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Yeh SM, Yoon M, Scott S, Chatterjee A, Hemara LM, Chen RKY, Wang T, Templeton K, Rikkerink EHA, Jayaraman J, Brendolise C. NbPTR1 confers resistance against Pseudomonas syringae pv. actinidiae in kiwifruit. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38899426 DOI: 10.1111/pce.15002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 06/04/2024] [Indexed: 06/21/2024]
Abstract
Pseudomonas syringae pv. actinidiae biovar 3 (Psa3) causes a devastating canker disease in yellow-fleshed kiwifruit (Actinidia chinensis). The effector HopZ5, which is present in all isolates of Psa3 causing global outbreaks of pandemic kiwifruit canker disease, triggers immunity in Nicotiana benthamiana and is not recognised in susceptible A. chinensis cultivars. In a search for N. benthamiana nonhost resistance genes against HopZ5, we found that the nucleotide-binding leucine-rich repeat receptor NbPTR1 recognised HopZ5. RPM1-interacting protein 4 orthologues from N. benthamiana and A. chinensis formed a complex with NbPTR1 and HopZ5 activity was able to disrupt this interaction. No functional orthologues of NbPTR1 were found in A. chinensis. NbPTR1 transformed into Psa3-susceptible A. chinensis var. chinensis 'Hort16A' plants introduced HopZ5-specific resistance against Psa3. Altogether, this study suggested that expressing NbPTR1 in Psa3-susceptible kiwifruit is a viable approach to acquiring resistance to Psa3 and it provides valuable information for engineering resistance in otherwise susceptible kiwifruit genotypes.
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Affiliation(s)
- Shin-Mei Yeh
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand
| | - Minsoo Yoon
- Bioprotection, The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand
| | - Sidney Scott
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand
| | - Abhishek Chatterjee
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand
| | - Lauren M Hemara
- Bioprotection, The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Ronan K Y Chen
- Food Innovation, The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston North, New Zealand
| | - Tianchi Wang
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand
| | - Kerry Templeton
- New Cultivar Innovation, The New Zealand Institute for Plant and Food Research Limited (PFR), Motueka, New Zealand
| | - Erik H A Rikkerink
- Bioprotection, The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand
| | - Jay Jayaraman
- Bioprotection, The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand
| | - Cyril Brendolise
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand
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Lukhovitskaya N, Brown K, Hua L, Pate AE, Carr JP, Firth AE. A novel ilarvirus protein CP-RT is expressed via stop codon readthrough and suppresses RDR6-dependent RNA silencing. PLoS Pathog 2024; 20:e1012034. [PMID: 38814986 PMCID: PMC11166343 DOI: 10.1371/journal.ppat.1012034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 06/11/2024] [Accepted: 05/03/2024] [Indexed: 06/01/2024] Open
Abstract
Ilarviruses are a relatively understudied but important group of plant RNA viruses that includes a number of crop pathogens. Their genomes comprise three RNA segments encoding two replicase subunits, movement protein, coat protein (CP), and (in some ilarvirus subgroups) a protein that suppresses RNA silencing. Here we report that, in many ilarviruses, RNA3 encodes an additional protein (termed CP-RT) as a result of ribosomal readthrough of the CP stop codon into a short downstream readthrough (RT) ORF. Using asparagus virus 2 as a model, we find that CP-RT is expressed in planta where it functions as a weak suppressor of RNA silencing. CP-RT expression is essential for persistent systemic infection in leaves and shoot apical meristem. CP-RT function is dependent on a putative zinc-finger motif within RT. Replacing the asparagus virus 2 RT with the RT of an ilarvirus from a different subgroup restored the ability to establish persistent infection. These findings open up a new avenue for research on ilarvirus silencing suppression, persistent meristem invasion and vertical transmission.
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Affiliation(s)
- Nina Lukhovitskaya
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Katherine Brown
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Lei Hua
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Adrienne E. Pate
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - John P. Carr
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Andrew E. Firth
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
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3
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Feng H, Jander G. Serine proteinase inhibitors from Nicotiana benthamiana, a nonpreferred host plant, inhibit the growth of Myzus persicae (green peach aphid). PEST MANAGEMENT SCIENCE 2024. [PMID: 38666388 DOI: 10.1002/ps.8148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/12/2024] [Accepted: 04/26/2024] [Indexed: 05/08/2024]
Abstract
BACKGROUND The green peach aphid (Myzus persicae) is a severe agricultural crop pest that has developed resistance to most current control methods, requiring the urgent development of novel strategies. Plant proteinase inhibitors (PINs) are small proteins that protect plants against pathogens and/or herbivores, likely by preventing efficient protein digestion. RESULTS We identified 67 protease genes in the transcriptomes of three M. persicae lineages (USDA-Red, G002 and G006). Comparison of gene expression levels in aphid guts and whole aphids showed that several proteases, including a highly expressed serine protease, are significantly overexpressed in the guts. Furthermore, we identified three genes encoding serine protease inhibitors (SerPIN-II1, 2 and 3) in Nicotiana benthamiana, which is a nonpreferred host for M. persicae. Using virus-induced gene silencing (VIGS) with a tobacco rattle virus (TRV) vector and overexpression with a turnip mosaic virus (TuMV) vector, we demonstrated that N. benthamiana SerPIN-II1 and SerPIN-II2 cause reduced survival and growth, but do not affect aphid protein content. Likewise, SerPIN-II3 overexpression reduced survival and growth, and serpin-II3 knockout mutations, which we generated using CRISPR/Cas9, increased survival and growth. Protein content was significantly increased in aphids fed on SerPIN-II3 overexpressing plants, yet it was decreased in aphids fed on serpin-II3 mutants. CONCLUSION Our results show that three PIN-IIs from N. benthamiana, a nonpreferred host plant, effectively inhibit M. persicae survival and growth, thereby representing a new resource for the development of aphid-resistant crop plants. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Honglin Feng
- Boyce Thompson Institute, Ithaca, NY, USA
- Department of Entomology, Louisiana State University AgCenter, Baton Rouge, LA, USA
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4
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Ko SR, Lee S, Koo H, Seo H, Yu J, Kim YM, Kwon SY, Shin AY. High-quality chromosome-level genome assembly of Nicotiana benthamiana. Sci Data 2024; 11:386. [PMID: 38627408 PMCID: PMC11021556 DOI: 10.1038/s41597-024-03232-0] [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: 12/18/2023] [Accepted: 04/05/2024] [Indexed: 04/19/2024] Open
Abstract
Nicotiana benthamiana is a fundamental model organism in plant research. Recent advancements in genomic sequencing have revealed significant intraspecific genetic variations. This study addresses the pressing need for a precise genome sequence specific to its geographic origin by presenting a comprehensive genome assembly of the N. benthamiana LAB strain from the Republic of Korea (NbKLAB). We compare this assembly with the widely used NbLAB360 strain, shedding light on essential genomic differences between them. The outcome is a high-quality, chromosome-level genome assembly comprising 19 chromosomes, spanning 2,762 Mb, with an N50 of 142.6 Mb. Comparative analyses revealed notable variations, including 46,215 protein-coding genes, with an impressive 99.5% BUSCO completeness score. Furthermore, the NbKLAB assembly substantially improved the QV from 33% for NbLAB360 to 49%. This refined chromosomal genome assembly for N. benthamiana, in conjunction with comparative insights, provides a valuable resource for genomics research and molecular biology. This accomplishment forms a strong foundation for in-depth exploration into the intricacies of plant genetics and genomics, improved precision, and a comparative framework.
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Affiliation(s)
- Seo-Rin Ko
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Sanghee Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Biosystems and Bioengineering Program, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon, 34113, Korea
| | - Hyunjin Koo
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | | | | | - Yong-Min Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
- Digital Biotech Innovation Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
| | - Suk-Yoon Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Biosystems and Bioengineering Program, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon, 34113, Korea.
| | - Ah-Young Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
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5
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Luo Y, Wang K, Zhu L, Zhang N, Si H. StMAPKK5 Positively Regulates Response to Drought and Salt Stress in Potato. Int J Mol Sci 2024; 25:3662. [PMID: 38612475 PMCID: PMC11011605 DOI: 10.3390/ijms25073662] [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: 02/13/2024] [Revised: 03/15/2024] [Accepted: 03/23/2024] [Indexed: 04/14/2024] Open
Abstract
MAPKKs, as one of the main members of the mitogen-activated protein kinase (MAPK) cascade pathway, are located in the middle of the cascade and are involved in many physiological processes of plant growth and development, as well as stress tolerance. Previous studies have found that StMAPKK5 is responsive to drought and salt stress. To further investigate the function and regulatory mechanism of StMAPKK5 in potato stress response, potato variety 'Atlantic' was subjected to drought and NaCl treatments, and the expression of the StMAPKK5 gene was detected by qRT-PCR. StMAPKK5 overexpression and RNA interference-mediated StMAPKK5 knockdown potato plants were constructed. The relative water content, superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) activities, as well as proline (Pro) and malondialdehyde (MDA) contents of plant leaves, were also assayed under drought and NaCl stress. The StMAPKK5 interacting proteins were identified and validated by yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC). The results showed that the expression of StMAPKK5 was significantly up-regulated under drought and NaCl stress conditions. The StMAPKK5 protein was localized in the nucleus, cytoplasm, and cell membrane. The expression of StMAPKK5 affected the relative water content, the enzymatic activities of SOD, CAT, and POD, and the proline and MDA contents of potatoes under drought and salt stress conditions. These results suggest that StMAPKK5 plays a significant role in regulating drought and salt tolerance in potato crop. Yeast two-hybrid (Y2H) screening identified four interacting proteins: StMYB19, StZFP8, StPUB-like, and StSKIP19. BiFC confirmed the authenticity of the interactions. These findings suggest that StMAPKK5 is crucial for potato growth, development, and response to adversity.
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Affiliation(s)
- Yu Luo
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (Y.L.); (K.W.); (N.Z.)
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
| | - Kaitong Wang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (Y.L.); (K.W.); (N.Z.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Liping Zhu
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
| | - Ning Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (Y.L.); (K.W.); (N.Z.)
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
| | - Huaijun Si
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (Y.L.); (K.W.); (N.Z.)
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
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6
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Wang J, Zhang Q, Tung J, Zhang X, Liu D, Deng Y, Tian Z, Chen H, Wang T, Yin W, Li B, Lai Z, Dinesh-Kumar SP, Baker B, Li F. High-quality assembled and annotated genomes of Nicotiana tabacum and Nicotiana benthamiana reveal chromosome evolution and changes in defense arsenals. MOLECULAR PLANT 2024; 17:423-437. [PMID: 38273657 DOI: 10.1016/j.molp.2024.01.008] [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: 09/14/2023] [Revised: 01/08/2024] [Accepted: 01/21/2024] [Indexed: 01/27/2024]
Abstract
Nicotiana tabacum and Nicotiana benthamiana are widely used models in plant biology research. However, genomic studies of these species have lagged. Here we report the chromosome-level reference genome assemblies for N. benthamiana and N. tabacum with an estimated 99.5% and 99.8% completeness, respectively. Sensitive transcription start and termination site sequencing methods were developed and used for accurate gene annotation in N. tabacum. Comparative analyses revealed evidence for the parental origins and chromosome structural changes, leading to hybrid genome formation of each species. Interestingly, the antiviral silencing genes RDR1, RDR6, DCL2, DCL3, and AGO2 were lost from one or both subgenomes in N. benthamiana, while both homeologs were kept in N. tabacum. Furthermore, the N. benthamiana genome encodes fewer immune receptors and signaling components than that of N. tabacum. These findings uncover possible reasons underlying the hypersusceptible nature of N. benthamiana. We developed the user-friendly Nicomics (http://lifenglab.hzau.edu.cn/Nicomics/) web server to facilitate better use of Nicotiana genomic resources as well as gene structure and expression analyses.
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Affiliation(s)
- Jubin Wang
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi Province, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330299, China
| | - Qingling Zhang
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Jeffrey Tung
- Plant Gene Expression Center, Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94706, USA
| | - Xi Zhang
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Dan Liu
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yingtian Deng
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Zhendong Tian
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Huilan Chen
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Taotao Wang
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Weixiao Yin
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Bo Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Zhibing Lai
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Savithramma P Dinesh-Kumar
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Barbara Baker
- Plant Gene Expression Center, Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94706, USA.
| | - Feng Li
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China.
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7
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Wang Y, Li X, Liu M, Zhou Y, Li F. Guide RNA scaffold variants enabled easy cloning of large gRNA cluster for multiplexed gene editing. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:460-471. [PMID: 37816147 PMCID: PMC10826992 DOI: 10.1111/pbi.14198] [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: 03/25/2023] [Revised: 07/20/2023] [Accepted: 09/23/2023] [Indexed: 10/12/2023]
Abstract
Cas9 protein-mediated gene editing has revolutionized genetic manipulation in most organisms. There are many cases where multiplexed gene editing is needed. Cas9 is capable of multiplex gene editing when expressed with multiple guide RNAs. Conventional cloning methods for multiplexed gene editing vector is not efficient due to repeated use of a single-guide RNA scaffold and inefficient ligation. In this study, we conducted structure-guided mutagenesis and random mutagenesis on the original sgRNA scaffold and identified a large number of functional sgRNA scaffold variants. With these scaffold variants and different tRNAs, fusion polymerase chain reaction protocol was developed to rapidly synthesize spacer-scaffold-tRNA-spacer units with up to 9 targets. In conjunction with golden gate cloning, gene editing vectors with up to 24 target sites were efficiently cloned in one-step cloning. One such gene editing vector targeting 12 genes in tomato were tested in stable transformation and 10 out of the 12 genes were found mutated in a single transgenic line. To facilitate the application of multiplexed gene editing using these scaffold variants and tRNAs from different species, a webserver was created to generate primer sets and provide template sequences for the synthesis of large sgRNA expression units based on the user-supplied target sequences and species.
