1
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Lacrampe N, Lugan R, Dumont D, Nicot PC, Lecompte F, Colombié S. Modelling metabolic fluxes of tomato stems reveals that nitrogen shapes central metabolism for defence against Botrytis cinerea. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4093-4110. [PMID: 38551810 DOI: 10.1093/jxb/erae140] [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: 09/12/2023] [Accepted: 03/28/2024] [Indexed: 07/11/2024]
Abstract
Among plant pathogens, the necrotrophic fungus Botrytis cinerea is one of the most prevalent, leading to severe crop damage. Studies related to its colonization of different plant species have reported variable host metabolic responses to infection. In tomato, high N availability leads to decreased susceptibility. Metabolic flux analysis can be used as an integrated method to better understand which metabolic adaptations lead to effective host defence and resistance. Here, we investigated the metabolic response of tomato infected by B. cinerea in symptomless stem tissues proximal to the lesions for 7 d post-inoculation, using a reconstructed metabolic model constrained by a large and consistent metabolic dataset acquired under four different N supplies. An overall comparison of 48 flux solution vectors of Botrytis- and mock-inoculated plants showed that fluxes were higher in Botrytis-inoculated plants, and the difference increased with a reduction in available N, accompanying an unexpected increase in radial growth. Despite higher fluxes, such as those involved in cell wall synthesis and other pathways, fluxes related to glycolysis, the tricarboxylic acid cycle, and amino acid and protein synthesis were limited under very low N, which might explain the enhanced susceptibility. Limiting starch synthesis and enhancing fluxes towards redox and specialized metabolism also contributed to defence independent of N supply.
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Affiliation(s)
- Nathalie Lacrampe
- PSH unit, INRAE, F-84914 Avignon, France
- UMR Qualisud, Avignon Université, F-84916 Avignon, France
| | | | | | | | | | - Sophie Colombié
- UMR 1332 BFP, INRAE, Univ Bordeaux, F-33883 Villenave d'Ornon, France
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2
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Wu X, Wang L, Xing Q, Zhao Y, Qi H. CmPIF8-CmERF27-CmACS10-mediated ethylene biosynthesis modulates red light-induced powdery mildew resistance in oriental melon. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38923433 DOI: 10.1111/pce.15015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 05/31/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024]
Abstract
Powdery mildew is a serious fungal disease in protected melon cultivation that affects the growth, development and production of melon plants. Previous studies have shown that red light can improve oriental melon seedlings resistance to powdery mildew. Here, after inoculation with Podosphaera xanthii, an obligate fungal pathogen eliciting powdery mildew, we found that red light pretreatment increased ethylene production and this improved the resistance of melon seedlings to powdery mildew, and the ethylene biosynthesis gene CmACS10 played an important role in this process. By analysing the CmACS10 promoter, screening yeast one-hybrid library, it was found that CmERF27 positively regulated the expression of CmACS10, increased powdery mildew resistance and interacted with PHYTOCHROME INTERACTING FACTOR8 (CmPIF8) at the protein level to participate in the regulation of ethylene biosynthesis to respond to the red light-induced resistance to P. xanthii, Furthermore, CmPIF8 also directly targeted the promoter of CmACS10, negatively participated in this process. In summary, this study revealed the specific mechanism by which the CmPIF8-CmERF27-CmACS10 module regulates red light-induced ethylene biosynthesis to resist P. xanthii infection, elucidate the interaction between light and plant hormones under biological stress, provide a reference and genetic resources for breeding of disease-resistant melon plants.
