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Mathur S, Singh D, Ranjan R. Recent advances in plant translational genomics for crop improvement. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 139:335-382. [PMID: 38448140 DOI: 10.1016/bs.apcsb.2023.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
The growing population, climate change, and limited agricultural resources put enormous pressure on agricultural systems. A plateau in crop yields is occurring and extreme weather events and urbanization threaten the livelihood of farmers. It is imperative that immediate attention is paid to addressing the increasing food demand, ensuring resilience against emerging threats, and meeting the demand for more nutritious, safer food. Under uncertain conditions, it is essential to expand genetic diversity and discover novel crop varieties or variations to develop higher and more stable yields. Genomics plays a significant role in developing abundant and nutrient-dense food crops. An alternative to traditional breeding approach, translational genomics is able to improve breeding programs in a more efficient and precise manner by translating genomic concepts into practical tools. Crop breeding based on genomics offers potential solutions to overcome the limitations of conventional breeding methods, including improved crop varieties that provide more nutritional value and are protected from biotic and abiotic stresses. Genetic markers, such as SNPs and ESTs, contribute to the discovery of QTLs controlling agronomic traits and stress tolerance. In order to meet the growing demand for food, there is a need to incorporate QTLs into breeding programs using marker-assisted selection/breeding and transgenic technologies. This chapter primarily focuses on the recent advances that are made in translational genomics for crop improvement and various omics techniques including transcriptomics, metagenomics, pangenomics, single cell omics etc. Numerous genome editing techniques including CRISPR Cas technology and their applications in crop improvement had been discussed.
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Affiliation(s)
- Shivangi Mathur
- Plant Molecular Biology Laboratory, Department of Botany, Faculty of Science, Dayalbagh Educational Institute, Agra, India
| | - Deeksha Singh
- Plant Molecular Biology Laboratory, Department of Botany, Faculty of Science, Dayalbagh Educational Institute, Agra, India
| | - Rajiv Ranjan
- Plant Molecular Biology Laboratory, Department of Botany, Faculty of Science, Dayalbagh Educational Institute, Agra, India.
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2
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Demirjian C, Razavi N, Yu G, Mayjonade B, Zhang L, Lonjon F, Chardon F, Carrere S, Gouzy J, Genin S, Macho AP, Roux F, Berthomé R, Vailleau F. An atypical NLR gene confers bacterial wilt susceptibility in Arabidopsis. PLANT COMMUNICATIONS 2023; 4:100607. [PMID: 37098653 PMCID: PMC10504594 DOI: 10.1016/j.xplc.2023.100607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 01/19/2023] [Accepted: 04/20/2023] [Indexed: 06/12/2023]
Abstract
Quantitative disease resistance (QDR) remains the most prevalent form of plant resistance in crop fields and wild habitats. Genome-wide association studies (GWAS) have proved to be successful in deciphering the quantitative genetic basis of complex traits such as QDR. To unravel the genetics of QDR to the devastating worldwide bacterial pathogen Ralstonia solanacearum, we performed a GWAS by challenging a highly polymorphic local mapping population of Arabidopsis thaliana with four R. solanacearum type III effector (T3E) mutants, identified as key pathogenicity determinants after a first screen on an A. thaliana core collection of 25 accessions. Although most quantitative trait loci (QTLs) were highly specific to the identity of the T3E mutant (ripAC, ripAG, ripAQ, and ripU), we finely mapped a common QTL located on a cluster of nucleotide-binding domain and leucine-rich repeat (NLR) genes that exhibited structural variation. We functionally validated one of these NLRs as a susceptibility factor in response to R. solanacearum, named it Bacterial Wilt Susceptibility 1 (BWS1), and cloned two alleles that conferred contrasting levels of QDR. Further characterization indicated that expression of BWS1 leads to suppression of immunity triggered by different R. solanacearum effectors. In addition, we showed a direct interaction between BWS1 and RipAC T3E, and BWS1 and SUPPRESSOR OF G2 ALLELE OF skp1 (SGT1b), the latter interaction being suppressed by RipAC. Together, our results highlight a putative role for BWS1 as a quantitative susceptibility factor directly targeted by the T3E RipAC, mediating negative regulation of the SGT1-dependent immune response.
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Affiliation(s)
- Choghag Demirjian
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Narjes Razavi
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Gang Yu
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | | | - Lu Zhang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Fabien Lonjon
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Fabien Chardon
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Sébastien Carrere
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Jérome Gouzy
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Stéphane Genin
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Alberto P Macho
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Fabrice Roux
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Richard Berthomé
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Fabienne Vailleau
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France.
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3
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Mapuranga J, Chang J, Zhang L, Zhang N, Yang W. Fungal Secondary Metabolites and Small RNAs Enhance Pathogenicity during Plant-Fungal Pathogen Interactions. J Fungi (Basel) 2022; 9:jof9010004. [PMID: 36675825 PMCID: PMC9862911 DOI: 10.3390/jof9010004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Fungal plant pathogens use proteinaceous effectors as well as newly identified secondary metabolites (SMs) and small non-coding RNA (sRNA) effectors to manipulate the host plant's defense system via diverse plant cell compartments, distinct organelles, and many host genes. However, most molecular studies of plant-fungal interactions have focused on secreted effector proteins without exploring the possibly equivalent functions performed by fungal (SMs) and sRNAs, which are collectively known as "non-proteinaceous effectors". Fungal SMs have been shown to be generated throughout the plant colonization process, particularly in the early biotrophic stages of infection. The fungal repertoire of non-proteinaceous effectors has been broadened by the discovery of fungal sRNAs that specifically target plant genes involved in resistance and defense responses. Many RNAs, particularly sRNAs involved in gene silencing, have been shown to transmit bidirectionally between fungal pathogens and their hosts. However, there are no clear functional approaches to study the role of these SM and sRNA effectors. Undoubtedly, fungal SM and sRNA effectors are now a treasured land to seek. Therefore, understanding the role of fungal SM and sRNA effectors may provide insights into the infection process and identification of the interacting host genes that are targeted by these effectors. This review discusses the role of fungal SMs and sRNAs during plant-fungal interactions. It will also focus on the translocation of sRNA effectors across kingdoms, the application of cross-kingdom RNA interference in managing plant diseases and the tools that can be used to predict and study these non-proteinaceous effectors.
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Kim CY, Song H, Lee YH. Ambivalent response in pathogen defense: A double-edged sword? PLANT COMMUNICATIONS 2022; 3:100415. [PMID: 35918895 PMCID: PMC9700132 DOI: 10.1016/j.xplc.2022.100415] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/29/2022] [Accepted: 07/25/2022] [Indexed: 05/16/2023]
Abstract
Plants possess effective immune systems that defend against most microbial attackers. Recent plant immunity research has focused on the classic binary defense model involving the pivotal role of small-molecule hormones in regulating the plant defense signaling network. Although most of our current understanding comes from studies that relied on information derived from a limited number of pathosystems, newer studies concerning the incredibly diverse interactions between plants and microbes are providing additional insights into other novel mechanisms. Here, we review the roles of both classical and more recently identified components of defense signaling pathways and stress hormones in regulating the ambivalence effect during responses to diverse pathogens. Because of their different lifestyles, effective defense against biotrophic pathogens normally leads to increased susceptibility to necrotrophs, and vice versa. Given these opposing forces, the plant potentially faces a trade-off when it mounts resistance to a specific pathogen, a phenomenon referred to here as the ambivalence effect. We also highlight a novel mechanism by which translational control of the proteins involved in the ambivalence effect can be used to engineer durable and broad-spectrum disease resistance, regardless of the lifestyle of the invading pathogen.