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Affiliation(s)
- Yaqi Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Xiaofei Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Minglei Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Yingjia Zhou
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Feng Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
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8
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Tezuka T, Nagai S, Matsuo C, Okamori T, Iizuka T, Marubashi W. Genetic Cause of Hybrid Lethality Observed in Reciprocal Interspecific Crosses between Nicotiana simulans and N. tabacum. Int J Mol Sci 2024; 25:1226. [PMID: 38279225 PMCID: PMC10817076 DOI: 10.3390/ijms25021226] [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: 12/22/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 01/28/2024] Open
Abstract
Hybrid lethality, a type of postzygotic reproductive isolation, is an obstacle to wide hybridization breeding. Here, we report the hybrid lethality that was observed in crosses between the cultivated tobacco, Nicotiana tabacum (section Nicotiana), and the wild tobacco species, Nicotiana simulans (section Suaveolentes). Reciprocal hybrid seedlings were inviable at 28 °C, and the lethality was characterized by browning of the hypocotyl and roots, suggesting that hybrid lethality is due to the interaction of nuclear genomes derived from each parental species, and not to a cytoplasmic effect. Hybrid lethality was temperature-sensitive and suppressed at 36 °C. However, when hybrid seedlings cultured at 36 °C were transferred to 28 °C, all of them showed hybrid lethality. After crossing between an N. tabacum monosomic line missing one copy of the Q chromosome and N. simulans, hybrid seedlings with or without the Q chromosome were inviable and viable, respectively. These results indicated that gene(s) on the Q chromosome are responsible for hybrid lethality and also suggested that N. simulans has the same allele at the Hybrid Lethality A1 (HLA1) locus responsible for hybrid lethality as other species in the section Suaveolentes. Haplotype analysis around the HLA1 locus suggested that there are at least six and two haplotypes containing Hla1-1 and hla1-2 alleles, respectively, in the section Suaveolentes.
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Affiliation(s)
- Takahiro Tezuka
- Graduate School of Agriculture, Osaka Metropolitan University, Sakai 599-8531, Osaka, Japan;
- Education and Research Field, School of Agriculture, Osaka Metropolitan University, Sakai 599-8531, Osaka, Japan
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai 599-8531, Osaka, Japan;
- School of Life and Environmental Sciences, Osaka Prefecture University, Sakai 599-8531, Osaka, Japan
| | - Shota Nagai
- Graduate School of Agriculture, Osaka Metropolitan University, Sakai 599-8531, Osaka, Japan;
| | - Chihiro Matsuo
- School of Life and Environmental Sciences, Osaka Prefecture University, Sakai 599-8531, Osaka, Japan
| | - Toshiaki Okamori
- School of Life and Environmental Sciences, Osaka Prefecture University, Sakai 599-8531, Osaka, Japan
| | - Takahiro Iizuka
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai 599-8531, Osaka, Japan;
| | - Wataru Marubashi
- School of Agriculture, Meiji University, Kawasaki 214-8571, Kanagawa, Japan;
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9
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Holtsclaw RE, Mahmud S, Koo AJ. Identification and characterization of GLYCEROLIPASE A1 for wound-triggered JA biosynthesis in Nicotiana benthamiana leaves. PLANT MOLECULAR BIOLOGY 2024; 114:4. [PMID: 38227103 DOI: 10.1007/s11103-023-01408-7] [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: 07/28/2023] [Accepted: 12/03/2023] [Indexed: 01/17/2024]
Abstract
Although many important discoveries have been made regarding the jasmonate signaling pathway, how jasmonate biosynthesis is initiated is still a major unanswered question in the field. Previous evidences suggest that jasmonate biosynthesis is limited by the availability of fatty acid precursor, such as ⍺-linolenic acid (⍺-LA). This indicates that the lipase responsible for releasing α-LA in the chloroplast, where early steps of jasmonate biosynthesis take place, is the key initial step in the jasmonate biosynthetic pathway. Nicotiana benthamiana glycerol lipase A1 (NbGLA1) is homologous to N. attenuata GLA1 (NaGLA1) which has been reported to be a major lipase in leaves for jasmonate biosynthesis. NbGLA1 was studied for its potential usefulness in a species that is more common in laboratories. Virus-induced gene silencing of both NbGLA1 and NbGLA2, another homolog, resulted in more than 80% reduction in jasmonic acid (JA) biosynthesis in wounded leaves. Overexpression of NbGLA1 utilizing an inducible vector system failed to increase JA, indicating that transcriptional induction of NbGLA1 is insufficient to trigger JA biosynthesis. However, co-treatment with wounding in addition to NbGLA1 induction increased JA accumulation several fold higher than the gene expression or wounding alone, indicating an enhancement of the enzyme activity by wounding. Domain-deletion of a 126-bp C-terminal region hypothesized to have regulatory roles increased NbGLA1-induced JA level. Together, the data show NbGLA1 to be a major lipase for wound-induced JA biosynthesis in N. benthamiana leaves and demonstrate the use of inducible promoter-driven construct of NbGLA1 in conjunction with its transient expression in N. benthamiana as a useful system to study its protein function.
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Affiliation(s)
- Rebekah E Holtsclaw
- Department of Biochemistry, University of Missouri, 65211, Columbia, MO, USA
- Rubi Laboratories, 94577, San Leandro, CA, USA
| | - Sakil Mahmud
- Department of Biochemistry, University of Missouri, 65211, Columbia, MO, USA
| | - Abraham J Koo
- Department of Biochemistry, University of Missouri, 65211, Columbia, MO, USA.
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10
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Yue J, Lu Y, Sun Z, Guo Y, San León D, Pasin F, Zhao M. Methyltransferase-like (METTL) homologues participate in Nicotiana benthamiana antiviral responses. PLANT SIGNALING & BEHAVIOR 2023; 18:2214760. [PMID: 37210738 DOI: 10.1080/15592324.2023.2214760] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/18/2023] [Accepted: 04/24/2023] [Indexed: 05/23/2023]
Abstract
Methyltransferase (MTase) enzymes catalyze the addition of a methyl group to a variety of biological substrates. MTase-like (METTL) proteins are Class I MTases whose enzymatic activities contribute to the epigenetic and epitranscriptomic regulation of multiple cellular processes. N6-adenosine methylation (m6A) is a common chemical modification of eukaryotic and viral RNA whose abundance is jointly regulated by MTases and METTLs, demethylases, and m6A binding proteins. m6A affects various cellular processes including RNA degradation, post-transcriptional processing, and antiviral immunity. Here, we used Nicotiana benthamiana and plum pox virus (PPV), an RNA virus of the Potyviridae family, to investigated the roles of MTases in plant-virus interaction. RNA sequencing analysis identified MTase transcripts that are differentially expressed during PPV infection; among these, accumulation of a METTL gene was significantly downregulated. Two N. benthamiana METTL transcripts (NbMETTL1 and NbMETTL2) were cloned and further characterized. Sequence and structural analyses of the two encoded proteins identified a conserved S-adenosyl methionine (SAM) binding domain, showing they are SAM-dependent MTases phylogenetically related to human METTL16 and Arabidopsis thaliana FIONA1. Overexpression of NbMETTL1 and NbMETTL2 caused a decrease of PPV accumulation. In sum, our results indicate that METTL homologues participate in plant antiviral responses.
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Affiliation(s)
- Jianying Yue
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Yan Lu
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhenqi Sun
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Yuqing Guo
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - David San León
- Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Fabio Pasin
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas - Universitat Politècnica de València (CSIC-UPV), Valencia, Spain
| | - Mingmin Zhao
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
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11
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Verdú-Navarro F, Moreno-Cid JA, Weiss J, Egea-Cortines M. The advent of plant cells in bioreactors. FRONTIERS IN PLANT SCIENCE 2023; 14:1310405. [PMID: 38148861 PMCID: PMC10749943 DOI: 10.3389/fpls.2023.1310405] [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: 10/09/2023] [Accepted: 12/01/2023] [Indexed: 12/28/2023]
Abstract
Ever since agriculture started, plants have been bred to obtain better yields, better fruits, or sustainable products under uncertain biotic and abiotic conditions. However, a new way to obtain products from plant cells emerged with the development of recombinant DNA technologies. This led to the possibility of producing exogenous molecules in plants. Furthermore, plant chemodiversity has been the main source of pharmacological molecules, opening a field of plant biotechnology directed to produce high quality plant metabolites. The need for different products by the pharma, cosmetics agriculture and food industry has pushed again to develop new procedures. These include cell production in bioreactors. While plant tissue and cell culture are an established technology, beginning over a hundred years ago, plant cell cultures have shown little impact in biotechnology projects, compared to bacterial, yeasts or animal cells. In this review we address the different types of bioreactors that are currently used for plant cell production and their usage for quality biomolecule production. We make an overview of Nicotiana tabacum, Nicotiana benthamiana, Oryza sativa, Daucus carota, Vitis vinifera and Physcomitrium patens as well-established models for plant cell culture, and some species used to obtain important metabolites, with an insight into the type of bioreactor and production protocols.
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Affiliation(s)
- Fuensanta Verdú-Navarro
- Bioprocessing R&D Department, Bionet, Parque Tecnológico Fuente Álamo, Fuente Álamo, Spain
- Genética Molecular, Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, Cartagena, Spain
| | - Juan A. Moreno-Cid
- Bioprocessing R&D Department, Bionet, Parque Tecnológico Fuente Álamo, Fuente Álamo, Spain
| | - Julia Weiss
- Genética Molecular, Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, Cartagena, Spain
| | - Marcos Egea-Cortines
- Genética Molecular, Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, Cartagena, Spain
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12
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Kim B, Yu W, Kim H, Dong Q, Choi S, Prokchorchick M, Macho AP, Sohn KH, Segonzac C. A plasma membrane nucleotide-binding leucine-rich repeat receptor mediates the recognition of the Ralstonia pseudosolanacearum effector RipY in Nicotiana benthamiana. PLANT COMMUNICATIONS 2023; 4:100640. [PMID: 37349986 PMCID: PMC10721487 DOI: 10.1016/j.xplc.2023.100640] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 06/01/2023] [Accepted: 06/18/2023] [Indexed: 06/24/2023]
Abstract
Bacterial wilt disease caused by several Ralstonia species is one of the most destructive diseases in Solanaceae crops. Only a few functional resistance genes against bacterial wilt have been cloned to date. Here, we show that the broadly conserved type III secreted effector RipY is recognized by the Nicotiana benthamiana immune system, leading to cell death induction, induction of defense-related gene expression, and restriction of bacterial pathogen growth. Using a multiplexed virus-induced gene-silencing-based N. benthamiana nucleotide-binding and leucine-rich repeat receptor (NbNLR) library, we identified a coiled-coil (CC) nucleotide-binding and leucine-rich repeat receptor (CNL) required for recognition of RipY, which we named RESISTANCE TO RALSTONIA SOLANACEARUM RIPY (RRS-Y). Genetic complementation assays in RRS-Y-silenced plants and stable rrs-y knockout mutants demonstrated that RRS-Y is sufficient to activate RipY-induced cell death and RipY-induced immunity to Ralstonia pseudosolanacearum. RRS-Y function is dependent on the phosphate-binding loop motif of the nucleotide-binding domain but independent of the characterized signaling components ENHANCED DISEASE SUSCEPTIBILITY 1, ACTIVATED DISEASE RESISTANCE 1, and N REQUIREMENT GENE 1 and the NLR helpers NB-LRR REQUIRED FOR HR-ASSOCIATED CELL DEATH-2, -3, and -4 in N. benthamiana. We further show that RRS-Y localization at the plasma membrane is mediated by two cysteine residues in the CC domain and is required for RipY recognition. RRS-Y also broadly recognizes RipY homologs across Ralstonia species. Lastly, we show that the C-terminal region of RipY is indispensable for RRS-Y activation. Together, our findings provide an additional effector/receptor pair system to deepen our understanding of CNL activation in plants.
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Affiliation(s)
- Boyoung Kim
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul 08826, Republic of Korea; Plant Immunity Research Center, Seoul National University, Seoul 08826, Republic of Korea
| | - Wenjia Yu
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Haseong Kim
- Plant Immunity Research Center, Seoul National University, Seoul 08826, Republic of Korea; Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Qian Dong
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Sera Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Maxim Prokchorchick
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Alberto P Macho
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Kee Hoon Sohn
- Plant Immunity Research Center, Seoul National University, Seoul 08826, Republic of Korea; Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Cécile Segonzac
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul 08826, Republic of Korea; Plant Immunity Research Center, Seoul National University, Seoul 08826, Republic of Korea; Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Republic of Korea; Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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13
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Tselika M, Belmezos N, Kallemi P, Andronis C, Chiumenti M, Navarro B, Lavigne M, Di Serio F, Kalantidis K, Katsarou K. PSTVd infection in Nicotiana benthamiana plants has a minor yet detectable effect on CG methylation. FRONTIERS IN PLANT SCIENCE 2023; 14:1258023. [PMID: 38023875 PMCID: PMC10645062 DOI: 10.3389/fpls.2023.1258023] [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: 07/13/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023]
Abstract
Viroids are small circular RNAs infecting a wide range of plants. They do not code for any protein or peptide and therefore rely on their structure for their biological cycle. Observed phenotypes of viroid infected plants are thought to occur through changes at the transcriptional/translational level of the host. A mechanism involved in such changes is RNA-directed DNA methylation (RdDM). Till today, there are contradictory works about viroids interference of RdDM. In this study, we investigated the epigenetic effect of viroid infection in Nicotiana benthamiana plants. Using potato spindle tuber viroid (PSTVd) as the triggering pathogen and via bioinformatic analyses, we identified endogenous gene promoters and transposable elements targeted by 24 nt host siRNAs that differentially accumulated in PSTVd-infected and healthy plants. The methylation status of these targets was evaluated following digestion with methylation-sensitive restriction enzymes coupled with PCR amplification, and bisulfite sequencing. In addition, we used Methylation Sensitive Amplification Polymorphism (MSAP) followed by sequencing (MSAP-seq) to study genomic DNA methylation of 5-methylcytosine (5mC) in CG sites upon viroid infection. In this study we identified a limited number of target loci differentially methylated upon PSTVd infection. These results enhance our understanding of the epigenetic host changes as a result of pospiviroid infection.
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Affiliation(s)
- Martha Tselika
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | | | - Paraskevi Kallemi
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Christos Andronis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Michela Chiumenti
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Matthieu Lavigne
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Kriton Kalantidis
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Konstantina Katsarou
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
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14
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Contreras MP, Lüdke D, Pai H, Toghani A, Kamoun S. NLR receptors in plant immunity: making sense of the alphabet soup. EMBO Rep 2023; 24:e57495. [PMID: 37602936 PMCID: PMC10561179 DOI: 10.15252/embr.202357495] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/22/2023] [Accepted: 08/03/2023] [Indexed: 08/22/2023] Open
Abstract
Plants coordinately use cell-surface and intracellular immune receptors to perceive pathogens and mount an immune response. Intracellular events of pathogen recognition are largely mediated by immune receptors of the nucleotide binding and leucine rich-repeat (NLR) classes. Upon pathogen perception, NLRs trigger a potent broad-spectrum immune reaction, usually accompanied by a form of programmed cell death termed the hypersensitive response. Some plant NLRs act as multifunctional singleton receptors which combine pathogen detection and immune signaling. However, NLRs can also function in higher order pairs and networks of functionally specialized interconnected receptors. In this article, we cover the basic aspects of plant NLR biology with an emphasis on NLR networks. We highlight some of the recent advances in NLR structure, function, and activation and discuss emerging topics such as modulator NLRs, pathogen suppression of NLRs, and NLR bioengineering. Multi-disciplinary approaches are required to disentangle how these NLR immune receptor pairs and networks function and evolve. Answering these questions holds the potential to deepen our understanding of the plant immune system and unlock a new era of disease resistance breeding.
