. But for TNL type, there are no significant differences in the orthologous gene pairs between the two species. Conclusion This study is first identification and characterization of NBS-encoding genes in B. rapa and B. oleracea based on whole genome sequences. Through tandem duplication and whole genome triplication analysis in B. oleracea, B. rapa and A. thaliana genomes, our study provides insight into the evolutionary history of NBS-encoding genes after divergence of A. thaliana and the Brassica lineage. These results together with expression pattern analysis of NBS-encoding orthologous genes provide useful resource for functional characterization of these genes and genetic improvement of relevant crops. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil crops, the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
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Meesters C, Kombrink E. Screening for bioactive small molecules by in vivo monitoring of luciferase-based reporter gene expression in Arabidopsis thaliana. Methods Mol Biol 2014; 1056:19-31. [PMID: 24306859 DOI: 10.1007/978-1-62703-592-7_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Chemical genetics is a scientific strategy that utilizes bioactive small molecules as experimental tools to dissect biological processes. Bioactive compounds occurring in nature represent an enormous diversity of structures that potentially can be used as activators or inhibitors of biochemical pathways, transport processes, regulatory networks, or developmental programs. Screening methods to identify bioactive small molecules can vary greatly, ranging from visual evaluation of phenotypic alterations to quantifying biometric traits such as enzyme activities. Here, we describe a general methodology that permits identification of compounds modulating the expression of reporter genes in Arabidopsis thaliana seedlings. The selection of luciferase-based reporter systems has the advantage that it allows in vivo imaging of reporter gene activity in a semiquantitative manner without affecting plant viability. We chose an Arabidopsis line harboring the luciferase reporter under the control of the jasmonate-inducible LOX2 promoter to screen for either activators or inhibitors of gene expression. The outlined assay conditions can readily be applied to Arabidopsis lines containing other reporter genes. Thereby screening for small molecules affecting different signaling pathways and/or phenotypic responses is possible.
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Affiliation(s)
- Christian Meesters
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
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Abstract
The generation of dominant gain-of-function mutants through activation tagging is a forward genetic approach that complements the screening of loss-of-function mutants and that has been successfully applied to studying the mechanisms of flower development. In addition, the functions of genes of interest can be further analyzed through reverse genetics. A commonly used method is gene overexpression, where strong, often ectopic expression can result in an opposite phenotype to that caused by a loss-of-function mutation. When overexpression is detrimental, the misexpression of a gene using tissue-specific promoters can be useful to study spatial-specific function. As flower development is a multistep process, it can be advantageous to control gene expression, or its protein product activity, in a temporal and/or spatial manner. This has been made possible through several inducible promoter systems, as well as by constructing chimeric fusions between the ligand binding domain of the glucocorticoid receptor (GR) and the protein of interest. Upon treatment with a steroid hormone at a specific time point, the fusion protein can enter the nucleus and activate downstream target genes. All these methods allow us to genetically manipulate gene expression during flower development. In this chapter, we describe methods to produce the expression constructs, method of screening, and more general applications of the techniques.
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Affiliation(s)
- Yifeng Xu
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
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