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Affiliation(s)
- Chi-Yeol Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea; Plant Immunity Research Center, Seoul National University, Seoul 08826, Korea; Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Hyeunjeong Song
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul 08826, Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea; Plant Immunity Research Center, Seoul National University, Seoul 08826, Korea; Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul 08826, Korea; Center for Fungal Genetic Resources, Seoul National University, Seoul 08826, Korea.
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5
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McCombe CL, Greenwood JR, Solomon PS, Williams SJ. Molecular plant immunity against biotrophic, hemibiotrophic, and necrotrophic fungi. Essays Biochem 2022; 66:581-593. [PMID: 35587147 PMCID: PMC9528087 DOI: 10.1042/ebc20210073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/04/2022] [Accepted: 05/03/2022] [Indexed: 11/17/2022]
Abstract
Pathogenic fungi use diverse infection strategies to obtain nutrients from plants. Biotrophic fungi feed only on living plant tissue, whereas necrotrophic fungi kill host cells to extract nutrients. To prevent disease, plants need to distinguish between pathogens with different life cycles, as a successful defense against a biotroph, which often involves programmed cell-death around the site of infection, is not an appropriate response to some necrotrophs. Plants utilize a vast collection of extracellular and intracellular receptors to detect the signatures of pathogen attack. In turn, pathogens are under strong selection to mask or avoid certain receptor responses while enhancing or manipulating other receptor responses to promote virulence. In this review, we focus on the plant receptors involved in resistance responses to fungal pathogens and highlight, with examples, how the infection strategy of fungal pathogens can determine if recognition responses are effective at preventing disease.
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Affiliation(s)
- Carl L McCombe
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Julian R Greenwood
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Peter S Solomon
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Simon J Williams
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, Australia
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Ngou BPM, Ding P, Jones JDG. Thirty years of resistance: Zig-zag through the plant immune system. THE PLANT CELL 2022; 34:1447-1478. [PMID: 35167697 PMCID: PMC9048904 DOI: 10.1093/plcell/koac041] [Citation(s) in RCA: 283] [Impact Index Per Article: 141.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/02/2022] [Indexed: 05/05/2023]
Abstract
Understanding the plant immune system is crucial for using genetics to protect crops from diseases. Plants resist pathogens via a two-tiered innate immune detection-and-response system. The first plant Resistance (R) gene was cloned in 1992 . Since then, many cell-surface pattern recognition receptors (PRRs) have been identified, and R genes that encode intracellular nucleotide-binding leucine-rich repeat receptors (NLRs) have been cloned. Here, we provide a list of characterized PRRs and NLRs. In addition to immune receptors, many components of immune signaling networks were discovered over the last 30 years. We review the signaling pathways, physiological responses, and molecular regulation of both PRR- and NLR-mediated immunity. Recent studies have reinforced the importance of interactions between the two immune systems. We provide an overview of interactions between PRR- and NLR-mediated immunity, highlighting challenges and perspectives for future research.
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Affiliation(s)
- Bruno Pok Man Ngou
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, UK
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Pingtao Ding
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, UK
- Institute of Biology Leiden, Leiden University, Leiden 2333 BE, The Netherlands
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, UK
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7
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Du D, Zhang C, Xing Y, Lu X, Cai L, Yun H, Zhang Q, Zhang Y, Chen X, Liu M, Sang X, Ling Y, Yang Z, Li Y, Lefebvre B, He G. The CC-NB-LRR OsRLR1 mediates rice disease resistance through interaction with OsWRKY19. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1052-1064. [PMID: 33368943 PMCID: PMC8131040 DOI: 10.1111/pbi.13530] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 12/07/2020] [Indexed: 05/20/2023]
Abstract
Nucleotide-binding site-leucine-rich repeat (NB-LRR) resistance proteins are critical for plant resistance to pathogens; however, their mechanism of activation and signal transduction is still not well understood. We identified a mutation in an as yet uncharacterized rice coiled-coil (CC)-NB-LRR, Oryza sativa RPM1-like resistance gene 1 (OsRLR1), which leads to hypersensitive response (HR)-like lesions on the leaf blade and broad-range resistance to the fungal pathogen Pyricularia oryzae (syn. Magnaporthe oryzae) and the bacterial pathogen Xanthomonas oryzae pv. oryzae, together with strong growth reduction. Consistently, OsRLR1-overexpression lines showed enhanced resistance to both pathogens. Moreover, we found that OsRLR1 mediates the defence response through direct interaction in the nucleus with the transcription factor OsWRKY19. Down-regulation of OsWRKY19 in the rlr1 mutant compromised the HR-like phenotype and resistance response, and largely restored plant growth. OsWRKY19 binds to the promoter of OsPR10 to activate the defence response. Taken together, our data highlight the role of a new residue involved in the NB-LRR activation mechanism, allowing identification of a new NB-LRR downstream signalling pathway.