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Affiliation(s)
| | - Daniel Lüdke
- The Sainsbury LaboratoryUniversity of East AngliaNorwichUK
| | - Hsuan Pai
- The Sainsbury LaboratoryUniversity of East AngliaNorwichUK
| | | | - Sophien Kamoun
- The Sainsbury LaboratoryUniversity of East AngliaNorwichUK
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15
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Vollheyde K, Dudley QM, Yang T, Oz MT, Mancinotti D, Fedi MO, Heavens D, Linsmith G, Chhetry M, Smedley MA, Harwood WA, Swarbreck D, Geu‐Flores F, Patron NJ. An improved Nicotiana benthamiana bioproduction chassis provides novel insights into nicotine biosynthesis. THE NEW PHYTOLOGIST 2023; 240:302-317. [PMID: 37488711 PMCID: PMC10952274 DOI: 10.1111/nph.19141] [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: 03/14/2023] [Accepted: 06/28/2023] [Indexed: 07/26/2023]
Abstract
The model plant Nicotiana benthamiana is an increasingly attractive organism for the production of high-value, biologically active molecules. However, N. benthamiana accumulates high levels of pyridine alkaloids, in particular nicotine, which complicates the downstream purification processes. Here, we report a new assembly of the N. benthamiana genome as well as the generation of low-nicotine lines by CRISPR/Cas9-based inactivation of berberine bridge enzyme-like proteins (BBLs). Triple as well as quintuple mutants accumulated three to four times less nicotine than the respective control lines. The availability of lines without functional BBLs allowed us to probe their catalytic role in nicotine biosynthesis, which has remained obscure. Notably, chiral analysis revealed that the enantiomeric purity of nicotine was fully lost in the quintuple mutants. In addition, precursor feeding experiments showed that these mutants cannot facilitate the specific loss of C6 hydrogen that characterizes natural nicotine biosynthesis. Our work delivers an improved N. benthamiana chassis for bioproduction and uncovers the crucial role of BBLs in the stereoselectivity of nicotine biosynthesis.
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Affiliation(s)
- Katharina Vollheyde
- Department of Plant and Environmental SciencesUniversity of Copenhagen1871 FrederiksbergCopenhagenDenmark
| | | | - Ting Yang
- Department of Plant and Environmental SciencesUniversity of Copenhagen1871 FrederiksbergCopenhagenDenmark
| | - Mehmet T. Oz
- Earlham Institute, Norwich Research ParkNorwichNorfolkNR4 7UZUK
| | - Davide Mancinotti
- Department of Plant and Environmental SciencesUniversity of Copenhagen1871 FrederiksbergCopenhagenDenmark
| | | | - Darren Heavens
- Earlham Institute, Norwich Research ParkNorwichNorfolkNR4 7UZUK
| | - Gareth Linsmith
- Earlham Institute, Norwich Research ParkNorwichNorfolkNR4 7UZUK
| | - Monika Chhetry
- John Innes Centre, Norwich Research ParkNorwichNorfolkNR4 7UHUK
| | - Mark A. Smedley
- John Innes Centre, Norwich Research ParkNorwichNorfolkNR4 7UHUK
| | | | - David Swarbreck
- Earlham Institute, Norwich Research ParkNorwichNorfolkNR4 7UZUK
| | - Fernando Geu‐Flores
- Department of Plant and Environmental SciencesUniversity of Copenhagen1871 FrederiksbergCopenhagenDenmark
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16
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Zhu F, Cao MY, Zhu PX, Zhang QP, Lam HM. Non-specific LIPID TRANSFER PROTEIN 1 enhances immunity against tobacco mosaic virus in Nicotiana benthamiana. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5236-5254. [PMID: 37246636 DOI: 10.1093/jxb/erad202] [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: 01/06/2023] [Accepted: 05/25/2023] [Indexed: 05/30/2023]
Abstract
Plant non-specific lipid transfer proteins (nsLTPs) are small, cysteine-rich proteins that play significant roles in biotic and abiotic stress responses; however, the molecular mechanism of their functions against viral infections remains unclear. In this study, we employed virus-induced gene-silencing and transgenic overexpression to functionally analyse a type-I nsLTP in Nicotiana benthamiana, NbLTP1, in the immunity response against tobacco mosaic virus (TMV). NbLTP1 was inducible by TMV infection, and its silencing increased TMV-induced oxidative damage and the production of reactive oxygen species (ROS), compromised local and systemic resistance to TMV, and inactivated the biosynthesis of salicylic acid (SA) and its downstream signaling pathway. The effects of NbLTP1-silencing were partially restored by application of exogenous SA. Overexpressing NbLTP1 activated genes related to ROS scavenging to increase cell membrane stability and maintain redox homeostasis, confirming that an early ROS burst followed by ROS suppression at the later phases of pathogenesis is essential for resistance to TMV infection. The cell-wall localization of NbLTP1 was beneficial to viral resistance. Overall, our results showed that NbLTP1 positively regulates plant immunity against viral infection through up-regulating SA biosynthesis and its downstream signaling component, NONEXPRESSOR OF PATHOGENESIS-RELATED 1 (NPR1), which in turn activates pathogenesis-related genes, and by suppressing ROS accumulation at the later phases of viral pathogenesis.
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Affiliation(s)
- Feng Zhu
- College of Plant Protection, Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Meng-Yao Cao
- College of Plant Protection, Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Peng-Xiang Zhu
- College of Plant Protection, Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Qi-Ping Zhang
- College of Plant Protection, Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Hon-Ming Lam
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
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17
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Lee S, Kim J, Kim MS, Min CW, Kim ST, Choi SB, Lee JH, Choi D. The Phytophthora nucleolar effector Pi23226 targets host ribosome biogenesis to induce necrotrophic cell death. PLANT COMMUNICATIONS 2023; 4:100606. [PMID: 37087572 PMCID: PMC10504586 DOI: 10.1016/j.xplc.2023.100606] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 03/15/2023] [Accepted: 04/19/2023] [Indexed: 05/03/2023]
Abstract
Pathogen effectors target diverse subcellular organelles to manipulate the plant immune system. Although the nucleolus has emerged as a stress marker and several effectors are localized in the nucleolus, the roles of nucleolar-targeted effectors remain elusive. In this study, we showed that Phytophthora infestans infection of Nicotiana benthamiana results in nucleolar inflation during the transition from the biotrophic to the necrotrophic phase. Multiple P. infestans effectors were localized in the nucleolus: Pi23226 induced cell death in N. benthamiana and nucleolar inflation similar to that observed in the necrotrophic stage of infection, whereas its homolog Pi23015 and a deletion mutant (Pi23226ΔC) did not induce cell death or affect nucleolar size. RNA immunoprecipitation and individual-nucleotide-resolution UV crosslinking and immunoprecipitation sequencing analysis indicated that Pi23226 bound to the 3' end of 25S rRNA precursors, resulting in accumulation of unprocessed 27S pre-rRNAs. The nucleolar stress marker NAC082 was strongly upregulated under Pi23226-expressing conditions. Pi23226 subsequently inhibited global protein translation in host cells by interacting with ribosomes. Pi23226 enhanced P. infestans pathogenicity, indicating that Pi23226-induced ribosome malfunction and cell death were beneficial for pathogenesis in the host. Our results provide evidence for the molecular mechanism underlying RNA-binding effector activity in host ribosome biogenesis and lead to new insights into the nucleolar action of effectors in pathogenesis.
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Affiliation(s)
- Soeui Lee
- Plant Immunity Research Center, Seoul National University, Seoul 08826, Republic of Korea; Plant Genomics and Breeding Institute, Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Jaehwan Kim
- Plant Immunity Research Center, Seoul National University, Seoul 08826, Republic of Korea; Plant Genomics and Breeding Institute, Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Myung-Shin Kim
- Plant Immunity Research Center, Seoul National University, Seoul 08826, Republic of Korea; Interdisciplinary Programs in Agricultural Genomics, College of Agriculture and Life Science, Seoul National University, Seoul 08826, Republic of Korea; Division of Bioscience and Bioinformatics, Myongji University, Yongin 449-728, Republic of Korea
| | - Cheol Woo Min
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
| | - Sang-Bong Choi
- Division of Bioscience and Bioinformatics, Myongji University, Yongin 449-728, Republic of Korea
| | - Joo Hyun Lee
- Plant Immunity Research Center, Seoul National University, Seoul 08826, Republic of Korea.
| | - Doil Choi
- Plant Immunity Research Center, Seoul National University, Seoul 08826, Republic of Korea; Plant Genomics and Breeding Institute, Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Science, Seoul National University, Seoul 08826, Republic of Korea.
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18
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Ranawaka B, An J, Lorenc MT, Jung H, Sulli M, Aprea G, Roden S, Llaca V, Hayashi S, Asadyar L, LeBlanc Z, Ahmed Z, Naim F, de Campos SB, Cooper T, de Felippes FF, Dong P, Zhong S, Garcia-Carpintero V, Orzaez D, Dudley KJ, Bombarely A, Bally J, Winefield C, Giuliano G, Waterhouse PM. A multi-omic Nicotiana benthamiana resource for fundamental research and biotechnology. NATURE PLANTS 2023; 9:1558-1571. [PMID: 37563457 PMCID: PMC10505560 DOI: 10.1038/s41477-023-01489-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 07/11/2023] [Indexed: 08/12/2023]
Abstract
Nicotiana benthamiana is an invaluable model plant and biotechnology platform with a ~3 Gb allotetraploid genome. To further improve its usefulness and versatility, we have produced high-quality chromosome-level genome assemblies, coupled with transcriptome, epigenome, microRNA and transposable element datasets, for the ubiquitously used LAB strain and a related wild accession, QLD. In addition, single nucleotide polymorphism maps have been produced for a further two laboratory strains and four wild accessions. Despite the loss of five chromosomes from the ancestral tetraploid, expansion of intergenic regions, widespread segmental allopolyploidy, advanced diploidization and evidence of recent bursts of Copia pseudovirus (Copia) mobility not seen in other Nicotiana genomes, the two subgenomes of N. benthamiana show large regions of synteny across the Solanaceae. LAB and QLD have many genetic, metabolic and phenotypic differences, including disparate RNA interference responses, but are highly interfertile and amenable to genome editing and both transient and stable transformation. The LAB/QLD combination has the potential to be as useful as the Columbia-0/Landsberg errecta partnership, utilized from the early pioneering days of Arabidopsis genomics to today.
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Affiliation(s)
- Buddhini Ranawaka
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia
| | - Jiyuan An
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia.
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia.
| | - Michał T Lorenc
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Hyungtaek Jung
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, Queensland, Australia
| | - Maria Sulli
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Research Centre, Rome, Italy
| | - Giuseppe Aprea
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Research Centre, Rome, Italy
| | - Sally Roden
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia
| | - Victor Llaca
- Genomics Technologies, Corteva Agriscience, Johnston, IA, USA
| | - Satomi Hayashi
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia
| | - Leila Asadyar
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia
| | - Zacharie LeBlanc
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Zuba Ahmed
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia
| | - Fatima Naim
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Samanta Bolzan de Campos
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Tal Cooper
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Felipe F de Felippes
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Pengfei Dong
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Silin Zhong
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Victor Garcia-Carpintero
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politècnica de Valencia, Valencia, Spain
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politècnica de Valencia, Valencia, Spain
| | - Kevin J Dudley
- School of Biology and Environmental Science, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- QUT Central Analytical Research Facility, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Aureliano Bombarely
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politècnica de Valencia, Valencia, Spain
- Università degli Studi di Milano, Milan, Italy
| | - Julia Bally
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia
| | - Christopher Winefield
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia.
- Department of Wine Food and Molecular Biosciences, Lincoln University, Lincoln, New Zealand.
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Research Centre, Rome, Italy
| | - Peter M Waterhouse
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia.
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia.
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19
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Ahn YJ, Kim H, Choi S, Mazo-Molina C, Prokchorchik M, Zhang N, Kim B, Mang H, Koehler N, Kim J, Lee S, Yoon H, Choi D, Kim MS, Segonzac C, Martin GB, Schultink A, Sohn KH. Ptr1 and ZAR1 immune receptors confer overlapping and distinct bacterial pathogen effector specificities. THE NEW PHYTOLOGIST 2023; 239:1935-1953. [PMID: 37334551 DOI: 10.1111/nph.19073] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 05/22/2023] [Indexed: 06/20/2023]
Abstract
Some nucleotide-binding and leucine-rich repeat receptors (NLRs) indirectly detect pathogen effectors by monitoring their host targets. In Arabidopsis thaliana, RIN4 is targeted by multiple sequence-unrelated effectors and activates immune responses mediated by RPM1 and RPS2. These effectors trigger cell death in Nicotiana benthamiana, but the corresponding NLRs have yet not been identified. To identify N. benthamiana NLRs (NbNLRs) that recognize Arabidopsis RIN4-targeting effectors, we conducted a rapid reverse genetic screen using an NbNLR VIGS library. We identified that the N. benthamiana homolog of Ptr1 (Pseudomonas tomato race 1) recognizes the Pseudomonas effectors AvrRpt2, AvrRpm1, and AvrB. We demonstrated that recognition of the Xanthomonas effector AvrBsT and the Pseudomonas effector HopZ5 is conferred independently by the N. benthamiana homolog of Ptr1 and ZAR1. Interestingly, the recognition of HopZ5 and AvrBsT is contributed unequally by Ptr1 and ZAR1 in N. benthamiana and Capsicum annuum. In addition, we showed that the RLCK XII family protein JIM2 is required for the NbZAR1-dependent recognition of AvrBsT and HopZ5. The recognition of sequence-unrelated effectors by NbPtr1 and NbZAR1 provides an additional example of convergently evolved effector recognition. Identification of key components involved in Ptr1 and ZAR1-mediated immunity could reveal unique mechanisms of expanded effector recognition.