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Affiliation(s)
- Xutong Wu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Education of Ministry and Liaoning Province/National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang, China
| | - Lixia Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Education of Ministry and Liaoning Province/National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang, China
| | - Qiaojuan Xing
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Yaping Zhao
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Education of Ministry and Liaoning Province/National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang, China
| | - Hongyan Qi
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Education of Ministry and Liaoning Province/National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang, China
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3
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Padilla-Padilla EA, De la Rosa C, Aragón W, Ávila-Sandoval AK, Torres M, Dorantes-Acosta AE, Arteaga-Vázquez MA, Formey D, Serrano M. Identification of Arabidopsis thaliana small RNAs responsive to the fungal pathogen Botrytis cinerea at an early stage of interaction. PLoS One 2024; 19:e0304790. [PMID: 38875250 PMCID: PMC11178217 DOI: 10.1371/journal.pone.0304790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 05/19/2024] [Indexed: 06/16/2024] Open
Abstract
In plants, small RNAs (sRNAs), mainly microRNAs (miRNAs) and small interfering RNAs (siRNAs), have been described as key regulators of plant development, growth, and abiotic and biotic responses. Despite reports indicating the involvement of certain sRNAs in regulating the interaction between Botrytis cinerea (a major necrotrophic fungal phytopathogen) and host plants, there remains a lack of analysis regarding the potential regulatory roles of plant sRNAs during early stages of the interaction despite early immune responses observed then during infection. We present the first transcriptome-wide analysis of small RNA expression on the early interaction between the necrotrophic fungus Botrytis cinerea and the model plant Arabidopsis thaliana. We found that evolutionary conserved A. thaliana miRNAs were the sRNAs that accumulated the most in the presence of B. cinerea. The upregulation of miR167, miR159 and miR319 was of particular interest because these, together with their target transcripts, are involved in the fine regulation of the plant hormone signaling pathways. We also describe that miR173, which triggers the production of secondary siRNAs from TAS1 and TAS2 loci, as well as secondary siRNAs derived from these loci, is upregulated in response to B. cinerea. Thus, at an early stage of the interaction there are transcriptional changes of sRNA-guided silencing pathway genes and of a subset of sRNAs that targeted genes from the PPR gene superfamily, and these may be important mechanisms regulating the interaction between A. thaliana and B. cinerea. This work provides the basis for a better understanding of the regulation mediated by sRNAs during early B. cinerea-plant interaction and may help in the development of more effective strategies for its control.
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Affiliation(s)
- Emir Alejandro Padilla-Padilla
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- Posgrado en Ciencias Biológicas, Unidad de Posgrado, Ciudad Universitaria, Coyoacán, Ciudad de México
| | - Carlos De la Rosa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Wendy Aragón
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- Instituto de Biociencias, Universidad Autónoma de Chiapas, Chiapas, México
| | - Ana Karen Ávila-Sandoval
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Martha Torres
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Ana Elena Dorantes-Acosta
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Xalapa, Veracruz, México
| | - Mario A Arteaga-Vázquez
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Xalapa, Veracruz, México
| | - Damien Formey
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Mario Serrano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
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Lee IH, Choi BY, Kim DS, Han H, Kim YH, Shim D. Temporal Transcriptome Profiling of Pinus densiflora Infected with Pine Wood Nematode Reveals Genetically Programmed Changes upon Pine Wilt Disease. PHYTOPATHOLOGY 2024; 114:982-989. [PMID: 38451552 DOI: 10.1094/phyto-10-23-0397-kc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Pine, an evergreen conifer, is widely distributed worldwide. It is economically, scientifically, and ecologically important. However, pine wilt disease (PWD) induced by the pine wood nematode (PWN) adversely affects pine trees. Many studies have been conducted on the PWN and its beetle vectors to prevent the spread of PWD. However, studies providing a comprehensive understanding of the pine tree transcriptome in response to PWN infection are lacking. Here, we performed temporal profiling of the pine tree transcriptome using PWD-infected red pine trees, Pinus densiflora, inoculated with the PWN by RNA sequencing. Our analysis revealed that defense-responsive genes involved in cell wall modification, jasmonic acid signaling, and phenylpropanoid-related processes were significantly enriched 2 weeks after PWD infection. Furthermore, some WRKY-type and MYB-type transcription factors were upregulated 2 weeks after PWD infection, suggesting that these transcription factors might be responsible for the genome-wide reprogramming of defense-responsive genes in the early PWD stage. Our comprehensive transcriptome analysis will assist in developing PWD-resistant pine trees and identifying genes to diagnose PWD at the early stage of infection, during which large-scale phenotypic changes are absent in PWD-infected pine trees.