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Affiliation(s)
- Dan Du
- Key Laboratory of Application and Safety Control of Genetically Modified CropsAcademy of Agricultural SciencesRice Research InstituteSouthwest UniversityChongqingChina
| | - Changwei Zhang
- Key Laboratory of Application and Safety Control of Genetically Modified CropsAcademy of Agricultural SciencesRice Research InstituteSouthwest UniversityChongqingChina
| | - Yadi Xing
- Key Laboratory of Application and Safety Control of Genetically Modified CropsAcademy of Agricultural SciencesRice Research InstituteSouthwest UniversityChongqingChina
- Agricultural CollegeZhengzhou UniversityZhengzhouChina
| | - Xin Lu
- Key Laboratory of Application and Safety Control of Genetically Modified CropsAcademy of Agricultural SciencesRice Research InstituteSouthwest UniversityChongqingChina
| | - Linjun Cai
- Key Laboratory of Application and Safety Control of Genetically Modified CropsAcademy of Agricultural SciencesRice Research InstituteSouthwest UniversityChongqingChina
| | - Han Yun
- Key Laboratory of Application and Safety Control of Genetically Modified CropsAcademy of Agricultural SciencesRice Research InstituteSouthwest UniversityChongqingChina
| | - Qiuli Zhang
- Key Laboratory of Application and Safety Control of Genetically Modified CropsAcademy of Agricultural SciencesRice Research InstituteSouthwest UniversityChongqingChina
| | - Yingying Zhang
- Key Laboratory of Application and Safety Control of Genetically Modified CropsAcademy of Agricultural SciencesRice Research InstituteSouthwest UniversityChongqingChina
| | - Xinlong Chen
- Key Laboratory of Application and Safety Control of Genetically Modified CropsAcademy of Agricultural SciencesRice Research InstituteSouthwest UniversityChongqingChina
| | - Mingming Liu
- Key Laboratory of Application and Safety Control of Genetically Modified CropsAcademy of Agricultural SciencesRice Research InstituteSouthwest UniversityChongqingChina
| | - Xianchun Sang
- Key Laboratory of Application and Safety Control of Genetically Modified CropsAcademy of Agricultural SciencesRice Research InstituteSouthwest UniversityChongqingChina
| | - Yinghua Ling
- Key Laboratory of Application and Safety Control of Genetically Modified CropsAcademy of Agricultural SciencesRice Research InstituteSouthwest UniversityChongqingChina
| | - Zhenglin Yang
- Key Laboratory of Application and Safety Control of Genetically Modified CropsAcademy of Agricultural SciencesRice Research InstituteSouthwest UniversityChongqingChina
| | - Yunfeng Li
- Key Laboratory of Application and Safety Control of Genetically Modified CropsAcademy of Agricultural SciencesRice Research InstituteSouthwest UniversityChongqingChina
| | - Benoit Lefebvre
- Key Laboratory of Application and Safety Control of Genetically Modified CropsAcademy of Agricultural SciencesRice Research InstituteSouthwest UniversityChongqingChina
- LIPM, INRAE, CNRSUniversité de ToulouseCastanet‐TolosanFrance
| | - Guanghua He
- Key Laboratory of Application and Safety Control of Genetically Modified CropsAcademy of Agricultural SciencesRice Research InstituteSouthwest UniversityChongqingChina
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Qin N, Zhang R, Zhang M, Niu Y, Fu S, Wang Y, Wang D, Chen Y, Zhao C, Chen Q, Lu H. Global Profiling of Dynamic Alternative Splicing Modulation in Arabidopsis Root upon Ralstonia solanacearum Infection. Genes (Basel) 2020; 11:genes11091078. [PMID: 32942673 PMCID: PMC7563316 DOI: 10.3390/genes11091078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/02/2020] [Accepted: 09/11/2020] [Indexed: 01/27/2023] Open
Abstract
Alternative splicing (AS) is an important mechanism by which eukaryotes regulate transcription and protein diversity. The dynamic changes in AS that occur on a genome-wide scale during interactions between plant roots and pathogens remain unknown. Here, we used the interaction between Arabidopsis and Ralstonia solanacearum as a model to explore the AS changes that take place during the response of roots to infection by means of high-throughput RNA-sequencing. We showed that dynamic changes in AS occur much earlier than changes at the level of transcription during R.solanacearum infection. Comparing genes that are regulated at the transcriptional and AS levels indicated that there are few common genes between differentially spliced genes (DSGs) and differentially expressed genes (DEGs). The functional gene ontology (GO) analysis identified that the enriched GO terms for the DSGs were different from those of the DEGs. The DSGs were over-represented in GO terms associated with post-transcriptional and translational regulations, suggesting that AS may act on RNA stability and during post-translation, thus affecting the output of plant defense molecules. Meanwhile, changes in DSGs were infection stage-specific. Furthermore, the nucleotide binding domain and leucine-rich repeat proteins and receptor-like kinases, key regulators in plant immunity, were shown to undergo dynamic changes in AS in response to R. solanacearum. Taken together, AS, along with transcription, modulates plant root defense to R. solanacearum through transcriptome reprogramming.
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Affiliation(s)
- Ning Qin
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; (N.Q.); (R.Z.); (M.Z.); (Y.N.); (S.F.); (Y.W.); (D.W.); (Y.C.); (C.Z.)
| | - Ruize Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; (N.Q.); (R.Z.); (M.Z.); (Y.N.); (S.F.); (Y.W.); (D.W.); (Y.C.); (C.Z.)
| | - Mancang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; (N.Q.); (R.Z.); (M.Z.); (Y.N.); (S.F.); (Y.W.); (D.W.); (Y.C.); (C.Z.)
| | - Yang Niu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; (N.Q.); (R.Z.); (M.Z.); (Y.N.); (S.F.); (Y.W.); (D.W.); (Y.C.); (C.Z.)
| | - Shouyang Fu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; (N.Q.); (R.Z.); (M.Z.); (Y.N.); (S.F.); (Y.W.); (D.W.); (Y.C.); (C.Z.)
| | - Yisa Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; (N.Q.); (R.Z.); (M.Z.); (Y.N.); (S.F.); (Y.W.); (D.W.); (Y.C.); (C.Z.)
| | - Dongdong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; (N.Q.); (R.Z.); (M.Z.); (Y.N.); (S.F.); (Y.W.); (D.W.); (Y.C.); (C.Z.)
| | - Yue Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; (N.Q.); (R.Z.); (M.Z.); (Y.N.); (S.F.); (Y.W.); (D.W.); (Y.C.); (C.Z.)
| | - Cuizhu Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; (N.Q.); (R.Z.); (M.Z.); (Y.N.); (S.F.); (Y.W.); (D.W.); (Y.C.); (C.Z.)
| | - Qin Chen
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China
- Correspondence: (Q.C.); (H.L.); Tel.: +86-18829010553 (H.L.)
| | - Haibin Lu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; (N.Q.); (R.Z.); (M.Z.); (Y.N.); (S.F.); (Y.W.); (D.W.); (Y.C.); (C.Z.)
- Correspondence: (Q.C.); (H.L.); Tel.: +86-18829010553 (H.L.)
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9
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Lorang J. Necrotrophic Exploitation and Subversion of Plant Defense: A Lifestyle or Just a Phase, and Implications in Breeding Resistance. PHYTOPATHOLOGY 2019; 109:332-346. [PMID: 30451636 DOI: 10.1094/phyto-09-18-0334-ia] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Breeding disease-resistant plants is a critical, environmentally friendly component of any strategy to sustainably feed and clothe the 9.8 billion people expected to live on Earth by 2050. Here, I review current literature detailing plant defense responses as they relate to diverse biological outcomes; disease resistance, susceptibility, and establishment of mutualistic plant-microbial relationships. Of particular interest is the degree to which these outcomes are a function of plant-associated microorganisms' lifestyles; biotrophic, hemibiotrophic, necrotrophic, or mutualistic. For the sake of brevity, necrotrophic pathogens and the necrotrophic phase of pathogenicity are emphasized in this review, with special attention given to the host-specific pathogens that exploit defense. Defense responses related to generalist necrotrophs and mutualists are discussed in the context of excellent reviews by others. In addition, host evolutionary trade-offs of disease resistance with other desirable traits are considered in the context of breeding for durable disease resistance.