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Affiliation(s)
- Ye Jin Ahn
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Haseong Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Korea
| | - Sera Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Carolina Mazo-Molina
- Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853, USA
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Maxim Prokchorchik
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Ning Zhang
- Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853, USA
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Boyoung Kim
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Korea
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul, 08826, Korea
| | - Hyunggon Mang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Naio Koehler
- Fortiphyte Inc., 3071 Research Drive, Richmond, CA, 94806, USA
| | - Jieun Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Soeui Lee
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Korea
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul, 08826, Korea
| | - Hayeon Yoon
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Doil Choi
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Korea
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul, 08826, Korea
| | - Min-Sung Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Cécile Segonzac
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Korea
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul, 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea
| | - Gregory B Martin
- Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853, USA
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Alex Schultink
- Fortiphyte Inc., 3071 Research Drive, Richmond, CA, 94806, USA
| | - Kee Hoon Sohn
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea
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20
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Wu Q, Tong C, Chen Z, Huang S, Zhao X, Hong H, Li J, Feng M, Wang H, Xu M, Yan Y, Cui H, Shen D, Ai G, Xu Y, Li J, Zhang H, Huang C, Zhang Z, Dong S, Wang X, Zhu M, Dinesh-Kumar SP, Tao X. NLRs derepress MED10b- and MED7-mediated repression of jasmonate-dependent transcription to activate immunity. Proc Natl Acad Sci U S A 2023; 120:e2302226120. [PMID: 37399403 PMCID: PMC10334756 DOI: 10.1073/pnas.2302226120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/23/2023] [Indexed: 07/05/2023] Open
Abstract
Plant intracellular nucleotide-binding domain, leucine-rich repeat-containing receptors (NLRs) activate a robust immune response upon detection of pathogen effectors. How NLRs induce downstream immune defense genes remains poorly understood. The Mediator complex plays a central role in transducing signals from gene-specific transcription factors to the transcription machinery for gene transcription/activation. In this study, we demonstrate that MED10b and MED7 of the Mediator complex mediate jasmonate-dependent transcription repression, and coiled-coil NLRs (CNLs) in Solanaceae modulate MED10b/MED7 to activate immunity. Using the tomato CNL Sw-5b, which confers resistance to tospovirus, as a model, we found that the CC domain of Sw-5b directly interacts with MED10b. Knockout/down of MED10b and other subunits including MED7 of the middle module of Mediator activates plant defense against tospovirus. MED10b was found to directly interact with MED7, and MED7 directly interacts with JAZ proteins, which function as transcriptional repressors of jasmonic acid (JA) signaling. MED10b-MED7-JAZ together can strongly repress the expression of JA-responsive genes. The activated Sw-5b CC interferes with the interaction between MED10b and MED7, leading to the activation of JA-dependent defense signaling against tospovirus. Furthermore, we found that CC domains of various other CNLs including helper NLR NRCs from Solanaceae modulate MED10b/MED7 to activate defense against different pathogens. Together, our findings reveal that MED10b/MED7 serve as a previously unknown repressor of jasmonate-dependent transcription repression and are modulated by diverse CNLs in Solanaceae to activate the JA-specific defense pathways.
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Affiliation(s)
- Qian Wu
- The Key Laboratory of Plant Immunity, Department of Plant Pathology, Nanjing Agricultural University, Nanjing210095, P. R. China
| | - Cong Tong
- The Key Laboratory of Plant Immunity, Department of Plant Pathology, Nanjing Agricultural University, Nanjing210095, P. R. China
| | - Zhengqiang Chen
- The Key Laboratory of Plant Immunity, Department of Plant Pathology, Nanjing Agricultural University, Nanjing210095, P. R. China
| | - Shen Huang
- The Key Laboratory of Plant Immunity, Department of Plant Pathology, Nanjing Agricultural University, Nanjing210095, P. R. China
| | - Xiaohui Zhao
- Salinity Agriculture Research Laboratory, Jiangsu Coastal Area Institute of Agricultural Sciences, Yancheng224002, P. R. China
| | - Hao Hong
- The Key Laboratory of Plant Immunity, Department of Plant Pathology, Nanjing Agricultural University, Nanjing210095, P. R. China
| | - Jia Li
- The Key Laboratory of Plant Immunity, Department of Plant Pathology, Nanjing Agricultural University, Nanjing210095, P. R. China
| | - Mingfeng Feng
- The Key Laboratory of Plant Immunity, Department of Plant Pathology, Nanjing Agricultural University, Nanjing210095, P. R. China
| | - Huiyuan Wang
- The Key Laboratory of Plant Immunity, Department of Plant Pathology, Nanjing Agricultural University, Nanjing210095, P. R. China
- Institute of Biotechnology, Zhejiang University, Hangzhou310058, P. R. China
| | - Min Xu
- The Key Laboratory of Plant Immunity, Department of Plant Pathology, Nanjing Agricultural University, Nanjing210095, P. R. China
| | - Yuling Yan
- The Key Laboratory of Plant Immunity, Department of Plant Pathology, Nanjing Agricultural University, Nanjing210095, P. R. China
| | - Hongmin Cui
- The Key Laboratory of Plant Immunity, Department of Plant Pathology, Nanjing Agricultural University, Nanjing210095, P. R. China
| | - Danyu Shen
- The Key Laboratory of Plant Immunity, Department of Plant Pathology, Nanjing Agricultural University, Nanjing210095, P. R. China
| | - Gan Ai
- The Key Laboratory of Plant Immunity, Department of Plant Pathology, Nanjing Agricultural University, Nanjing210095, P. R. China
| | - Yi Xu
- The Key Laboratory of Plant Immunity, Department of Plant Pathology, Nanjing Agricultural University, Nanjing210095, P. R. China
| | - Junming Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, P. R. China
| | - Hui Zhang
- Institute of Horticulture Science, Shanghai Academy of Agricultural Sciences, Shanghai201403, P. R. China
| | - Changjun Huang
- Yunnan Academy of Tobacco Agricultural Sciences, Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Kunming650021, P. R. China
| | - Zhongkai Zhang
- Yunnan Provincial Key Laboratory of Agri-Biotechnology, Institute of Biotechnology and Genetic Resources, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan650223, P. R. China
| | - Suomeng Dong
- The Key Laboratory of Plant Immunity, Department of Plant Pathology, Nanjing Agricultural University, Nanjing210095, P. R. China
| | - Xuan Wang
- The Key Laboratory of Plant Immunity, Department of Plant Pathology, Nanjing Agricultural University, Nanjing210095, P. R. China
| | - Min Zhu
- The Key Laboratory of Plant Immunity, Department of Plant Pathology, Nanjing Agricultural University, Nanjing210095, P. R. China
| | - Savithramma P. Dinesh-Kumar
- Department of Plant Biology and The Genome Center College of Biological Sciences, University of California, Davis, CA95616
| | - Xiaorong Tao
- The Key Laboratory of Plant Immunity, Department of Plant Pathology, Nanjing Agricultural University, Nanjing210095, P. R. China
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21
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Wu Y, Li D, Hu Y, Li H, Ramstein GP, Zhou S, Zhang X, Bao Z, Zhang Y, Song B, Zhou Y, Zhou Y, Gagnon E, Särkinen T, Knapp S, Zhang C, Städler T, Buckler ES, Huang S. Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding. Cell 2023; 186:2313-2328.e15. [PMID: 37146612 DOI: 10.1016/j.cell.2023.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 02/20/2023] [Accepted: 04/05/2023] [Indexed: 05/07/2023]
Abstract
Hybrid potato breeding will transform the crop from a clonally propagated tetraploid to a seed-reproducing diploid. Historical accumulation of deleterious mutations in potato genomes has hindered the development of elite inbred lines and hybrids. Utilizing a whole-genome phylogeny of 92 Solanaceae and its sister clade species, we employ an evolutionary strategy to identify deleterious mutations. The deep phylogeny reveals the genome-wide landscape of highly constrained sites, comprising ∼2.4% of the genome. Based on a diploid potato diversity panel, we infer 367,499 deleterious variants, of which 50% occur at non-coding and 15% at synonymous sites. Counterintuitively, diploid lines with relatively high homozygous deleterious burden can be better starting material for inbred-line development, despite showing less vigorous growth. Inclusion of inferred deleterious mutations increases genomic-prediction accuracy for yield by 24.7%. Our study generates insights into the genome-wide incidence and properties of deleterious mutations and their far-reaching consequences for breeding.
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Affiliation(s)
- Yaoyao Wu
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
| | - Dawei Li
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; State Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Yong Hu
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, Yunnan 650500, China
| | - Hongbo Li
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Guillaume P Ramstein
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus 8000, Denmark
| | - Shaoqun Zhou
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Xinyan Zhang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Zhigui Bao
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | - Yu Zhang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; School of Agriculture, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Baoxing Song
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261000, China
| | - Yao Zhou
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100094, China
| | - Yongfeng Zhou
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Edeline Gagnon
- Technische Universität München, TUM School of Life Sciences, Emil-Ramann-Strasse 2, 85354 Freising, Germany
| | - Tiina Särkinen
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Sandra Knapp
- Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Chunzhi Zhang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Thomas Städler
- Institute of Integrative Biology and Zurich-Basel Plant Science Center, ETH Zurich, 8092 Zurich, Switzerland
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA; USDA-ARS, Ithaca, NY 14853, USA
| | - Sanwen Huang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; State Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China.
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22
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Feng H, Chen W, Hussain S, Shakir S, Tzin V, Adegbayi F, Ugine T, Fei Z, Jander G. Horizontally transferred genes as RNA interference targets for aphid and whitefly control. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:754-768. [PMID: 36577653 PMCID: PMC10037149 DOI: 10.1111/pbi.13992] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/14/2022] [Accepted: 12/22/2022] [Indexed: 06/01/2023]
Abstract
RNA interference (RNAi)-based technologies are starting to be commercialized as a new approach for agricultural pest control. Horizontally transferred genes (HTGs), which have been transferred into insect genomes from viruses, bacteria, fungi or plants, are attractive targets for RNAi-mediated pest control. HTGs are often unique to a specific insect family or even genus, making it unlikely that RNAi constructs targeting such genes will have negative effects on ladybugs, lacewings and other beneficial predatory insect species. In this study, we sequenced the genome of a red, tobacco-adapted isolate of Myzus persicae (green peach aphid) and bioinformatically identified 30 HTGs. We then used plant-mediated virus-induced gene silencing (VIGS) to show that several HTGs of bacterial and plant origin are important for aphid growth and/or survival. Silencing the expression of fungal-origin HTGs did not affect aphid survivorship but decreased aphid reproduction. Importantly, although there was uptake of plant-expressed RNA by Coccinella septempunctata (seven-spotted ladybugs) via the aphids that they consumed, we did not observe negative effects on ladybugs from aphid-targeted VIGS constructs. To demonstrate that this approach is more broadly applicable, we also targeted five Bemisia tabaci (whitefly) HTGs using VIGS and demonstrated that knockdown of some of these genes affected whitefly survival. As functional HTGs have been identified in the genomes of numerous pest species, we propose that these HTGs should be explored further as efficient and safe targets for control of insect pests using plant-mediated RNA interference.
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Affiliation(s)
| | - Wenbo Chen
- Boyce Thompson InstituteIthacaNYUSA
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative BiologyZhejiang UniversityHangzhouChina
| | - Sonia Hussain
- Boyce Thompson InstituteIthacaNYUSA
- Present address:
National Institute for Biotechnology and Genetic Engineering CollegePakistan Institute of Engineering and Applied SciencesFaisalabadPakistan
| | - Sara Shakir
- Boyce Thompson InstituteIthacaNYUSA
- Present address:
Gembloux Agro‐Bio Tech InstituteThe University of LiegeGemblouxBelgium
| | - Vered Tzin
- Boyce Thompson InstituteIthacaNYUSA
- Present address:
Jacob Blaustein Institutes for Desert ResearchBen‐Gurion University of the NegevSede BoqerIsrael
| | - Femi Adegbayi
- Boyce Thompson InstituteIthacaNYUSA
- Present address:
Drexel University College of MedicinePhiladelphiaPAUSA
| | - Todd Ugine
- Department of EntomologyCornell UniversityIthacaNYUSA
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23
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Uranga M, Aragonés V, Daròs JA, Pasin F. Heritable CRISPR-Cas9 editing of plant genomes using RNA virus vectors. STAR Protoc 2023; 4:102091. [PMID: 36853698 PMCID: PMC9943877 DOI: 10.1016/j.xpro.2023.102091] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/05/2022] [Accepted: 01/17/2023] [Indexed: 02/11/2023] Open
Abstract
Viral vectors hold enormous potential for genome editing in plants as transient delivery vehicles of CRISPR-Cas components. Here, we describe a protocol to assemble plant viral vectors for single-guide RNA (sgRNA) delivery. The obtained viral constructs are based on compact T-DNA binary vectors of the pLX series and are delivered into Cas9-expressing plants through agroinoculation. This approach allows rapidly assessing sgRNA design for plant genome targeting, as well as the recovery of progeny with heritable mutations at targeted loci. For complete details on the use and execution of this protocol, please refer to Uranga et al. (2021)1 and Aragonés et al. (2022).2.
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Affiliation(s)
- Mireia Uranga
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas - Universitat Politècnica de València, Avenida de los Naranjos s/n, 46022 Valencia, Spain.
| | - Verónica Aragonés
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas - Universitat Politècnica de València, Avenida de los Naranjos s/n, 46022 Valencia, Spain.
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas - Universitat Politècnica de València, Avenida de los Naranjos s/n, 46022 Valencia, Spain.
| | - Fabio Pasin
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas - Universitat Politècnica de València, Avenida de los Naranjos s/n, 46022 Valencia, Spain.
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24
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Zhong X, Li J, Yang L, Wu X, Xu H, Hu T, Wang Y, Wang Y, Wang Z. Genome-wide identification and expression analysis of wall-associated kinase (WAK) and WAK-like kinase gene family in response to tomato yellow leaf curl virus infection in Nicotiana benthamiana. BMC PLANT BIOLOGY 2023; 23:146. [PMID: 36927306 PMCID: PMC10021985 DOI: 10.1186/s12870-023-04112-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Tomato yellow leaf curl virus (TYLCV) is a major monopartite virus in the family Geminiviridae and has caused severe yield losses in tomato and tobacco planting areas worldwide. Wall-associated kinases (WAKs) and WAK-like kinases (WAKLs) are a subfamily of the receptor-like kinase family implicated in cell wall signaling and transmitting extracellular signals to the cytoplasm, thereby regulating plant growth and development and resistance to abiotic and biotic stresses. Recently, many studies on WAK/WAKL family genes have been performed in various plants under different stresses; however, identification and functional survey of the WAK/WAKL gene family of Nicotiana benthamiana have not yet been performed, even though its genome has been sequenced for several years. Therefore, in this study, we aimed to identify the WAK/WAKL gene family in N. benthamiana and explore their possible functions in response to TYLCV infection. RESULTS Thirty-eight putative WAK/WAKL genes were identified and named according to their locations in N. benthamiana. Phylogenetic analysis showed that NbWAK/WAKLs are clustered into five groups. The protein motifs and gene structure compositions of NbWAK/WAKLs appear to be highly conserved among the phylogenetic groups. Numerous cis-acting elements involved in phytohormone and/or stress responses were detected in the promoter regions of NbWAK/WAKLs. Moreover, gene expression analysis revealed that most of the NbWAK/WAKLs are expressed in at least one of the examined tissues, suggesting their possible roles in regulating the growth and development of plants. Virus-induced gene silencing and quantitative PCR analyses demonstrated that NbWAK/WAKLs are implicated in regulating the response of N. benthamiana to TYLCV, ten of which were dramatically upregulated in locally or systemically infected leaves of N. benthamiana following TYLCV infection. CONCLUSIONS Our study lays an essential base for the further exploration of the potential functions of NbWAK/WAKLs in plant growth and development and response to viral infections in N. benthamiana.