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Affiliation(s)
- Il Hwan Lee
- Department of Forest Bio-Resources, National Institute of Forest Science, Suwon 16631, Republic of Korea
| | - Bae Young Choi
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Dong Soo Kim
- Forest Biomaterials Research Center, National Institute of Forest Science, Jinju 52817, Republic of Korea
| | - Hyelim Han
- Division of Forest Insect Pests and Diseases, National Institute of Forest Science, Seoul 02455, Republic of Korea
| | - Yun-Hee Kim
- Department of Biology Education, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Donghwan Shim
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
- Center for Genome Engineering, Institute for Basic Sciences, Daejeon 34126, Republic of Korea
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5
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Evans KV, Ransom E, Nayakoti S, Wilding B, Mohd Salleh F, Gržina I, Erber L, Tse C, Hill C, Polanski K, Holland A, Bukhat S, Herbert RJ, de Graaf BHJ, Denby K, Buchanan-Wollaston V, Rogers HJ. Expression of the Arabidopsis redox-related LEA protein, SAG21 is regulated by ERF, NAC and WRKY transcription factors. Sci Rep 2024; 14:7756. [PMID: 38565965 PMCID: PMC10987515 DOI: 10.1038/s41598-024-58161-0] [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: 07/31/2023] [Accepted: 03/26/2024] [Indexed: 04/04/2024] Open
Abstract
SAG21/LEA5 is an unusual late embryogenesis abundant protein in Arabidopsis thaliana, that is primarily mitochondrially located and may be important in regulating translation in both chloroplasts and mitochondria. SAG21 expression is regulated by a plethora of abiotic and biotic stresses and plant growth regulators indicating a complex regulatory network. To identify key transcription factors regulating SAG21 expression, yeast-1-hybrid screens were used to identify transcription factors that bind the 1685 bp upstream of the SAG21 translational start site. Thirty-three transcription factors from nine different families bound to the SAG21 promoter, including members of the ERF, WRKY and NAC families. Key binding sites for both NAC and WRKY transcription factors were tested through site directed mutagenesis indicating the presence of cryptic binding sites for both these transcription factor families. Co-expression in protoplasts confirmed the activation of SAG21 by WRKY63/ABO3, and SAG21 upregulation elicited by oligogalacturonide elicitors was partially dependent on WRKY63, indicating its role in SAG21 pathogen responses. SAG21 upregulation by ethylene was abolished in the erf1 mutant, while wound-induced SAG21 expression was abolished in anac71 mutants, indicating SAG21 expression can be regulated by several distinct transcription factors depending on the stress condition.
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Affiliation(s)
- Kelly V Evans
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
| | - Elspeth Ransom
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
| | - Swapna Nayakoti
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
| | - Ben Wilding
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
| | - Faezah Mohd Salleh
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
- Investigative and Forensic Sciences Research Group, Universiti Teknologi Malaysia, 81310, Johor Bahru, Johor, Malaysia
| | - Irena Gržina
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
| | - Lieselotte Erber
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
| | - Carmen Tse
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
| | - Claire Hill
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | | | - Alistair Holland
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
| | - Sherien Bukhat
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
| | - Robert J Herbert
- School of Science and the Environment, University of Worcester, Henwick Grove, Worcester, WR2 6AJ, UK
| | - Barend H J de Graaf
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
| | - Katherine Denby
- Department of Biology, Centre for Novel Agricultural Products (CNAP), University of York, Heslington, York, YO10 5DD, UK
| | | | - Hilary J Rogers
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK.
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6
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Robuschi L, Mariani O, Perk EA, Cerrudo I, Villarreal F, Laxalt AM. Arabidopsis thaliana phosphoinositide-specific phospholipase C 2 is required for Botrytis cinerea proliferation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 340:111971. [PMID: 38160760 DOI: 10.1016/j.plantsci.2023.111971] [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: 06/29/2023] [Revised: 11/24/2023] [Accepted: 12/28/2023] [Indexed: 01/03/2024]
Abstract
Phospholipase C (PLC) plays a key role in lipid signaling during plant development and stress responses. PLC activation is one of the earliest responses during pathogen perception. Arabidopsis thaliana contains seven PLC encoding genes (AtPLC1 to AtPLC7) and two pseudogenes (AtPLC8 and AtPLC9), being AtPLC2 the most abundant isoform with constitutive expression in all plant organs. PLC has been linked to plant defense signaling, in particular to the production of reactive oxygen species (ROS). Previously, we demonstrated that AtPLC2 is involved in ROS production via the NADPH oxidase isoforms RBOHD activation during stomata plant immunity. Here we studied the role of AtPLC2 on plant resistance against the necrotrophic fungus Botrytis cinerea, a broad host-range and serious agricultural pathogen. We show that the AtPLC2-silenced (amiR PLC2) or null mutant (plc2-1) plants developed smaller B. cinerea lesions. Moreover, plc2-1 showed less ROS production and an intensified SA-dependent signaling upon infection, indicating that B. cinerea uses AtPLC2-triggered responses for a successful proliferation. Therefore, AtPLC2 is a susceptibility (S) gene that facilitates B. cinerea infection and proliferation.