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Affiliation(s)
- Jennifer Lorang
- Department of Botany, 2082 Cordley Hall, Oregon State University, Corvallis 97331
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10
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Aglawe SB, Barbadikar KM, Mangrauthia SK, Madhav MS. New breeding technique "genome editing" for crop improvement: applications, potentials and challenges. 3 Biotech 2018; 8:336. [PMID: 30073121 PMCID: PMC6056351 DOI: 10.1007/s13205-018-1355-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 07/14/2018] [Indexed: 12/26/2022] Open
Abstract
Crop improvement is a continuous process in agriculture which ensures ample supply of food, fodder and fiber to burgeoning world population. Despite tremendous success in plant breeding and transgenesis to improve the yield-related traits, there have been several limitations primarily with the specificity in genetic modifications and incompatibility of host species. Because of this, new breeding techniques (NBTs) are gaining worldwide attention for crop improvement programs. Among the NBTs, genome editing (GE) using site-directed nucleases (SDNs) is an important and potential technique that overcomes limitations associated with classical breeding and transgenesis. These SDNs specifically target a compatible region in the gene/genome. The meganucleases (MgN), zinc finger nucleases (ZFN), transcription activator-like effectors nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated endonuclease (Cas) are being successfully employed for GE. These can be used for desired or targeted modifications of the native endogenous gene(s) or targeted insertion of cis/trans elements in the genomes of recipient organisms. Applications of these techniques appear to be endless ever since their discovery and several modifications in original technologies have further brought precision and accuracy in these methods. In this review, we present an overview of GE using SDNs with an emphasis on CRISPR/Cas system, their advantages, limitations and also practical considerations while designing experiments have been discussed. The review also emphasizes on the possible applications of CRISPR for improving economic traits in crop plants.
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Affiliation(s)
- Supriya B. Aglawe
- Biotechnology Section, ICAR-Indian Institute of Rice Research (IIRR), Rajendranagar, Hyderabad, 500030 India
| | - Kalyani M. Barbadikar
- Biotechnology Section, ICAR-Indian Institute of Rice Research (IIRR), Rajendranagar, Hyderabad, 500030 India
| | - Satendra K. Mangrauthia
- Biotechnology Section, ICAR-Indian Institute of Rice Research (IIRR), Rajendranagar, Hyderabad, 500030 India
| | - M. Sheshu Madhav
- Biotechnology Section, ICAR-Indian Institute of Rice Research (IIRR), Rajendranagar, Hyderabad, 500030 India
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11
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Vleeshouwers VGAA, Oliver RP. Effectors as Tools in Disease Resistance Breeding Against Biotrophic, Hemibiotrophic, and Necrotrophic Plant Pathogens. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 2015:40-50. [PMID: 27839074 DOI: 10.1094/mpmi-10-13-0313-ta.testissue] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
One of most important challenges in plant breeding is improving resistance to the plethora of pathogens that threaten our crops. The ever-growing world population, changing pathogen populations, and fungicide resistance issues have increased the urgency of this task. In addition to a vital inflow of novel resistance sources into breeding programs, the functional characterization and deployment of resistance also needs improvement. Therefore, plant breeders need to adopt new strategies and techniques. In modern resistance breeding, effectors are emerging as tools to accelerate and improve the identification, functional characterization, and deployment of resistance genes. Since genome-wide catalogues of effectors have become available for various pathogens, including biotrophs as well as necrotrophs, effector-assisted breeding has been shown to be successful for various crops. "Effectoromics" has contributed to classical resistance breeding as well as for genetically modified approaches. Here, we present an overview of how effector-assisted breeding and deployment is being exploited for various pathosystems.
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Affiliation(s)
- Vivianne G A A Vleeshouwers
- 1 Wageningen UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Richard P Oliver
- 2 Australian Centre for Necrotrophic Fungal Pathogens, Curtin University, Perth WA 6845, Australia
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Vleeshouwers VGAA, Oliver RP. Effectors as Tools in Disease Resistance Breeding Against Biotrophic, Hemibiotrophic, and Necrotrophic Plant Pathogens. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 2015:17-27. [PMID: 27839075 DOI: 10.1094/mpmi-10-13-0313-cr.testissue] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
One of most important challenges in plant breeding is improving resistance to the plethora of pathogens that threaten our crops. The ever-growing world population, changing pathogen populations, and fungicide resistance issues have increased the urgency of this task. In addition to a vital inflow of novel resistance sources into breeding programs, the functional characterization and deployment of resistance also needs improvement. Therefore, plant breeders need to adopt new strategies and techniques. In modern resistance breeding, effectors are emerging as tools to accelerate and improve the identification, functional characterization, and deployment of resistance genes. Since genome-wide catalogues of effectors have become available for various pathogens, including biotrophs as well as necrotrophs, effector-assisted breeding has been shown to be successful for various crops. "Effectoromics" has contributed to classical resistance breeding as well as for genetically modified approaches. Here, we present an overview of how effector-assisted breeding and deployment is being exploited for various pathosystems.
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Affiliation(s)
- Vivianne G A A Vleeshouwers
- 1 Wageningen UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Richard P Oliver
- 2 Australian Centre for Necrotrophic Fungal Pathogens, Curtin University, Perth WA 6845, Australia
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13
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Vleeshouwers VGAA, Oliver RP. Effectors as tools in disease resistance breeding against biotrophic, hemibiotrophic, and necrotrophic plant pathogens. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:196-206. [PMID: 24405032 DOI: 10.1094/mpmi-10-13-0313-ia] [Citation(s) in RCA: 204] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
One of most important challenges in plant breeding is improving resistance to the plethora of pathogens that threaten our crops. The ever-growing world population, changing pathogen populations, and fungicide resistance issues have increased the urgency of this task. In addition to a vital inflow of novel resistance sources into breeding programs, the functional characterization and deployment of resistance also needs improvement. Therefore, plant breeders need to adopt new strategies and techniques. In modern resistance breeding, effectors are emerging as tools to accelerate and improve the identification, functional characterization, and deployment of resistance genes. Since genome-wide catalogues of effectors have become available for various pathogens, including biotrophs as well as necrotrophs, effector-assisted breeding has been shown to be successful for various crops. "Effectoromics" has contributed to classical resistance breeding as well as for genetically modified approaches. Here, we present an overview of how effector-assisted breeding and deployment is being exploited for various pathosystems.
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Condon BJ, Leng Y, Wu D, Bushley KE, Ohm RA, Otillar R, Martin J, Schackwitz W, Grimwood J, MohdZainudin N, Xue C, Wang R, Manning VA, Dhillon B, Tu ZJ, Steffenson BJ, Salamov A, Sun H, Lowry S, LaButti K, Han J, Copeland A, Lindquist E, Barry K, Schmutz J, Baker SE, Ciuffetti LM, Grigoriev IV, Zhong S, Turgeon BG. Comparative genome structure, secondary metabolite, and effector coding capacity across Cochliobolus pathogens. PLoS Genet 2013; 9:e1003233. [PMID: 23357949 PMCID: PMC3554632 DOI: 10.1371/journal.pgen.1003233] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 11/14/2012] [Indexed: 11/17/2022] Open
Abstract
The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five percent of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25× higher than those between inbred lines and 50× lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP-encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence.