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Affiliation(s)
- Xueting Zhong
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Jiapeng Li
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Lianlian Yang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Xiaoyin Wu
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Hong Xu
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Tao Hu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Yajun Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Yaqin Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Zhanqi Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
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25
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Kurotani KI, Hirakawa H, Shirasawa K, Tanizawa Y, Nakamura Y, Isobe S, Notaguchi M. Genome Sequence and Analysis of Nicotiana benthamiana, the Model Plant for Interactions between Organisms. PLANT & CELL PHYSIOLOGY 2023; 64:248-257. [PMID: 36755428 PMCID: PMC9977260 DOI: 10.1093/pcp/pcac168] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/28/2022] [Accepted: 12/07/2022] [Indexed: 06/18/2023]
Abstract
Nicotiana benthamiana is widely used as a model plant for dicotyledonous angiosperms. In fact, the strains used in research are highly susceptible to a wide range of viruses. Accordingly, these strains are subject to plant pathology and plant-microbe interactions. In terms of plant-plant interactions, N. benthamiana is one of the plants that exhibit grafting affinity with plants from different families. Thus, N. benthamiana is a good model for plant biology and has been the subject of genome sequencing analyses for many years. However, N. benthamiana has a complex allopolyploid genome, and its previous reference genome is fragmented into 141,000 scaffolds. As a result, molecular genetic analysis is difficult to perform. To improve this effort, de novo whole-genome assembly was performed in N. benthamiana with Hifi reads, and 1,668 contigs were generated with a total length of 3.1 Gb. The 21 longest scaffolds, regarded as pseudomolecules, contained a 2.8-Gb sequence, occupying 95.6% of the assembled genome. A total of 57,583 high-confidence gene sequences were predicted. Based on a comparison of the genome structures between N. benthamiana and N. tabacum, N. benthamiana was found to have more complex chromosomal rearrangements, reflecting the age of interspecific hybridization. To verify the accuracy of the annotations, the cell wall modification genes involved in grafting were analyzed, which revealed not only the previously indeterminate untranslated region, intron and open reading frame sequences but also the genomic locations of their family genes. Owing to improved genome assembly and annotation, N. benthamiana would increasingly be more widely accessible.
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Affiliation(s)
- Ken-ichi Kurotani
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
| | - Hideki Hirakawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Kenta Shirasawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Yasuhiro Tanizawa
- Research Organization of Information and Systems, National Institute of Genetics, Yata, Mishima, 411-8540 Japan
| | - Yasukazu Nakamura
- Research Organization of Information and Systems, National Institute of Genetics, Yata, Mishima, 411-8540 Japan
| | - Sachiko Isobe
- *Corresponding authors: Sachiko Isobe, E-mail, ; Michitaka Notaguchi, E-mail,
| | - Michitaka Notaguchi
- *Corresponding authors: Sachiko Isobe, E-mail, ; Michitaka Notaguchi, E-mail,
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Garcia AGK, Steinbrenner AD. Bringing Plant Immunity to Light: A Genetically Encoded, Bioluminescent Reporter of Pattern-Triggered Immunity in Nicotiana benthamiana. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:139-149. [PMID: 36583694 DOI: 10.1094/mpmi-07-22-0160-ta] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Plants rely on innate immune systems to defend against a wide variety of biotic attackers. Key components of innate immunity include cell-surface pattern-recognition receptors (PRRs), which recognize pest- and pathogen-associated molecular patterns (PAMPs). Unlike other classes of receptors that often have visible cell-death immune outputs upon activation, PRRs generally lack rapid methods for assessing function. Here, we describe a genetically encoded bioluminescent reporter of immune activation by heterologously expressed PRRs in the model organism Nicotiana benthamiana. We characterized N. benthamiana transcriptome changes in response to Agrobacterium tumefaciens and subsequent PAMP treatment to identify pattern-triggered immunity (PTI)-associated marker genes, which were then used to generate promoter-luciferase fusion fungal bioluminescence pathway (FBP) constructs. A reporter construct termed pFBP_2xNbLYS1::LUZ allows for robust detection of PTI activation by heterologously expressed PRRs. Consistent with known PTI signaling pathways, reporter activation by receptor-like protein (RLP) PRRs is dependent on the known adaptor of RLP PRRs, i.e., SOBIR1. The FBP reporter minimizes the amount of labor, reagents, and time needed to assay function of PRRs and displays robust sensitivity at biologically relevant PAMP concentrations, making it ideal for high throughput screens. The tools described in this paper will be powerful for investigations of PRR function and characterization of the structure-function of plant cell-surface receptors. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2023.
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Affiliation(s)
- Anthony G K Garcia
- Department of Biology, University of Washington, Seattle, WA 98195, U.S.A
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McCray TN, Azim MF, Burch-Smith TM. The dicot homolog of maize PPR103 carries a C-terminal DYW domain and is required for C-to-U editing of chloroplast RNA transcripts. RESEARCH SQUARE 2023:rs.3.rs-2574001. [PMID: 36865278 PMCID: PMC9980218 DOI: 10.21203/rs.3.rs-2574001/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
In plants, cytidine-to-uridine (C-to-U) editing is a crucial step in processing mitochondria and chloroplast-encoded transcripts. This editing requires nuclear-encoded proteins including members of the pentatricopeptide (PPR) family, especially PLS-type proteins carrying the DYW domain. IPI1/emb175/PPR103 is a nuclear gene encoding a PLS-type PPR protein essential for survival in Arabidopsis thaliana and maize. Arabidopsis IPI1 was identified as likely interacting with ISE2, a chloroplast-localized RNA helicase associated with C-to-U RNA editing in Arabidopsis and maize. Notably, while the Arabidopsis and Nicotiana IPI1 homologs possess complete DYW motifs at their C-termini, the maize homolog, ZmPPR103, lacks this triplet of residues which are essential for editing. We examined the function of ISE2 and IPI1 in chloroplast RNA processing in N. benthamiana. A combination of deep sequencing and Sanger sequencing revealed C-to-U editing at 41 sites in 18 transcripts, with 34 sites conserved in the closely related N. tabacum. Virus induced gene silencing of NbISE2 or NbIPI1 led to defective C-to-U revealed that they have overlapping roles at editing a site in the rpoB transcript but have distinct roles in editing other transcripts. This finding contrasts with maize ppr103 mutants that showed no defects in editing. The results indicate that NbISE2 and NbIPI1 are important for C-to-U editing in N. benthamiana chloroplasts, and they may function in a complex to edit specific sites while having antagonistic effects on editing others. That NbIPI1, carrying a DYW domain, is involved in organelle C-to-U RNA editing supports previous work showing that this domain catalyzes RNA editing.
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Affiliation(s)
- Tyra N. McCray
- School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996
- Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN 37996
| | - Mohammad F. Azim
- Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN 37996
- Donald Danforth Plant Science Center, St. Louis, MO 63132
| | - Tessa M. Burch-Smith
- School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996
- Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN 37996
- Donald Danforth Plant Science Center, St. Louis, MO 63132
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Zhang FB, Ji SX, Yang JG, Wang XW, Han WH. Genome-wide analysis of MYB family in Nicotiana benthamiana and the functional role of the key members in resistance to Bemisia tabaci. Int J Biol Macromol 2023; 235:123759. [PMID: 36812971 DOI: 10.1016/j.ijbiomac.2023.123759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/06/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023]
Abstract
MYB transcription factors (TFs) play a key role in plant resistance to abiotic and biotical stresses. However, little is currently known about their involvement in the plant defense to piercing-sucking insects. Here, we studied the MYB TFs that responded to and resisted Bemisia tabaci whitefly in the model plant Nicotiana benthamiana. Firstly, a total of 453 NbMYB TFs in N. benthamiana genome were identified and 182 R2R3-MYB TFs were analyzed for molecular characteristics, phylogenetic analysis, genetic structure, motif composition, and cis-elements. Then, six stress-related NbMYB genes were selected for further study. The expression pattern shows they were highly expressed in mature leaves and intensively induced upon whitefly attack. Combined with bioinformatic analysis, overexpression, β-Glucuronidase (GUS) assay, and virus-induced silencing tests, we determined the transcriptional regulation of these NbMYBs on the genes in lignin biosynthesis and SA-signaling pathways. Meanwhile, we tested the performance of whitefly on plants with increased or silenced NbMYB genes expression and found that NbMYB42, NbMYB107, NbMYB163, and NbMYB423 were resistant to whitefly. Our results contribute to a comprehensive understanding of the MYB TFs in N. benthamiana. Furthermore, our findings will facilitate further studies on the role of MYB TFs in the interaction between plants and piercing-sucking insects.
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Affiliation(s)
- Feng-Bin Zhang
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shun-Xia Ji
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jin-Guang Yang
- Key Laboratory of Tobacco Pest Monitoring, Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Xiao-Wei Wang
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wen-Hao Han
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China.
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Sun L, Cao S, Zheng N, Kao TH. Analyses of Cullin1 homologs reveal functional redundancy in S-RNase-based self-incompatibility and evolutionary relationships in eudicots. THE PLANT CELL 2023; 35:673-699. [PMID: 36478090 PMCID: PMC9940881 DOI: 10.1093/plcell/koac357] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
In Petunia (Solanaceae family), self-incompatibility (SI) is regulated by the polymorphic S-locus, which contains the pistil-specific S-RNase and multiple pollen-specific S-Locus F-box (SLF) genes. SLFs assemble into E3 ubiquitin ligase complexes known as Skp1-Cullin1-F-box complexes (SCFSLF). In pollen tubes, these complexes collectively mediate ubiquitination and degradation of all nonself S-RNases, but not self S-RNase, resulting in cross-compatible, but self-incompatible, pollination. Using Petunia inflata, we show that two pollen-expressed Cullin1 (CUL1) proteins, PiCUL1-P and PiCUL1-B, function redundantly in SI. This redundancy is lost in Petunia hybrida, not because of the inability of PhCUL1-B to interact with SSK1, but due to a reduction in the PhCUL1-B transcript level. This is possibly caused by the presence of a DNA transposon in the PhCUL1-B promoter region, which was inherited from Petunia axillaris, one of the parental species of Pe. hybrida. Phylogenetic and syntenic analyses of Cullin genes in various eudicots show that three Solanaceae-specific CUL1 genes share a common origin, with CUL1-P dedicated to S-RNase-related reproductive processes. However, CUL1-B is a dispersed duplicate of CUL1-P present only in Petunia, and not in the other species of the Solanaceae family examined. We suggest that the CUL1s involved (or potentially involved) in the SI response in eudicots share a common origin.
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Affiliation(s)
- Linhan Sun
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Shiyun Cao
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, Washington 98195, USA
| | - Ning Zheng
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, Washington 98195, USA
| | - Teh-hui Kao
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Huang YW, Sun CI, Hu CC, Tsai CH, Meng M, Lin NS, Dinesh-Kumar SP, Hsu YH. A viral movement protein co-opts endoplasmic reticulum luminal-binding protein and calreticulin to promote intracellular movement. PLANT PHYSIOLOGY 2023; 191:904-924. [PMID: 36459587 PMCID: PMC9922411 DOI: 10.1093/plphys/kiac547] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
Intracellular movement is an important step for the initial spread of virus in plants during infection. This process requires virus-encoded movement proteins (MPs) and their interaction with host factors. Despite the large number of known host factors involved in the movement of different viruses, little is known about host proteins that interact with one of the MPs encoded by potexviruses, the triple-gene-block protein 3 (TGBp3). The main obstacle lies in the relatively low expression level of potexviral TGBp3 in hosts and the weak or transient nature of interactions. Here, we used TurboID-based proximity labeling to identify the network of proteins directly or indirectly interacting with the TGBp3 of a potexvirus, Bamboo mosaic virus (BaMV). Endoplasmic reticulum (ER) luminal-binding protein 4 and calreticulin 3 of Nicotiana benthamiana (NbBiP4 and NbCRT3, respectively) associated with the functional TGBp3-containing BaMV movement complexes, but not the movement-defective mutant, TGBp3M. Fluorescent microscopy revealed that TGBp3 colocalizes with NbBiP4 or NbCRT3 and the complexes move together along ER networks to cell periphery in N. benthamiana. Loss- and gain-of-function experiments revealed that NbBiP4 or NbCRT3 is required for the efficient spread and accumulation of BaMV in infected leaves. In addition, overexpression of NbBiP4 or NbCRT3 enhanced the targeting of BaMV TGBp1 to plasmodesmata (PD), indicating that NbBiP4 and NbCRT3 interact with TGBp3 to promote the intracellular transport of virion cargo to PD that facilitates virus cell-to-cell movement. Our findings revealed additional roles for NbBiP4 and NbCRT3 in BaMV intracellular movement through ER networks or ER-derived vesicles to PD, which enhances the spread of BaMV in N. benthamiana.