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Affiliation(s)
- Luciana Robuschi
- Instituto de Investigaciones Biológicas, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Mar del Plata, 7600 Mar del Plata, Argentina
| | - Oriana Mariani
- Plant Nutrition Laboratory, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Strasse, 06120 Halle (Saale), Germany
| | - Enzo A Perk
- Instituto de Investigaciones Biológicas, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Mar del Plata, 7600 Mar del Plata, Argentina
| | - Ignacio Cerrudo
- Instituto de Investigaciones Biológicas, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Mar del Plata, 7600 Mar del Plata, Argentina
| | - Fernando Villarreal
- Instituto de Investigaciones Biológicas, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Mar del Plata, 7600 Mar del Plata, Argentina
| | - Ana M Laxalt
- Instituto de Investigaciones Biológicas, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Mar del Plata, 7600 Mar del Plata, Argentina.
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7
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Deokar AA, Sagi M, Tar’an B. Genetic Analysis of Partially Resistant and Susceptible Chickpea Cultivars in Response to Ascochyta rabiei Infection. Int J Mol Sci 2024; 25:1360. [PMID: 38279360 PMCID: PMC10816841 DOI: 10.3390/ijms25021360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/06/2024] [Accepted: 01/19/2024] [Indexed: 01/28/2024] Open
Abstract
The molecular mechanism involved in chickpea (Cicer arietinum L.) resistance to the necrotrophic fungal pathogen Ascochyta rabiei is not well documented. A. rabiei infection can cause severe damage in chickpea, resulting in significant economic losses. Understanding the resistance mechanism against ascochyta blight can help to define strategies to develop resistant cultivars. In this study, differentially expressed genes from two partially resistant cultivars (CDC Corinne and CDC Luna) and a susceptible cultivar (ICCV 96029) to ascochyta blight were identified in the early stages (24, 48 and 72 h) of A. rabiei infection using RNA-seq. Altogether, 3073 genes were differentially expressed in response to A. rabiei infection across different time points and cultivars. A larger number of differentially expressed genes (DEGs) were found in CDC Corinne and CDC Luna than in ICCV 96029. Various transcription factors including ERF, WRKY, bHLH and MYB were differentially expressed in response to A. rabiei infection. Genes involved in pathogen detection and immune signalings such as receptor-like kinases (RLKs), Leucine-Rich Repeat (LRR)-RLKs, and genes associated with the post-infection defence response were differentially expressed among the cultivars. GO functional enrichment and pathway analysis of the DEGs suggested that the biological processes such as metabolic process, response to stimulus and catalytic activity were overrepresented in both resistant and susceptible chickpea cultivars. The expression patterns of eight randomly selected genes revealed by RNA-seq were confirmed by quantitative PCR (qPCR) analysis. The results provide insights into the complex molecular mechanism of the chickpea defence in response to the A. rabiei infection.
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Affiliation(s)
| | | | - Bunyamin Tar’an
- Crop Development Centre, Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
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8
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Ma LJ, Liu X, Guo L, Luo Y, Zhang B, Cui X, Yang K, Cai J, Liu F, Ma N, Yang FQ, He X, Shi SP, Wan JB. Discovery of plant chemical defence mediated by a two-component system involving β-glucosidase in Panax species. Nat Commun 2024; 15:602. [PMID: 38238334 PMCID: PMC10796634 DOI: 10.1038/s41467-024-44854-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 01/07/2024] [Indexed: 01/22/2024] Open
Abstract
Plants usually produce defence metabolites in non-active forms to minimize the risk of harm to themselves and spatiotemporally activate these defence metabolites upon pathogen attack. This so-called two-component system plays a decisive role in the chemical defence of various plants. Here, we discovered that Panax notoginseng, a valuable medicinal plant, has evolved a two-component chemical defence system composed of a chloroplast-localized β-glucosidase, denominated PnGH1, and its substrates 20(S)-protopanaxadiol ginsenosides. The β-glucosidase and its substrates are spatially separated in cells under physiological conditions, and ginsenoside hydrolysis is therefore activated only upon chloroplast disruption, which is caused by the induced exoenzymes of pathogenic fungi upon exposure to plant leaves. This activation of PnGH1-mediated hydrolysis results in the production of a series of less-polar ginsenosides by selective hydrolysis of an outer glucose at the C-3 site, with a broader spectrum and more potent antifungal activity in vitro and in vivo than the precursor molecules. Furthermore, such β-glucosidase-mediated hydrolysis upon fungal infection was also found in the congeneric species P. quinquefolium and P. ginseng. Our findings reveal a two-component chemical defence system in Panax species and offer insights for developing botanical pesticides for disease management in Panax species.