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Affiliation(s)
- Bradford J. Condon
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - Yueqiang Leng
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
| | - Dongliang Wu
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - Kathryn E. Bushley
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Robin A. Ohm
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Robert Otillar
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Joel Martin
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Wendy Schackwitz
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - NurAinIzzati MohdZainudin
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Chunsheng Xue
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Rui Wang
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
| | - Viola A. Manning
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Braham Dhillon
- Department of Forest Sciences, University of British Columbia, Vancouver, Canada
| | - Zheng Jin Tu
- Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Brian J. Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Asaf Salamov
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Hui Sun
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Steve Lowry
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Kurt LaButti
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - James Han
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Alex Copeland
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Erika Lindquist
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Kerrie Barry
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Jeremy Schmutz
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Scott E. Baker
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Lynda M. Ciuffetti
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Igor V. Grigoriev
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Shaobin Zhong
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
| | - B. Gillian Turgeon
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
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Lorang J, Kidarsa T, Bradford CS, Gilbert B, Curtis M, Tzeng SC, Maier C, Wolpert TJ. Tricking the guard: exploiting plant defense for disease susceptibility. Science 2012; 338:659-62. [PMID: 23087001 PMCID: PMC4125361 DOI: 10.1126/science.1226743] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Typically, pathogens deploy virulence effectors to disable defense. Plants defeat effectors with resistance proteins that guard effector targets. We found that a pathogen exploits a resistance protein by activating it to confer susceptibility in Arabidopsis. The guard mechanism of plant defense is recapitulated by interactions among victorin (an effector produced by the necrotrophic fungus Cochliobolus victoriae), TRX-h5 (a defense-associated thioredoxin), and LOV1 (an Arabidopsis susceptibility protein). In LOV1's absence, victorin inhibits TRX-h5, resulting in compromised defense but not disease by C. victoriae. In LOV1's presence, victorin binding to TRX-h5 activates LOV1 and elicits a resistance-like response that confers disease susceptibility. We propose that victorin is, or mimics, a conventional pathogen virulence effector that was defeated by LOV1 and confers virulence to C. victoriae solely because it incites defense.
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Affiliation(s)
- J. Lorang
- Department of Botany and Plant Pathology and Center for Gene Research and
Biotechnology, Oregon State University, Corvallis, OR 97331-2902
| | - T. Kidarsa
- Department of Botany and Plant Pathology and Center for Gene Research and
Biotechnology, Oregon State University, Corvallis, OR 97331-2902
| | - C. S. Bradford
- Department of Botany and Plant Pathology and Center for Gene Research and
Biotechnology, Oregon State University, Corvallis, OR 97331-2902
| | - B. Gilbert
- Department of Botany and Plant Pathology and Center for Gene Research and
Biotechnology, Oregon State University, Corvallis, OR 97331-2902
| | - M. Curtis
- Department of Botany and Plant Pathology and Center for Gene Research and
Biotechnology, Oregon State University, Corvallis, OR 97331-2902
| | | | | | - T. J. Wolpert
- Department of Botany and Plant Pathology and Center for Gene Research and
Biotechnology, Oregon State University, Corvallis, OR 97331-2902
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16
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Meyer Y, Belin C, Delorme-Hinoux V, Reichheld JP, Riondet C. Thioredoxin and glutaredoxin systems in plants: molecular mechanisms, crosstalks, and functional significance. Antioxid Redox Signal 2012; 17:1124-60. [PMID: 22531002 DOI: 10.1089/ars.2011.4327] [Citation(s) in RCA: 216] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Thioredoxins (Trx) and glutaredoxins (Grx) constitute families of thiol oxidoreductases. Our knowledge of Trx and Grx in plants has dramatically increased during the last decade. The release of the Arabidopsis genome sequence revealed an unexpectedly high number of Trx and Grx genes. The availability of several genomes of vascular and nonvascular plants allowed the establishment of a clear classification of the genes and the chronology of their appearance during plant evolution. Proteomic approaches have been developed that identified the putative Trx and Grx target proteins which are implicated in all aspects of plant growth, including basal metabolism, iron/sulfur cluster formation, development, adaptation to the environment, and stress responses. Analyses of the biochemical characteristics of specific Trx and Grx point to a strong specificity toward some target enzymes, particularly within plastidial Trx and Grx. In apparent contradiction with this specificity, genetic approaches show an absence of phenotype for most available Trx and Grx mutants, suggesting that redundancies also exist between Trx and Grx members. Despite this, the isolation of mutants inactivated in multiple genes and several genetic screens allowed the demonstration of the involvement of Trx and Grx in pathogen response, phytohormone pathways, and at several control points of plant development. Cytosolic Trxs are reduced by NADPH-thioredoxin reductase (NTR), while the reduction of Grx depends on reduced glutathione (GSH). Interestingly, recent development integrating biochemical analysis, proteomic data, and genetics have revealed an extensive crosstalk between the cytosolic NTR/Trx and GSH/Grx systems. This crosstalk, which occurs at multiple levels, reveals the high plasticity of the redox systems in plants.
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Affiliation(s)
- Yves Meyer
- Laboratoire Génome et Développement des Plantes, Université de Perpignan, Perpignan, France
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17
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Stergiopoulos I, Collemare J, Mehrabi R, De Wit PJGM. Phytotoxic secondary metabolites and peptides produced by plant pathogenic Dothideomycete fungi. FEMS Microbiol Rev 2012; 37:67-93. [PMID: 22931103 DOI: 10.1111/j.1574-6976.2012.00349.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 07/01/2012] [Accepted: 07/19/2012] [Indexed: 01/25/2023] Open
Abstract
Many necrotrophic plant pathogenic fungi belonging to the class of Dothideomycetes produce phytotoxic metabolites and peptides that are usually required for pathogenicity. Phytotoxins that affect a broad range of plant species are known as non-host-specific toxins (non-HSTs), whereas HSTs affect only a particular plant species or more often genotypes of that species. For pathogens producing HSTs, pathogenicity and host specificity are largely defined by the ability to produce the toxin, while plant susceptibility is dependent on the presence of the toxin target. Non-HSTs are not the main determinants of pathogenicity but contribute to virulence of the producing pathogen. Dothideomycetes are remarkable for the production of toxins, particularly HSTs because they are the only fungal species known so far to produce them. The synthesis, regulation, and mechanisms of action of the most important HSTs and non-HSTs will be discussed. Studies on the mode of action of HSTs have highlighted the induction of programed cell death (PCD) as an important mechanism. We discuss HST-induced PCD and the plant hypersensitive response upon recognition of avirulence factors that share common pathways. In this respect, although nucleotide-binding-site-leucine-rich repeat types of resistance proteins mediate resistance against biotrophs, they can also contribute to susceptibility toward necrotrophs.