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Affiliation(s)
- Ying-Wen Huang
- Graduate Institute of Biotechnology, National Chung Hisng University, Taichung 40227, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
| | - Chu-I Sun
- Graduate Institute of Biotechnology, National Chung Hisng University, Taichung 40227, Taiwan
| | - Chung-Chi Hu
- Graduate Institute of Biotechnology, National Chung Hisng University, Taichung 40227, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
| | - Ching-Hsiu Tsai
- Graduate Institute of Biotechnology, National Chung Hisng University, Taichung 40227, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
| | - Menghsiao Meng
- Graduate Institute of Biotechnology, National Chung Hisng University, Taichung 40227, Taiwan
| | - Na-Sheng Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Savithramma P Dinesh-Kumar
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, California 95616, USA
| | - Yau-Heiu Hsu
- Graduate Institute of Biotechnology, National Chung Hisng University, Taichung 40227, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
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31
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Chase MW, Samuel R, Leitch AR, Guignard MS, Conran JG, Nollet F, Fletcher P, Jakob A, Cauz-Santos LA, Vignolle G, Dodsworth S, Christenhusz MJM, Buril MT, Paun O. Down, then up: non-parallel genome size changes and a descending chromosome series in a recent radiation of the Australian allotetraploid plant species, Nicotiana section Suaveolentes (Solanaceae). ANNALS OF BOTANY 2023; 131:123-142. [PMID: 35029647 PMCID: PMC9904355 DOI: 10.1093/aob/mcac006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 01/11/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS The extent to which genome size and chromosome numbers evolve in concert is little understood, particularly after polyploidy (whole-genome duplication), when a genome returns to a diploid-like condition (diploidization). We study this phenomenon in 46 species of allotetraploid Nicotiana section Suaveolentes (Solanaceae), which formed <6 million years ago and radiated in the arid centre of Australia. METHODS We analysed newly assessed genome sizes and chromosome numbers within the context of a restriction site-associated nuclear DNA (RADseq) phylogenetic framework. KEY RESULTS RADseq generated a well-supported phylogenetic tree, in which multiple accessions from each species formed unique genetic clusters. Chromosome numbers and genome sizes vary from n = 2x = 15 to 24 and 2.7 to 5.8 pg/1C nucleus, respectively. Decreases in both genome size and chromosome number occur, although neither consistently nor in parallel. Species with the lowest chromosome numbers (n = 15-18) do not possess the smallest genome sizes and, although N. heterantha has retained the ancestral chromosome complement, n = 2x = 24, it nonetheless has the smallest genome size, even smaller than that of the modern representatives of ancestral diploids. CONCLUSIONS The results indicate that decreases in genome size and chromosome number occur in parallel down to a chromosome number threshold, n = 20, below which genome size increases, a phenomenon potentially explained by decreasing rates of recombination over fewer chromosomes. We hypothesize that, more generally in plants, major decreases in genome size post-polyploidization take place while chromosome numbers are still high because in these stages elimination of retrotransposons and other repetitive elements is more efficient. Once such major genome size change has been accomplished, then dysploid chromosome reductions take place to reorganize these smaller genomes, producing species with small genomes and low chromosome numbers such as those observed in many annual angiosperms, including Arabidopsis.
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Affiliation(s)
- Mark W Chase
- Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK
- Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Rosabelle Samuel
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | | | - John G Conran
- ACEBB & SGC, School of Biological Sciences, The University of Adelaide, SA 5005Australia
| | - Felipe Nollet
- Universidade Federal Rural de Pernambuco, Centro de Ciências Biológicas, Departamento de Botânica, Rua Manuel de Medeiros, S/N, Dois Irmãos, 52171-900 Recife, Pernambuco, Brazil
| | - Paul Fletcher
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Aljaž Jakob
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Luiz A Cauz-Santos
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Gabriel Vignolle
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Steven Dodsworth
- School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Maarten J M Christenhusz
- Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
| | - Maria Teresa Buril
- ACEBB & SGC, School of Biological Sciences, The University of Adelaide, SA 5005Australia
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
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Characterization and expression analysis of bHLH transcription factors reveal their putative regulatory effects on nectar spur development in Aquilegia species. Gene 2023; 852:147057. [PMID: 36410606 DOI: 10.1016/j.gene.2022.147057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/27/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022]
Abstract
Nectar spur is a hollow extension of certain flower parts and shows strikingly diverse size and shape in Aquilegia. Nectar spur development is involved in cell division and expansion processes. The basic helix-loop-helix (bHLH) transcription factors (TFs) control a diversity of organ morphogenesis, including cell division and cell expansion processes. However, the role of bHLH genes in nectar spur development in Aquilegia is mainly unknown. We conducted a genome-wide identification of the bHLH gene family in Aquilegia to determine structural characteristics and phylogenetic relationships, and to analyze expression profiles of these genes during the development of nectar spur in spurless and spurred species. A total of 120 AqbHLH genes were identified from the Aquilegia coerulea genome. The phylogenetic tree showed that AqbHLH proteins were divided into 15 subfamilies, among which S7 and S8 subfamilies occurred marked expansion. The AqbHLH genes in the same clade had similar motif composition and gene structure characteristics. Conserved residue analysis indicated nineteen residues with conservation of more than 50% were found in the four conserved regions. In the upstream sequence of AqbHLH genes, the light-responsive element was the most abundant cis-acting element. Eighteen AqbHLH genes showed syntenic relationships, and eight genes from four syntenic pairs underwent tandem duplications. According to the expression profiling analysis by public RNA-Seq data and qRT-PCR results, five AqbHLH genes, including AqbHLH027, AqbHLH046, AqbHLH082, AqbHLH083 and AqbHLH092, were differentially expressed between different tissues in A. coerulea at early developmental stages, as well as between spurless and spurred Aquilegia species. Of them, AqbHLH046 was not only highly expressed in spur compared with blade, but also showed higher expression levels in spurred species than spurless specie, suggesting it plays an essential role in the development of spur by regulating cell division. This study lays a foundation to investigate the function of AqbHLH genes family in nectar spur development, and has potential implications for speciation and genetic breeding in the genus Aquilegia.
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Choi JW, Choi HH, Park YS, Jang MJ, Kim S. Comparative and expression analyses of AP2/ERF genes reveal copy number expansion and potential functions of ERF genes in Solanaceae. BMC PLANT BIOLOGY 2023; 23:48. [PMID: 36683040 PMCID: PMC9869560 DOI: 10.1186/s12870-022-04017-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND The AP2/ERF gene family is a superfamily of transcription factors that are important in the response of plants to abiotic stress and development. However, comprehensive research of the AP2/ERF genes in the Solanaceae family is lacking. RESULTS Here, we updated the annotation of AP2/ERF genes in the genomes of eight Solanaceae species, as well as Arabidopsis thaliana and Oryza sativa. We identified 2,195 AP2/ERF genes, of which 368 (17%) were newly identified. Based on phylogenetic analyses, we observed expansion of the copy number of these genes, especially those belonging to specific Ethylene-Responsive Factor (ERF) subgroups of the Solanaceae. From the results of chromosomal location and synteny analyses, we identified that the AP2/ERF genes of the pepper (Capsicum annuum), the tomato (Solanum lycopersicum), and the potato (Solanum tuberosum) belonging to ERF subgroups form a tandem array and most of them are species-specific without orthologs in other species, which has led to differentiation of AP2/ERF gene repertory among Solanaceae. We suggest that these genes mainly emerged through recent gene duplication after the divergence of these species. Transcriptome analyses showed that the genes have a putative function in the response of the pepper and tomato to abiotic stress, especially those in ERF subgroups. CONCLUSIONS Our findings will provide comprehensive information on AP2/ERF genes and insights into the structural, evolutionary, and functional understanding of the role of these genes in the Solanaceae.
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Affiliation(s)
- Jin-Wook Choi
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Republic of Korea
| | - Hyeon Ho Choi
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Republic of Korea
| | - Young-Soo Park
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Republic of Korea
| | - Min-Jeong Jang
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Republic of Korea
| | - Seungill Kim
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Republic of Korea.
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Wu FH, Hsu CT, Lin CS. Targeted Insertion in Nicotiana benthamiana Genomes via Protoplast Regeneration. Methods Mol Biol 2023; 2653:297-315. [PMID: 36995634 DOI: 10.1007/978-1-0716-3131-7_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Insertion of a specific sequence in a targeted region for precise editing is still a major challenge in plants. Current protocols rely on inefficient homology-directed repair or non-homologous end-joining with modified double-stranded oligodeoxyribonucleotides (dsODNs) as donors. We developed a simple protocol that eliminates the need for expensive equipment, chemicals, modifications of donor DNA, and complicated vector construction. The protocol uses polyethylene glycol (PEG)-calcium to deliver low-cost, unmodified single-stranded oligodeoxyribonucleotides (ssODNs) and CRISPR/Cas9 ribonucleoprotein (RNP) complexes into Nicotiana benthamiana protoplasts. Regenerated plants were obtained from edited protoplasts with an editing frequency of up to 50% at the target locus. The inserted sequence was inherited to the next generation; this method thus opens the possibility for the future exploration of genomes by targeted insertion in plants.
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Affiliation(s)
- Fu-Hui Wu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Chen-Tran Hsu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Choun-Sea Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
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Çalışır K, Krczal G, Uslu VV. Small RNA-seq dataset of wild type and 16C Nicotiana benthamiana leaves sprayed with naked dsRNA using the high-pressure spraying technique. Data Brief 2022; 45:108706. [PMID: 36426005 PMCID: PMC9679692 DOI: 10.1016/j.dib.2022.108706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 10/14/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
Double-stranded RNA (dsRNA) applications have emerged as promising alternatives to chemical plant pesticides. It has been proposed that the protective effect of dsRNA is mediated by the RNA interference (RNAi) mechanism. Small RNAs (sRNAs) are one of the landmarks of RNAi mechanisms. Two classes of sRNAs appear upon RNAi, triggered by dsRNA: The cleavage products of the dsRNA mapping directly to the dsRNA sequence and the transitive sRNAs mapping to the target transcript outside of the dsRNA sequence. Therefore, the sRNA-seq data obtained from dsRNA-treated plants have been exclusively analysed in the context of the target genes and the outcome has been considered essential to evaluate the underlying mechanism of dsRNA mediated plant protection. Using high-pressure spraying technology (HPST), we have applied a GFP targeting 139bp-long dsRNA on wild type (WT) and GFP expressing (16C) Nicotiana benthamiana plants in biological triplicates. As a control, we applied water with HPST on 16C N. benthamiana. We have acquired sRNA-seq data on the treated and control leaves 5 days post spraying. In this dataset, we have expanded our sRNA-seq analysis from the target GFP transgene sequence to the whole transcriptome of N. benthamiana to provide the community with a resource for the small RNA landscape after high-pressure spraying in 16C and WT samples. Furthermore, we have provided a comparison of sRNA landscape between WT and 16C lines.
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36
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Valli AA, Gonzalo-Magro I, Sanchez DH. Rearranged Endogenized Plant Pararetroviruses as Evidence of Heritable RNA-based Immunity. Mol Biol Evol 2022; 40:6794085. [PMID: 36322467 PMCID: PMC9868043 DOI: 10.1093/molbev/msac240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 09/05/2022] [Accepted: 10/25/2022] [Indexed: 01/24/2023] Open
Abstract
Eukaryotic genomics frequently revealed historical spontaneous endogenization events of external invading nucleic acids, such as viral elements. In plants, an extensive occurrence of endogenous plant pararetroviruses (EPRVs) is usually believed to endow hosts with an additional layer of internal suppressive weaponry. However, an actual demonstration of this activity remains speculative. We analyzed the EPRV component and accompanying silencing effectors of Solanum lycopersicum, documenting that intronic/intergenic pararetroviral integrations bearing inverted-repeats fuel the plant's RNA-based immune system with suitable transcripts capable of evoking a silencing response. A surprisingly small set of rearrangements explained a substantial fraction of pararetroviral-derived endogenous small-interfering (si)RNAs, enriched in 22-nt forms typically associated with anti-viral post-transcriptional gene silencing. We provide preliminary evidence that such genetic and immunological signals may be found in other species outside the genus Solanum. Based on molecular dating, bioinformatics, and empirical explorations, we propose that homology-dependent silencing emerging from particular immuno-competent rearranged chromosomal areas that constitute an adaptive heritable trans-acting record of past infections, with potential impact against the unlocking of plant latent EPRVs and cognate-free pararetroviruses.
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Affiliation(s)
| | - Irene Gonzalo-Magro
- Centro Nacional de Biotecnología (CNB-CSIC), Calle Darwin 3, 28049 Madrid, Spain
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Welch T, Bayon C, Rudd JJ, Kanyuka K, Kettles GJ. Induction of distinct plant cell death programs by secreted proteins from the wheat pathogen Zymoseptoria tritici. Sci Rep 2022; 12:17880. [PMID: 36284131 PMCID: PMC9596407 DOI: 10.1038/s41598-022-22660-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/18/2022] [Indexed: 01/20/2023] Open
Abstract
Cell death processes in eukaryotes shape normal development and responses to the environment. For plant-microbe interactions, initiation of host cell death plays an important role in determining disease outcomes. Cell death pathways are frequently initiated following detection of pathogen-derived molecules which can lead to resistance or susceptibility to disease depending on pathogen lifestyle. We previously identified several small secreted proteins (SSPs) from the wheat-infecting fungus Zymoseptoria tritici that induce rapid cell death in Nicotiana benthamiana following Agrobacterium-mediated delivery and expression (agroinfiltration). Here we investigated whether the execution of host cells was mechanistically similar in response to different Z. tritici SSPs. Using RNA sequencing, we found that transient expression of four Z. tritici SSPs led to massive transcriptional reprogramming within 48 h of agroinfiltration. We observed that distinct host gene expression profiles were induced dependent on whether cell death occurs in a cell surface immune receptor-dependent or -independent manner. These gene expression profiles involved differential transcriptional networks mediated by WRKY, NAC and MYB transcription factors. In addition, differential expression of genes belonging to different classes of receptor-like proteins and receptor-like kinases was observed. These data suggest that different Z. tritici SSPs trigger differential transcriptional reprogramming in plant cells.