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Affiliation(s)
- Li-Juan Ma
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Xiao Liu
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Liwei Guo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yuan Luo
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Beibei Zhang
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, China
| | - Xiaoxue Cui
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Kuan Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Jing Cai
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Fang Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Ni Ma
- Department of Product Development, Wenshan Sanqi Institute of Science and Technology, Wenshan University, Wenshan, Yunnan, China
| | - Feng-Qing Yang
- Department of Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Chongqing University, 401331, Chongqing, China
| | - Xiahong He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China.
- Ministry of Education Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Southwest Forestry University, 650224, Kunming, Yunnan, China.
| | - She-Po Shi
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China.
| | - Jian-Bo Wan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China.
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9
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García-Soto I, Formey D, Mora-Toledo A, Cárdenas L, Aragón W, Tromas A, Duque-Ortiz A, Jiménez-Bremont JF, Serrano M. AtRAC7/ROP9 Small GTPase Regulates A. thaliana Immune Systems in Response to B. cinerea Infection. Int J Mol Sci 2024; 25:591. [PMID: 38203762 PMCID: PMC10779071 DOI: 10.3390/ijms25010591] [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: 10/19/2023] [Revised: 11/17/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Botrytis cinerea is a necrotrophic fungus that can cause gray mold in over 1400 plant species. Once it is detected by Arabidopsis thaliana, several defense responses are activated against this fungus. The proper activation of these defenses determines plant susceptibility or resistance. It has been proposed that the RAC/ROP small GTPases might serve as a molecular link in this process. In this study, we investigate the potential role of the Arabidopsis RAC7 gene during infection with B. cinerea. For that, we evaluated A. thaliana RAC7-OX lines, characterized by the overexpression of the RAC7 gene. Our results reveal that these RAC7-OX lines displayed increased susceptibility to B. cinerea infection, with enhanced fungal colonization and earlier lesion development. Additionally, they exhibited heightened sensitivity to bacterial infections caused by Pseudomonas syringae and Pectobacterium brasiliense. By characterizing plant canonical defense mechanisms and performing transcriptomic profiling, we determined that RAC7-OX lines impaired the plant transcriptomic response before and during B. cinerea infection. Global pathway analysis of differentially expressed genes suggested that RAC7 influences pathogen perception, cell wall homeostasis, signal transduction, and biosynthesis and response to hormones and antimicrobial compounds through actin filament modulation. Herein, we pointed out, for first time, the negative role of RAC7 small GTPase during A. thaliana-B. cinerea interaction.
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Affiliation(s)
- Ivette García-Soto
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico; (D.F.); (A.M.-T.)
- Programa de Doctorado en Ciencias Bioquímicas, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico
| | - Damien Formey
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico; (D.F.); (A.M.-T.)
| | - Angélica Mora-Toledo
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico; (D.F.); (A.M.-T.)
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Coyoacan 04510, Ciudad de México, Mexico
| | - Luis Cárdenas
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico;
| | - Wendy Aragón
- Instituto de Biociencias, Universidad Autónoma de Chiapas, Blvd. Príncipe Akishino s/n, Tapachula 30798, Chiapas, Mexico;
| | - Alexandre Tromas
- La Cité College, Bureau de la Recherche et de l’Innovation, Ottawa, ON K1K 4R3, Canada;
| | - Arianna Duque-Ortiz
- Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), San Luis Potosí 78216, San Luis Potosí, Mexico; (A.D.-O.); (J.F.J.-B.)
| | - Juan Francisco Jiménez-Bremont
- Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), San Luis Potosí 78216, San Luis Potosí, Mexico; (A.D.-O.); (J.F.J.-B.)
| | - Mario Serrano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico; (D.F.); (A.M.-T.)