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18
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Berkey R, Bendigeri D, Xiao S. Sphingolipids and plant defense/disease: the "death" connection and beyond. FRONTIERS IN PLANT SCIENCE 2012; 3:68. [PMID: 22639658 PMCID: PMC3355615 DOI: 10.3389/fpls.2012.00068] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 03/22/2012] [Indexed: 05/19/2023]
Abstract
Sphingolipids comprise a major class of structural materials and lipid signaling molecules in all eukaryotic cells. Over the past two decades, there has been a phenomenal growth in the study of sphingolipids (i.e., sphingobiology) at an average rate of ∼1000 research articles per year. Sphingolipid studies in plants, though accounting for only a small fraction (∼6%) of the total number of publications, have also enjoyed proportionally rapid growth in the past decade. Concomitant with the growth of sphingobiology, there has also been tremendous progress in our understanding of the molecular mechanisms of plant innate immunity. In this review, we (i) cross examine and analyze the major findings that establish and strengthen the intimate connections between sphingolipid metabolism and plant programmed cell death (PCD) associated with plant defense or disease; (ii) highlight and compare key bioactive sphingolipids involved in the regulation of plant PCD and possibly defense; (iii) discuss the potential role of sphingolipids in polarized membrane/protein trafficking and formation of lipid rafts as subdomains of cell membranes in relation to plant defense; and (iv) where possible, attempt to identify potential parallels for immunity-related mechanisms involving sphingolipids across kingdoms.
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Affiliation(s)
- Robert Berkey
- Institute for Bioscience and Biotechnology Research, University of MarylandRockville, MD, USA
- Department of Plant Sciences and Landscape Architecture, University of MarylandCollege Park, MD, USA
| | - Dipti Bendigeri
- Institute for Bioscience and Biotechnology Research, University of MarylandRockville, MD, USA
- Department of Plant Sciences and Landscape Architecture, University of MarylandCollege Park, MD, USA
| | - Shunyuan Xiao
- Institute for Bioscience and Biotechnology Research, University of MarylandRockville, MD, USA
- Department of Plant Sciences and Landscape Architecture, University of MarylandCollege Park, MD, USA
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19
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Tan KC, Ferguson-Hunt M, Rybak K, Waters ODC, Stanley WA, Bond CS, Stukenbrock EH, Friesen TL, Faris JD, McDonald BA, Oliver RP. Quantitative variation in effector activity of ToxA isoforms from Stagonospora nodorum and Pyrenophora tritici-repentis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2012; 25:515-22. [PMID: 22250581 DOI: 10.1094/mpmi-10-11-0273] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
ToxA is a proteinaceous necrotrophic effector produced by Stagonospora nodorum and Pyrenophora tritici-repentis. In this study, all eight mature isoforms of the ToxA protein were purified and compared. Circular dichroism spectra indicated that all isoforms were structurally intact and had indistinguishable secondary structural features. ToxA isoforms were infiltrated into wheat lines that carry the sensitivity gene Tsn1. It was observed that different wheat lines carrying identical Tsn1 alleles varied in sensitivity to ToxA. All ToxA isoforms induced necrosis when introduced into any Tsn1 wheat line but we observed quantitative variation in effector activity, with the least-active version found in isolates of P. tritici-repentis. Pathogen sporulation increased with higher doses of ToxA. The isoforms that induced the most rapid necrosis also induced the most sporulation, indicating that pathogen fitness is affected by differences in ToxA activity. We show that differences in toxin activity encoded by a single gene can contribute to the quantitative inheritance of necrotrophic virulence. Our findings support the hypothesis that the variation at ToxA results from selection that favors increased toxin activity.
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Affiliation(s)
- Kar-Chun Tan
- Environment and Agriculture, Curtin University, Bentley WA 6102, Australia
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20
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Giuliano Garisto Donzelli B, Krasnoff SB, Moon YS, Sun-Moon Y, Churchill ACL, Gibson DM. Genetic basis of destruxin production in the entomopathogen Metarhizium robertsii. Curr Genet 2012; 58:105-16. [PMID: 22367459 DOI: 10.1007/s00294-012-0368-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 02/04/2012] [Indexed: 01/12/2023]
Abstract
Destruxins are among the most exhaustively researched secondary metabolites of entomopathogenic fungi, yet definitive evidence for their roles in pathogenicity and virulence has yet to be shown. To establish the genetic bases for the biosynthesis of this family of depsipeptides, we identified a 23,792-bp gene in Metarhizium robertsii ARSEF 2575 containing six complete nonribosomal peptide synthetase modules, with an N-methyltransferase domain in each of the last two modules. This domain arrangement is consistent with the positioning of the adjacent amino acids N-methyl-L: -valine and N-methyl-L: -alanine within the depsipeptide structure of destruxin. DXS expression levels in vitro and in vivo exhibited comparable patterns, beginning at low levels during the early growth phases and increasing with time. Targeted gene knockout using Agrobacterium-mediated transformation produced mutants that failed to synthesize destruxins, in comparison with wild type and ectopic control strains, indicating the involvement of this gene in destruxin biosynthesis. The destruxin synthetase (DXS) disruption mutant was as virulent as the control strain when conidial inoculum was topically applied to larvae of Spodoptera exigua, Galleria mellonella, and Tenebrio molitor indicating that destruxins are dispensable for virulence in these insect hosts. The DXS mutants exhibited no other detectable changes in morphology and development.
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Affiliation(s)
- Bruno Giuliano Garisto Donzelli
- Biological Integrated Pest Management Research Unit, Robert W. Holley Center for Agriculture and Health, USDA-ARS, 538 Tower Road, Ithaca, NY 14853, USA.
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21
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Vartapetian AB, Tuzhikov AI, Chichkova NV, Taliansky M, Wolpert TJ. A plant alternative to animal caspases: subtilisin-like proteases. Cell Death Differ 2011; 18:1289-97. [PMID: 21546909 DOI: 10.1038/cdd.2011.49] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Activities displaying caspase cleavage specificity have been well documented in various plant programmed cell death (PCD) models. However, plant genome analyses have not revealed clear orthologues of caspase genes, indicating that enzyme(s) structurally unrelated yet possessing caspase specificity have functions in plant PCD. Here, we review recent data showing that some caspase-like activities are attributable to the plant subtilisin-like proteases, saspases and phytaspases. These proteases hydrolyze a range of tetrapeptide caspase substrates following the aspartate residue. Data obtained with saspases implicate them in the proteolytic degradation of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) during biotic and abiotic PCD, whereas phytaspase overproducing and silenced transgenics provide evidence that phytaspase regulates PCD during both abiotic (oxidative and osmotic stresses) and biotic (virus infection) insults. Like caspases, phytaspases and saspases are synthesized as proenzymes, which are autocatalytically processed to generate a mature enzyme. However, unlike caspases, phytaspases and saspases appear to be constitutively processed and secreted from healthy plant cells into the intercellular space. Apoplastic localization presumably prevents enzyme-mediated protein fragmentation in the absence of PCD. In response to death-inducing stimuli, phytaspase has been shown to re-localize to the cell interior. Thus, plant PCD-related proteases display both common (D-specific protein fragmentation during PCD) and distinct (enzyme structure and activity regulation) features with animal PCD-related proteases.