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Affiliation(s)
- Thomas Welch
- grid.6572.60000 0004 1936 7486Birmingham Institute of Forest Research, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK ,grid.6572.60000 0004 1936 7486School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - Carlos Bayon
- grid.418374.d0000 0001 2227 9389Wheat Pathogenomics Team, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ UK
| | - Jason J. Rudd
- grid.418374.d0000 0001 2227 9389Wheat Pathogenomics Team, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ UK
| | - Kostya Kanyuka
- grid.17595.3f0000 0004 0383 6532Cambridge Crop Research, National Institute of Agricultural Botany (NIAB), 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Graeme J. Kettles
- grid.6572.60000 0004 1936 7486Birmingham Institute of Forest Research, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK ,grid.6572.60000 0004 1936 7486School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
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Wu L, Xiao H, Zhao L, Cheng Q. CRISPR/Cas9-mediated generation of fls2 mutant in Nicotiana benthamiana for investigating the flagellin recognition spectrum of diverse FLS2 receptors. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1853-1855. [PMID: 35880295 PMCID: PMC9491447 DOI: 10.1111/pbi.13898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/11/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Ling Wu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
| | - Hongju Xiao
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
| | - Lijuan Zhao
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
| | - Qiang Cheng
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
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Wang L, Tan H, Medina-Puche L, Wu M, Garnelo Gomez B, Gao M, Shi C, Jimenez-Gongora T, Fan P, Ding X, Zhang D, Ding Y, Rosas-Díaz T, Liu Y, Aguilar E, Fu X, Lozano-Durán R. Combinatorial interactions between viral proteins expand the potential functional landscape of the tomato yellow leaf curl virus proteome. PLoS Pathog 2022; 18:e1010909. [PMID: 36256684 PMCID: PMC9633003 DOI: 10.1371/journal.ppat.1010909] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 11/03/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022] Open
Abstract
Viruses manipulate the cells they infect in order to replicate and spread. Due to strict size restrictions, viral genomes have reduced genetic space; how the action of the limited number of viral proteins results in the cell reprogramming observed during the infection is a long-standing question. Here, we explore the hypothesis that combinatorial interactions may expand the functional landscape of the viral proteome. We show that the proteins encoded by a plant-infecting DNA virus, the geminivirus tomato yellow leaf curl virus (TYLCV), physically associate with one another in an intricate network, as detected by a number of protein-protein interaction techniques. Importantly, our results indicate that intra-viral protein-protein interactions can modify the subcellular localization of the proteins involved. Using one particular pairwise interaction, that between the virus-encoded C2 and CP proteins, as proof-of-concept, we demonstrate that the combination of viral proteins leads to novel transcriptional effects on the host cell. Taken together, our results underscore the importance of studying viral protein function in the context of the infection. We propose a model in which viral proteins might have evolved to extensively interact with other elements within the viral proteome, enlarging the potential functional landscape available to the pathogen. Viruses are obligate intracellular parasites that depend on the molecular machinery of their host cell to complete their life cycle. For this purpose, viruses co-opt host processes, modulating or redirecting them. Most viruses have small genomes, and hence limited coding capacity. During the viral invasion, virus-encoded proteins will be produced in large amounts and coexist in the infected cell, which enables physical or functional interactions among viral proteins, potentially expanding the virus-host functional interface by increasing the number of potential targets in the host cell and/or synergistically modulating the cellular environment. Examples of interactions between viral proteins have been recently documented for both animal and plant viruses; however, the hypothesis that viral proteins might have a combinatorial effect, which would lead to the acquisition of novel functions, lacks systematic experimental validation. Here, we use the geminivirus tomato yellow leaf curl virus (TYLCV), a plant-infecting virus with reduced proteome and causing devastating diseases in crops, to test the idea that combinatorial interactions between viral proteins exist and might underlie an expansion of the functional landscape of the viral proteome. Our results indicate that viral proteins prevalently interact with one another in the context of the infection, which can result in the acquisition of novel functions.
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Affiliation(s)
- Liping Wang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Huang Tan
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
- Department of Plant Biochemistry, Center for Plant Molecular Biology (ZMBP), Eberhard Karls University, Tübingen, Germany
| | - Laura Medina-Puche
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- Department of Plant Biochemistry, Center for Plant Molecular Biology (ZMBP), Eberhard Karls University, Tübingen, Germany
| | - Mengshi Wu
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Borja Garnelo Gomez
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Man Gao
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Chaonan Shi
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- Department of Plant Biochemistry, Center for Plant Molecular Biology (ZMBP), Eberhard Karls University, Tübingen, Germany
| | - Tamara Jimenez-Gongora
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Pengfei Fan
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Xue Ding
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Dan Zhang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Yi Ding
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Tábata Rosas-Díaz
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yujing Liu
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Emmanuel Aguilar
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC), Area de Genética, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos s/n, Málaga, Spain
| | - Xing Fu
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Rosa Lozano-Durán
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- Department of Plant Biochemistry, Center for Plant Molecular Biology (ZMBP), Eberhard Karls University, Tübingen, Germany
- * E-mail:
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Kourelis J, Contreras MP, Harant A, Pai H, Lüdke D, Adachi H, Derevnina L, Wu CH, Kamoun S. The helper NLR immune protein NRC3 mediates the hypersensitive cell death caused by the cell-surface receptor Cf-4. PLoS Genet 2022; 18:e1010414. [PMID: 36137148 PMCID: PMC9543701 DOI: 10.1371/journal.pgen.1010414] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 10/07/2022] [Accepted: 09/06/2022] [Indexed: 11/18/2022] Open
Abstract
Cell surface pattern recognition receptors (PRRs) activate immune responses that can include the hypersensitive cell death. However, the pathways that link PRRs to the cell death response are poorly understood. Here, we show that the cell surface receptor-like protein Cf-4 requires the intracellular nucleotide-binding domain leucine-rich repeat containing receptor (NLR) NRC3 to trigger a confluent cell death response upon detection of the fungal effector Avr4 in leaves of Nicotiana benthamiana. This NRC3 activity requires an intact N-terminal MADA motif, a conserved signature of coiled-coil (CC)-type plant NLRs that is required for resistosome-mediated immune responses. A chimeric protein with the N-terminal α1 helix of Arabidopsis ZAR1 swapped into NRC3 retains the capacity to mediate Cf-4 hypersensitive cell death. Pathogen effectors acting as suppressors of NRC3 can suppress Cf-4-triggered hypersensitive cell-death. Our findings link the NLR resistosome model to the hypersensitive cell death caused by a cell surface PRR.
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Affiliation(s)
- Jiorgos Kourelis
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Mauricio P. Contreras
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Adeline Harant
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Hsuan Pai
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Daniel Lüdke
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Hiroaki Adachi
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Lida Derevnina
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Chih-Hang Wu
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
- * E-mail: (CHW); (SK)
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
- * E-mail: (CHW); (SK)
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41
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Choi JW, Kim HE, Kim S. Two different domain architectures generate structural and functional diversity among bZIP genes in the Solanaceae family. FRONTIERS IN PLANT SCIENCE 2022; 13:967546. [PMID: 36061789 PMCID: PMC9437623 DOI: 10.3389/fpls.2022.967546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/01/2022] [Indexed: 05/27/2023]
Abstract
The bZIP gene family is one of the largest transcription factor families and has important roles in plant growth, development, and stress responses. However, bZIP genes in the Solanaceae family have not been extensively investigated. Here, we conducted genome-wide re-annotation in nine Solanaceae species and Arabidopsis thaliana. We annotated 935 bZIP genes, including 107 (11%) that were newly identified. Structural analyses of bZIP genes in the Solanaceae family revealed that the bZIP domain displayed two types of architectures depending on the presence of an additional domain, suggesting that these architectures generate diversified structures and functions. Motif analyses indicated that the two types of bZIP genes had distinct sequences adjacent to the bZIP domain. Phylogenetic analyses suggested that the two types of bZIP genes distinctly evolved and ultimately adapted in different lineages. Transcriptome analyses in pepper (Capsicum annuum) and tomato (Solanum lycopersicum) revealed putative functional diversity between the two types of bZIP genes in response to various abiotic stresses. This study extensively updated bZIP gene family annotations and provided novel evolutionary and functional evidence for the role of bZIP genes in Solanaceae plants. Our findings provide evolutionary and functional characteristics of bZIP genes for a better understanding of their roles in Solanaceae plants.
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Wang N, Yin Z, Zhao Y, Li Z, Dou D, Wei L. Two divergent immune receptors of the allopolyploid Nicotiana benthamiana reinforce the recognition of a fungal microbe-associated molecular pattern VdEIX3. FRONTIERS IN PLANT SCIENCE 2022; 13:968562. [PMID: 36046591 PMCID: PMC9421165 DOI: 10.3389/fpls.2022.968562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
The allotetraploid Solanaceae plant Nicotiana benthamiana contains two closely related receptor-like proteins (RLPs), NbEIX2 and NbRXEG1, which regulate the recognition of VdEIX3 and PsXEG1, respectively. VdEIX3, PsXEG1, and their homologs represent two types of microbe-associated molecular patterns (MAMPs) that are widespread in diverse pathogens. Here, we report that NbRXEG1 also participates in VdEIX3 recognition. Both eix2 and rxeg1 single mutants exhibited significantly impaired but not abolished ability to mediate VdEIX3-triggered immune responses, which are nearly abolished in eix2 rxeg1 double mutants. Moreover, a dominant negative mutant of eix2 that contains a 60 bp deletion failed to respond to VdEIX3 and could suppress VdEIX3-induced cell death in the wild-type N. benthamiana. Further phylogenetic analyses showed that NbEIX2 and NbRXEG1 are obtained from different diploid ancestors by hybridization. These results demonstrate that the allotetraploid N. benthamiana recognizes two types of MAMPs by two homologous but diverged RLPs, which provides a model in which an allopolyploid plant probably exhibits defense hybrid vigor by acquiring divergent immune receptors from different ancestors.
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Affiliation(s)
- Nan Wang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Zhiyuan Yin
- College of Plant Protection, China Agricultural University, Beijing, China
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Yaning Zhao
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Zhengpeng Li
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huaian, China
| | - Daolong Dou
- College of Plant Protection, China Agricultural University, Beijing, China
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Lihui Wei
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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Huang Y, Chen I, Kao Y, Hsu Y, Tsai C. The gibberellic acid derived from the plastidial MEP pathway is involved in the accumulation of Bamboo mosaic virus. THE NEW PHYTOLOGIST 2022; 235:1543-1557. [PMID: 35524450 PMCID: PMC9543464 DOI: 10.1111/nph.18210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/12/2022] [Indexed: 06/14/2023]
Abstract
A gene upregulated in Nicotiana benthamiana after Bamboo mosaic virus (BaMV) infection was revealed as 1-deoxy-d-xylulose-5-phosphate reductoisomerase (NbDXR). DXR is the key enzyme in the 2-C-methyl-d-erythritol-4-phosphate (MEP) pathway that catalyzes the conversion of 1-deoxy-d-xylulose 5-phosphate to 2-C-methyl-d-erythritol-4-phosphate. Knockdown and overexpression of NbDXR followed by BaMV inoculation revealed that NbDXR is involved in BaMV accumulation. Treating leaves with fosmidomycin, an inhibitor of DXR function, reduced BaMV accumulation. Subcellular localization confirmed that DXR is a chloroplast-localized protein by confocal microscopy. Furthermore, knockdown of 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate reductase, one of the enzymes in the MEP pathway, also reduced BaMV accumulation. The accumulation of BaMV increased significantly in protoplasts treated with isopentenyl pyrophosphate. Thus, the metabolites of the MEP pathway could be involved in BaMV infection. To identify the critical components involved in BaMV accumulation, we knocked down the crucial enzyme of isoprenoid synthesis, NbGGPPS11 or NbGGPPS2. Only NbGGPPS2 was involved in BaMV infection. The geranylgeranyl pyrophosphate (GGPP) synthesized by NbGGPPS2 is known for gibberellin synthesis. We confirmed this result by supplying gibberellic acid exogenously on leaves, which increased BaMV accumulation. The de novo synthesis of gibberellic acid could assist BaMV accumulation.
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Affiliation(s)
- Ying‐Ping Huang
- Graduate Institute of BiotechnologyNational Chung Hsing UniversityTaichung402Taiwan
| | - I‐Hsuan Chen
- Graduate Institute of BiotechnologyNational Chung Hsing UniversityTaichung402Taiwan
| | - Yu‐Shun Kao
- Graduate Institute of BiotechnologyNational Chung Hsing UniversityTaichung402Taiwan
| | - Yau‐Heiu Hsu
- Graduate Institute of BiotechnologyNational Chung Hsing UniversityTaichung402Taiwan
- Advaced Plant Biotechnology CenterNational Chung Hsing UniversityTaichung402Taiwan
| | - Ching‐Hsiu Tsai
- Graduate Institute of BiotechnologyNational Chung Hsing UniversityTaichung402Taiwan
- Advaced Plant Biotechnology CenterNational Chung Hsing UniversityTaichung402Taiwan
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Saado I, Chia KS, Betz R, Alcântara A, Pettkó-Szandtner A, Navarrete F, D'Auria JC, Kolomiets MV, Melzer M, Feussner I, Djamei A. Effector-mediated relocalization of a maize lipoxygenase protein triggers susceptibility to Ustilago maydis. THE PLANT CELL 2022; 34:2785-2805. [PMID: 35512341 PMCID: PMC9252493 DOI: 10.1093/plcell/koac105] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 02/17/2022] [Indexed: 05/07/2023]
Abstract
As the gall-inducing smut fungus Ustilago maydis colonizes maize (Zea mays) plants, it secretes a complex effector blend that suppresses host defense responses, including production of reactive oxygen species (ROS) and redirects host metabolism to facilitate colonization. We show that the U. maydis effector ROS burst interfering protein 1 (Rip1), which is involved in pathogen-associated molecular pattern (PAMP)-triggered suppression of host immunity, is functionally conserved in several other monocot-infecting smut fungi. We also have identified a conserved C-terminal motif essential for Rip1-mediated PAMP-triggered suppression of the ROS burst. The maize susceptibility factor lipoxygenase 3 (Zmlox3) bound by Rip1 was relocalized to the nucleus, leading to partial suppression of the ROS burst. Relocalization was independent of its enzymatic activity, revealing a distinct function for ZmLox3. Most importantly, whereas Zmlox3 maize mutant plants showed increased resistance to U. maydis wild-type strains, rip1 deletion strains infecting the Zmlox3 mutant overcame this effect. This could indicate that Rip1-triggered host resistance depends on ZmLox3 to be suppressed and that lox3 mutation-based resistance of maize to U. maydis requires functional Rip1. Together, our results reveal that Rip1 acts in several cellular compartments to suppress immunity and that targeting of ZmLox3 by Rip1 is responsible for the suppression of Rip1-dependent reduced susceptibility of maize to U. maydis.