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Affiliation(s)
- A B Vartapetian
- A N Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
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22
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Horbach R, Navarro-Quesada AR, Knogge W, Deising HB. When and how to kill a plant cell: infection strategies of plant pathogenic fungi. JOURNAL OF PLANT PHYSIOLOGY 2011; 168:51-62. [PMID: 20674079 DOI: 10.1016/j.jplph.2010.06.014] [Citation(s) in RCA: 203] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Revised: 06/16/2010] [Accepted: 06/18/2010] [Indexed: 05/23/2023]
Abstract
Fungi cause severe diseases on a broad range of crop and ornamental plants, leading to significant economical losses. Plant pathogenic fungi exhibit a huge variability in their mode of infection, differentiation and function of infection structures and nutritional strategy. In this review, advances in understanding mechanisms of biotrophy, necrotrophy and hemibiotrophic lifestyles are described. Special emphasis is given to the biotrophy-necrotrophy switch of hemibiotrophic pathogens, and to biosynthesis, chemical diversity and mode of action of various fungal toxins produced during the infection process.
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Affiliation(s)
- Ralf Horbach
- Martin-Luther-University Halle-Wittenberg, Faculty of Natural Sciences III, Institute for Agricultural and Nutritional Sciences, Phytopathology and Plant Protection, Betty-Heimann-Strasse 3, Halle (Saale), Germany
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23
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Deller S, Hammond-Kosack KE, Rudd JJ. The complex interactions between host immunity and non-biotrophic fungal pathogens of wheat leaves. JOURNAL OF PLANT PHYSIOLOGY 2011; 168:63-71. [PMID: 20688416 DOI: 10.1016/j.jplph.2010.05.024] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 05/28/2010] [Accepted: 05/30/2010] [Indexed: 05/18/2023]
Abstract
Significant progress has been made in elucidating the mechanisms used by plants to recognize pathogens and activate "immune" responses. A "first line" of defense can be triggered through recognition of conserved Pathogen or Microbe Associated Molecular Patterns (PAMPs or MAMPs), resulting in activation of basal (or non-host) plant defenses, referred to as PAMP-triggered immunity (PTI). Disease resistance responses can also subsequently be triggered via gene-for-gene type interactions between pathogen avirulence effector genes and plant disease resistance genes (Avr-R), giving rise to effector triggered immunity (ETI). The majority of the conceptual advances in understanding these systems have been made using model systems, such as Arabidopsis, tobacco, or tomato in combination with biotrophic pathogens that colonize living plant tissues. In contrast, how these disease resistance mechanisms interact with non-biotrophic (hemibiotrophic or necrotrophic) fungal pathogens that thrive on dying host tissue during successful infection, is less clear. Several lines of recent evidence have begun to suggest that these organisms may actually exploit components of plant immunity in order to infect, successfully colonize and reproduce within host tissues. One underlying mechanism for this strategy has been proposed, which has been referred to as effector triggered susceptibility (ETS). This review aims to highlight the complexity of interactions between plant recognition and defense activation towards non-biotrophic pathogens, with particular emphasis on three important fungal diseases of wheat (Triticum aestivum) leaves.
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Affiliation(s)
- Siân Deller
- Centre for Pest and Disease Management, Rothamsted Research, Harpenden, Herts, UK
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24
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Hok S, Attard A, Keller H. Getting the most from the host: how pathogens force plants to cooperate in disease. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2010; 23:1253-9. [PMID: 20636104 DOI: 10.1094/mpmi-04-10-0103] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plant diseases caused by pathogenic microorganisms remain a major limitation in many crop production systems. Nonetheless, constitutive and inducible defense mechanisms render most plants inaccessible to pathogens, making disease an exception rather than a common outcome of plant-microbe interactions. Defense mechanisms and associated pathogen resistance were thus of key interest to many plant pathologists, and many of the molecular mechanisms underlying resistance have been elucidated over the last few decades. In recent years, the analysis of physiological and molecular determinants accounting for successful infection and eventual disease has become a topic of prime scientific interest. The hunt is now on for pathogen effectors subverting the host cell and for the plant compatibility functions manipulated by these effectors. An understanding of the molecular mechanisms underlying successful infection should make it possible to develop new crop protection strategies based on interference with compatibility to prevent disease. This review is addressing plant susceptibility and highlights a number of host processes that have been shown to be induced or subverted to facilitate infection. In particular, we focus on those processes that appear to be manipulated by filamentous fungal and oomycete pathogens.
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Affiliation(s)
- Sophie Hok
- Plant-Oomycete Interaction Group, UMR-Interactions Biotiques et Santé Végétale, INRA1301-CNRS6243-Université Nice-Sophia Antipolis, Sohia Antipolis, France
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Pavan S, Jacobsen E, Visser RGF, Bai Y. Loss of susceptibility as a novel breeding strategy for durable and broad-spectrum resistance. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2010; 25:1-12. [PMID: 20234841 PMCID: PMC2837247 DOI: 10.1007/s11032-009-9323-6] [Citation(s) in RCA: 176] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Accepted: 07/31/2009] [Indexed: 05/18/2023]
Abstract
Recent studies on plant immunity have suggested that a pathogen should suppress induced plant defense in order to infect a plant species, which otherwise would have been a nonhost to the pathogen. For this purpose, pathogens exploit effector molecules to interfere with different layers of plant defense responses. In this review, we summarize the latest findings on plant factors that are activated by pathogen effectors to suppress plant immunity. By looking from a different point of view into host and nonhost resistance, we propose a novel breeding strategy: disabling plant disease susceptibility genes (S-genes) to achieve durable and broad-spectrum resistance.
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Affiliation(s)
- Stefano Pavan
- Graduate School Experimental Plant Sciences, Wageningen UR-Plant Breeding, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Department of Agroforestry, Environmental Biology and Chemistry, Section of Genetics and Plant Breeding, University of Bari, Via Amendola 165/A, 70126 Bari, Italy
| | - Evert Jacobsen
- Graduate School Experimental Plant Sciences, Wageningen UR-Plant Breeding, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Richard G. F. Visser
- Graduate School Experimental Plant Sciences, Wageningen UR-Plant Breeding, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Yuling Bai
- Graduate School Experimental Plant Sciences, Wageningen UR-Plant Breeding, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Barrett LG, Kniskern JM, Bodenhausen N, Zhang W, Bergelson J. Continua of specificity and virulence in plant host-pathogen interactions: causes and consequences. THE NEW PHYTOLOGIST 2009; 183:513-529. [PMID: 19563451 DOI: 10.1111/j.1469-8137.2009.02927.x] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Ecological, evolutionary and molecular models of interactions between plant hosts and microbial pathogens are largely based around a concept of tightly coupled interactions between species pairs. However, highly pathogenic and obligate associations between host and pathogen species represent only a fraction of the diversity encountered in natural and managed systems. Instead, many pathogens can infect a wide range of hosts, and most hosts are exposed to more than one pathogen species, often simultaneously. Furthermore, outcomes of pathogen infection vary widely because host plants vary in resistance and tolerance to infection, while pathogens are also variable in their ability to grow on or within hosts. Environmental heterogeneity further increases the potential for variation in plant host-pathogen interactions by influencing the degree and fitness consequences of infection. Here, we describe these continua of specificity and virulence inherent within plant host-pathogen interactions. Using this framework, we describe and contrast the genetic and environmental mechanisms that underlie this variation, outline consequences for epidemiology and community structure, explore likely ecological and evolutionary drivers, and highlight several key areas for future research.
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Affiliation(s)
- Luke G Barrett
- Department of Ecology and Evolution, University of Chicago, 1101 E. 57th Street, Chicago, IL 60637, USA
| | - Joel M Kniskern
- Department of Ecology and Evolution, University of Chicago, 1101 E. 57th Street, Chicago, IL 60637, USA
| | - Natacha Bodenhausen
- Department of Ecology and Evolution, University of Chicago, 1101 E. 57th Street, Chicago, IL 60637, USA
| | - Wen Zhang
- Department of Ecology and Evolution, University of Chicago, 1101 E. 57th Street, Chicago, IL 60637, USA
| | - Joy Bergelson
- Department of Ecology and Evolution, University of Chicago, 1101 E. 57th Street, Chicago, IL 60637, USA
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27
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Wroblewski T, Caldwell KS, Piskurewicz U, Cavanaugh KA, Xu H, Kozik A, Ochoa O, McHale LK, Lahre K, Jelenska J, Castillo JA, Blumenthal D, Vinatzer BA, Greenberg JT, Michelmore RW. Comparative large-scale analysis of interactions between several crop species and the effector repertoires from multiple pathovars of Pseudomonas and Ralstonia. PLANT PHYSIOLOGY 2009; 150:1733-49. [PMID: 19571308 PMCID: PMC2719141 DOI: 10.1104/pp.109.140251] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2009] [Accepted: 06/23/2009] [Indexed: 05/18/2023]
Abstract
Bacterial plant pathogens manipulate their hosts by injection of numerous effector proteins into host cells via type III secretion systems. Recognition of these effectors by the host plant leads to the induction of a defense reaction that often culminates in a hypersensitive response manifested as cell death. Genes encoding effector proteins can be exchanged between different strains of bacteria via horizontal transfer, and often individual strains are capable of infecting multiple hosts. Host plant species express diverse repertoires of resistance proteins that mediate direct or indirect recognition of bacterial effectors. As a result, plants and their bacterial pathogens should be considered as two extensive coevolving groups rather than as individual host species coevolving with single pathovars. To dissect the complexity of this coevolution, we cloned 171 effector-encoding genes from several pathovars of Pseudomonas and Ralstonia. We used Agrobacterium tumefaciens-mediated transient assays to test the ability of each effector to induce a necrotic phenotype on 59 plant genotypes belonging to four plant families, including numerous diverse accessions of lettuce (Lactuca sativa) and tomato (Solanum lycopersicum). Known defense-inducing effectors (avirulence factors) and their homologs commonly induced extensive necrosis in many different plant species. Nonhost species reacted to multiple effector proteins from an individual pathovar more frequently and more intensely than host species. Both homologous and sequence-unrelated effectors could elicit necrosis in a similar spectrum of plants, suggesting common effector targets or targeting of the same pathways in the plant cell.
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Affiliation(s)
- Tadeusz Wroblewski
- Genome Center and Department of Plant Sciences, University of California, Davis, California 95616, USA
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Tör M, Lotze MT, Holton N. Receptor-mediated signalling in plants: molecular patterns and programmes. JOURNAL OF EXPERIMENTAL BOTANY 2009; 60:3645-54. [PMID: 19628572 PMCID: PMC2766824 DOI: 10.1093/jxb/erp233] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Accepted: 07/01/2009] [Indexed: 05/18/2023]
Abstract
A highly evolved surveillance system in plants is able to detect a broad range of signals originating from pathogens, damaged tissues, or altered developmental processes, initiating sophisticated molecular mechanisms that result in defence, wound healing, and development. Microbe-associated molecular pattern molecules (MAMPs), damage-associated molecular pattern molecules (DAMPs), virulence factors, secreted proteins, and processed peptides can be recognized directly or indirectly by this surveillance system. Nucleotide binding-leucine rich repeat proteins (NB-LRR) are intracellular receptors and have been targeted by breeders for decades to elicit resistance to crop pathogens in the field. Receptor-like kinases (RLKs) or receptor like proteins (RLPs) are membrane bound signalling molecules with an extracellular receptor domain. They provide an early warning system for the presence of potential pathogens and activate protective immune signalling in plants. In addition, they act as a signal amplifier in the case of tissue damage, establishing symbiotic relationships and effecting developmental processes. The identification of several important ligands for the RLK-type receptors provided an opportunity to understand how plants differentiate, how they distinguish beneficial and detrimental stimuli, and how they co-ordinate the role of various types of receptors under varying environmental conditions. The diverse roles of extra-and intracellular plant receptors are examined here and the recent findings on how they promote defence and development is reviewed.
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Affiliation(s)
- Mahmut Tör
- Warwick HRI, University of Warwick, Wellesbourne Campus, UK.
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Friesen TL, Faris JD, Solomon PS, Oliver RP. Host-specific toxins: effectors of necrotrophic pathogenicity. Cell Microbiol 2008; 10:1421-8. [PMID: 18384660 DOI: 10.1111/j.1462-5822.2008.01153.x] [Citation(s) in RCA: 186] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Host-specific toxins (HSTs) are defined as pathogen effectors that induce toxicity and promote disease only in the host species and only in genotypes of that host expressing a specific and often dominant susceptibility gene. They are a feature of a small but well-studied group of fungal plant pathogens. Classical HST pathogens include species of Cochliobolus, Alternaria and Pyrenophora. Recent studies have shown that Stagonospora nodorum produces at least four separate HSTs that interact with four of the many quantitative resistance loci found in the host, wheat. Rationalization of fungal phylogenetics has placed these pathogens in the Pleosporales order of the class Dothideomycetes. It is possible that all HST pathogens lie in this order. Strong evidence of the recent lateral gene transfer of the ToxA gene from S. nodorum to Pyrenophora tritici-repentis has been obtained. Hallmarks of lateral gene transfer are present for all the studied HST genes although definitive proof is lacking. We therefore suggest that the Pleosporales pathogens may have a conserved propensity to acquire HST genes by lateral transfer.
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Affiliation(s)
- Timothy L Friesen
- USDA-ARS, Cereal Crops Research Unit, Red River Valley Agricultural Research Center, Northern Crop Science Laboratory, Fargo, ND 58105, USA
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