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Affiliation(s)
- Indira Saado
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences (OEAW), Vienna BioCenter 7(VBC),Vienna 1030, Austria
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland D-06466, Germany
| | - Khong-Sam Chia
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences (OEAW), Vienna BioCenter 7(VBC),Vienna 1030, Austria
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland D-06466, Germany
| | - Ruben Betz
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences (OEAW), Vienna BioCenter 7(VBC),Vienna 1030, Austria
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland D-06466, Germany
| | - André Alcântara
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences (OEAW), Vienna BioCenter 7(VBC),Vienna 1030, Austria
| | | | - Fernando Navarrete
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences (OEAW), Vienna BioCenter 7(VBC),Vienna 1030, Austria
| | - John C D'Auria
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland D-06466, Germany
| | | | - Michael Melzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland D-06466, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, University of Göttingen, Albrecht-von-Haller Institute for Plant Sciences and Goettingen Center for Molecular Biosciences (GZMB), Göttingen 37077, Germany
| | - Armin Djamei
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences (OEAW), Vienna BioCenter 7(VBC),Vienna 1030, Austria
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland D-06466, Germany
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45
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Feng H, Acosta-Gamboa L, Kruse LH, Tracy JD, Chung SH, Nava Fereira AR, Shakir S, Xu H, Sunter G, Gore MA, Casteel CL, Moghe GD, Jander G. Acylsugars protect Nicotiana benthamiana against insect herbivory and desiccation. PLANT MOLECULAR BIOLOGY 2022; 109:505-522. [PMID: 34586580 DOI: 10.1007/s11103-021-01191-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 09/12/2021] [Indexed: 06/13/2023]
Abstract
KEY MESSAGE Nicotiana benthamiana acylsugar acyltransferase (ASAT) is required for protection against desiccation and insect herbivory. Knockout mutations provide a new resource for investigation of plant-aphid and plant-whitefly interactions. Nicotiana benthamiana is used extensively as a transient expression platform for functional analysis of genes from other species. Acylsugars, which are produced in the trichomes, are a hypothesized cause of the relatively high insect resistance that is observed in N. benthamiana. We characterized the N. benthamiana acylsugar profile, bioinformatically identified two acylsugar acyltransferase genes, ASAT1 and ASAT2, and used CRISPR/Cas9 mutagenesis to produce acylsugar-deficient plants for investigation of insect resistance and foliar water loss. Whereas asat1 mutations reduced accumulation, asat2 mutations caused almost complete depletion of foliar acylsucroses. Three hemipteran and three lepidopteran herbivores survived, gained weight, and/or reproduced significantly better on asat2 mutants than on wildtype N. benthamiana. Both asat1 and asat2 mutations reduced the water content and increased leaf temperature. Our results demonstrate the specific function of two ASAT proteins in N. benthamiana acylsugar biosynthesis, insect resistance, and desiccation tolerance. The improved growth of aphids and whiteflies on asat2 mutants will facilitate the use of N. benthamiana as a transient expression platform for the functional analysis of insect effectors and resistance genes from other plant species. Similarly, the absence of acylsugars in asat2 mutants will enable analysis of acylsugar biosynthesis genes from other Solanaceae by transient expression.
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Affiliation(s)
- Honglin Feng
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Lucia Acosta-Gamboa
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Lars H Kruse
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Jake D Tracy
- Plant-Microbe Biology and Plant Pathology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA
| | | | - Alba Ruth Nava Fereira
- Department of Biology, University of Texas San Antonio, San Antonio, TX, 78249, USA
- Department of Biological Sciences, Northern Illinois University, Dekalb, IL, 60115, USA
| | - Sara Shakir
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
- Gembloux Agro-Bio Tech Institute, The University of Liege, Gembloux, Belgium
| | - Hongxing Xu
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
- College of Life Science, The Shaanxi Normal University, Xi'an, China
| | - Garry Sunter
- Department of Biology, University of Texas San Antonio, San Antonio, TX, 78249, USA
- Department of Biological Sciences, Northern Illinois University, Dekalb, IL, 60115, USA
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Clare L Casteel
- Plant-Microbe Biology and Plant Pathology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Gaurav D Moghe
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Georg Jander
- Boyce Thompson Institute, Ithaca, NY, 14853, USA.
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46
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Uetz P, Melnik S, Grünwald-Gruber C, Strasser R, Stoger E. CRISPR/Cas9-mediated knockout of a prolyl-4-hydroxylase subfamily in Nicotiana benthamiana using DsRed2 for plant selection. Biotechnol J 2022; 17:e2100698. [PMID: 35427441 DOI: 10.1002/biot.202100698] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 04/01/2022] [Accepted: 04/11/2022] [Indexed: 11/08/2022]
Abstract
The properties of host plants used for molecular farming can be modified by CRISPR/Cas9 genome editing to improve the quality and yield of recombinant proteins. However, it is often necessary to target multiple genes simultaneously, particularly when using host plants with large and complex genomes. This is the case for Nicotiana benthamiana, an allotetraploid relative of tobacco frequently used for transient protein expression. A multiplex genome editing system incorporating the DsRed2 fluorescent marker for the identification and selection of transgenic plants was established. As proof of principle, NbP4H4 was targeted encoding a prolyl-4-hydroxylase involved in protein O-linked glycosylation. Using preselected gRNAs with efficiencies confirmed by transient expression, transgenic plant lines with knockout mutations in all four NbP4H4 genes were obtained. Leaf fluorescence was then used to screen for the absence of the SpCas9 transgene in T1 plants, and transgene-free lines with homozygous or biallelic mutations were identified. The analysis of plant-produced recombinant IgA1 as a reporter protein revealed changes in the number of peptides containing hydroxyproline residues and pentoses in the knockout plants. The selection of efficient gRNAs combined with the DsRed2 marker reduces the effort needed to generate N. benthamiana mutants and simplifies the screening processes to obtain transgene-free progeny.
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Affiliation(s)
- Pia Uetz
- Institute of Plant Biotechnology and Cell Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Stanislav Melnik
- Institute of Plant Biotechnology and Cell Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Clemens Grünwald-Gruber
- Core Facility Mass Spectrometry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Richard Strasser
- Institute of Plant Biotechnology and Cell Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Eva Stoger
- Institute of Plant Biotechnology and Cell Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
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47
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Cauz‐Santos LA, Dodsworth S, Samuel R, Christenhusz MJM, Patel D, Shittu T, Jakob A, Paun O, Chase MW. Genomic insights into recent species divergence in Nicotiana benthamiana and natural variation in Rdr1 gene controlling viral susceptibility. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:7-18. [PMID: 35535507 PMCID: PMC9543217 DOI: 10.1111/tpj.15801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/05/2022] [Accepted: 05/07/2022] [Indexed: 05/31/2023]
Abstract
One of the most commonly encountered and frequently cited laboratory organisms worldwide is classified taxonomically as Nicotiana benthamiana (Solanaceae), an accession of which, typically referred to as LAB, is renowned for its unique susceptibility to a wide range of plant viruses and hence capacity to be transformed using a variety of methods. This susceptibility is the result of an insertion and consequent loss of function in the RNA-dependent RNA polymerase 1 (Rdr1) gene. However, the origin and age of LAB and the evolution of N. benthamiana across its wide distribution in Australia remain relatively underexplored. Here, we have used multispecies coalescent methods on genome-wide single nucleotide polymorphisms (SNPs) to assess species limits, phylogenetic relationships and divergence times within N. benthamiana. Our results show that the previous taxonomic concept of this species in fact comprises five geographically, morphologically and genetically distinct species, one of which includes LAB. We provide clear evidence that LAB is closely related to accessions collected further north in the Northern Territory; this species split much earlier, c. 1.1 million years ago, from their common ancestor than the other four in this clade and is morphologically the most distinctive. We also found that the Rdr1 gene insertion is variable among accessions from the northern portions of the Northern Territory. Furthermore, this long-isolated species typically grows in sheltered sites in subtropical/tropical monsoon areas of northern Australia, contradicting the previously advanced hypothesis that this species is an extremophile that has traded viral resistance for precocious development.
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Affiliation(s)
- Luiz A. Cauz‐Santos
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14A‐1030ViennaAustria
| | - Steven Dodsworth
- School of Biological SciencesUniversity of PortsmouthKing Henry Building, King Henry 1 StreetPortsmouthPO1 2DYUK
- School of Life SciencesUniversity of Bedfordshire, University SquareLutonBedfordshireLU1 3JUUK
| | - Rosabelle Samuel
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14A‐1030ViennaAustria
| | | | - Denise Patel
- School of Life SciencesUniversity of Bedfordshire, University SquareLutonBedfordshireLU1 3JUUK
| | - Taiwo Shittu
- School of Life SciencesUniversity of Bedfordshire, University SquareLutonBedfordshireLU1 3JUUK
| | - Aljaž Jakob
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14A‐1030ViennaAustria
| | - Ovidiu Paun
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14A‐1030ViennaAustria
| | - Mark W. Chase
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14A‐1030ViennaAustria
- Royal Botanic GardensKewRichmondTW9 3DSUK
- Department of Environment and AgricultureCurtin UniversityPerthWestern AustraliaAustralia
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48
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Yokoyama R, de Oliveira MVV, Takeda-Kimura Y, Ishihara H, Alseekh S, Arrivault S, Kukshal V, Jez JM, Stitt M, Fernie AR, Maeda HA. Point mutations that boost aromatic amino acid production and CO 2 assimilation in plants. SCIENCE ADVANCES 2022; 8:eabo3416. [PMID: 35675400 PMCID: PMC9176744 DOI: 10.1126/sciadv.abo3416] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/19/2022] [Indexed: 06/15/2023]
Abstract
Aromatic compounds having unusual stability provide high-value chemicals and considerable promise for carbon storage. Terrestrial plants can convert atmospheric CO2 into diverse and abundant aromatic compounds. However, it is unclear how plants control the shikimate pathway that connects the photosynthetic carbon fixation with the biosynthesis of aromatic amino acids, the major precursors of plant aromatic natural products. This study identified suppressor of tyra2 (sota) mutations that deregulate the first step in the plant shikimate pathway by alleviating multiple effector-mediated feedback regulation in Arabidopsis thaliana. The sota mutant plants showed hyperaccumulation of aromatic amino acids accompanied by up to a 30% increase in net CO2 assimilation. The identified mutations can be used to enhance plant-based, sustainable conversion of atmospheric CO2 to high-energy and high-value aromatic compounds.
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Affiliation(s)
- Ryo Yokoyama
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Hirofumi Ishihara
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Stéphanie Arrivault
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Vandna Kukshal
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Joseph M. Jez
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Mark Stitt
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Hiroshi A. Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
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49
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Baldrich P, Bélanger S, Kong S, Pokhrel S, Tamim S, Teng C, Schiebout C, Gurazada SGR, Gupta P, Patel P, Razifard H, Nakano M, Dusia A, Meyers BC, Frank MH. The evolutionary history of small RNAs in Solanaceae. PLANT PHYSIOLOGY 2022; 189:644-665. [PMID: 35642548 PMCID: PMC9157080 DOI: 10.1093/plphys/kiac089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/07/2022] [Indexed: 06/01/2023]
Abstract
The Solanaceae or "nightshade" family is an economically important group with remarkable diversity. To gain a better understanding of how the unique biology of the Solanaceae relates to the family's small RNA (sRNA) genomic landscape, we downloaded over 255 publicly available sRNA data sets that comprise over 2.6 billion reads of sequence data. We applied a suite of computational tools to predict and annotate two major sRNA classes: (1) microRNAs (miRNAs), typically 20- to 22-nucleotide (nt) RNAs generated from a hairpin precursor and functioning in gene silencing and (2) short interfering RNAs (siRNAs), including 24-nt heterochromatic siRNAs typically functioning to repress repetitive regions of the genome via RNA-directed DNA methylation, as well as secondary phased siRNAs and trans-acting siRNAs generated via miRNA-directed cleavage of a polymerase II-derived RNA precursor. Our analyses described thousands of sRNA loci, including poorly understood clusters of 22-nt siRNAs that accumulate during viral infection. The birth, death, expansion, and contraction of these sRNA loci are dynamic evolutionary processes that characterize the Solanaceae family. These analyses indicate that individuals within the same genus share similar sRNA landscapes, whereas comparisons between distinct genera within the Solanaceae reveal relatively few commonalities.
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Affiliation(s)
- Patricia Baldrich
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | | | - Shuyao Kong
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Suresh Pokhrel
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
- Division of Plant Science and Technology, University of Missouri, Columbia, Missouri 65211, USA
| | - Saleh Tamim
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19711, USA
| | - Chong Teng
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | | | - Sai Guna Ranjan Gurazada
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19711, USA
- Corteva Agriscience, Wilmington, Delaware 19805, USA
| | - Pallavi Gupta
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- Institute for Data Science & Informatics, University of Missouri, Columbia, Missouri 65211, USA
| | - Parth Patel
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19711, USA
| | - Hamid Razifard
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Mayumi Nakano
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Ayush Dusia
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19711, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- Division of Plant Science and Technology, University of Missouri, Columbia, Missouri 65211, USA
| | - Margaret H Frank
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
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50
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Park IW, Hwang IS, Oh EJ, Kwon CT, Oh CS. Nicotiana benthamiana, a Surrogate Host to Study Novel Virulence Mechanisms of Gram-Positive Bacteria, Clavibacter michiganensis, and C. capsici in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:876971. [PMID: 35620684 PMCID: PMC9127732 DOI: 10.3389/fpls.2022.876971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/25/2022] [Indexed: 06/11/2023]
Abstract
Clavibacter michiganensis is a Gram-positive bacterium that causes bacterial canker and wilting in host plants like tomato. Two major virulence genes encoding a cellulase (celA) and a putative serine protease (pat-1) have been reported. Here we show that Nicotiana benthamiana, a commonly used model plant for studying molecular plant-pathogen interactions, is a surrogate host of C. michiganensis and C. capsici. When a low concentration of two Clavibacter species, C. michiganensis and C. capsici, were infiltrated into N. benthamiana leaves, they caused blister-like lesions closely associated with cell death and the generation of reactive oxygen species and proliferated significantly like a pathogenic bacterium. By contrast, they did not cause any disease symptoms in N. tabacum leaves. The celA and pat-1 mutants of C. michiganensis still caused blister-like lesions and cankers like the wild-type strain. When a high concentration of two Clavibacter species and two mutant strains were infiltrated into N. benthamiana leaves, all of them caused strong and rapid necrosis. However, only C. michiganensis strains, including the celA and pat-1 mutants, caused wilting symptoms when it was injected into stems. When two Clavibacter species and two mutants were infiltrated into N. tabacum leaves at the high concentration, they (except for the pat-1 mutant) caused a strong hypersensitive response. These results indicate that C. michiganensis causes blister-like lesions, canker, and wilting in N. benthamiana, and celA and pat-1 genes are not necessary for the development of these symptoms. Overall, N. benthamiana is a surrogate host of Clavibacter species, and their novel virulence factors are responsible for disease development in this plant.
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Affiliation(s)
- In Woong Park
- Department of Horticultural Biotechnology, Kyung Hee University, Yongin, South Korea
| | - In Sun Hwang
- Department of Horticultural Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Eom-Ji Oh
- Department of Horticultural Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Choon-Tak Kwon
- Department of Horticultural Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Chang-Sik Oh
- Department of Horticultural Biotechnology, Kyung Hee University, Yongin, South Korea
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin, South Korea
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