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10
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Felemban A, Moreno JC, Mi J, Ali S, Sham A, AbuQamar SF, Al-Babili S. The apocarotenoid β-ionone regulates the transcriptome of Arabidopsis thaliana and increases its resistance against Botrytis cinerea. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:541-560. [PMID: 37932864 DOI: 10.1111/tpj.16510] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 11/08/2023]
Abstract
Carotenoids are isoprenoid pigments indispensable for photosynthesis. Moreover, they are the precursor of apocarotenoids, which include the phytohormones abscisic acid (ABA) and strigolactones (SLs) as well as retrograde signaling molecules and growth regulators, such as β-cyclocitral and zaxinone. Here, we show that the application of the volatile apocarotenoid β-ionone (β-I) to Arabidopsis plants at micromolar concentrations caused a global reprogramming of gene expression, affecting thousands of transcripts involved in stress tolerance, growth, hormone metabolism, pathogen defense, and photosynthesis. This transcriptional reprogramming changes, along with induced changes in the level of the phytohormones ABA, jasmonic acid, and salicylic acid, led to enhanced Arabidopsis resistance to the widespread necrotrophic fungus Botrytis cinerea (B.c.) that causes the gray mold disease in many crop species and spoilage of harvested fruits. Pre-treatment of tobacco and tomato plants with β-I followed by inoculation with B.c. confirmed the effect of β-I in increasing the resistance to this pathogen in crop plants. Moreover, we observed reduced susceptibility to B.c. in fruits of transgenic tomato plants overexpressing LYCOPENE β-CYCLASE, which contains elevated levels of endogenous β-I, providing a further evidence for its effect on B.c. infestation. Our work unraveled β-I as a further carotenoid-derived regulatory metabolite and indicates the possibility of establishing this natural volatile as an environmentally friendly bio-fungicide to control B.c.
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Affiliation(s)
- Abrar Felemban
- The Bioactives Laboratory, Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Plant Science Program, Biological and Environmental Science and Engineering Division, 4700 King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Juan C Moreno
- The Bioactives Laboratory, Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Plant Science Program, Biological and Environmental Science and Engineering Division, 4700 King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Jianing Mi
- The Bioactives Laboratory, Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Plant Science Program, Biological and Environmental Science and Engineering Division, 4700 King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Shawkat Ali
- Kentville Research and Development Center, Agriculture and Agri-Food Canada, Kentville, Nova Scotia, B4N 1J5, Canada
| | - Arjun Sham
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Synan F AbuQamar
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Salim Al-Babili
- The Bioactives Laboratory, Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Plant Science Program, Biological and Environmental Science and Engineering Division, 4700 King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
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11
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Kawade K, Tabeta H, Ferjani A, Hirai MY. The Roles of Functional Amino Acids in Plant Growth and Development. PLANT & CELL PHYSIOLOGY 2023; 64:1482-1493. [PMID: 37489637 DOI: 10.1093/pcp/pcad071] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 06/04/2023] [Accepted: 07/03/2023] [Indexed: 07/26/2023]
Abstract
Plants incorporate acquired carbon and nitrogen into amino acid metabolism, whereby the building blocks of proteins and the precursors of various metabolites are produced. This fundamental demand requires tight amino acid metabolism to sustain physiological homeostasis. There is increasing evidence that amino acid metabolism undergoes plastic alteration to orchestrate specific growth and developmental events. Consequently, there has been a gradual exploration of the interface at which amino acid metabolism and plant morphogenesis are mutually affected. This research progress offers an opportunity to explore amino acid metabolism, with the goal to understand how it can be modulated to serve special cellular needs and regulate specific growth and developmental pathways. Continuous improvements in the sensitivity and coverage of metabolomics technology, along with the development of chemoinformatics, have allowed the investigation of these research questions. In this review, we summarize the roles of threonine, serine, arginine and γ-aminobutyric acid as representative examples of amino acids relevant to specific developmental processes in plants ('functional amino acids'). Our objective is to expand perspectives regarding amino acid metabolism beyond the conventional view that it is merely life-supporting machinery.
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Affiliation(s)
- Kensuke Kawade
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama, 338-8570 Japan
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045 Japan
| | | | - Ali Ferjani
- Department of Biology, Tokyo Gakugei University, 4-1-1 Nukuikita-machi, Koganei, Tokyo, 184-8501 Japan
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045 Japan
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902 Japan
| | - Masami Yokota Hirai
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045 Japan
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
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12
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Soto-Cardinault C, Childs KL, Góngora-Castillo E. Network Analysis of Publicly Available RNA-seq Provides Insights into the Molecular Mechanisms of Plant Defense against Multiple Fungal Pathogens in Arabidopsis thaliana. Genes (Basel) 2023; 14:2223. [PMID: 38137044 PMCID: PMC10743233 DOI: 10.3390/genes14122223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/06/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Fungal pathogens can have devastating effects on global crop production, leading to annual economic losses ranging from 10% to 23%. In light of climate change-related challenges, researchers anticipate an increase in fungal infections as a result of shifting environmental conditions. However, plants have developed intricate molecular mechanisms for effective defense against fungal attacks. Understanding these mechanisms is essential to the development of new strategies for protecting crops from multiple fungi threats. Public omics databases provide valuable resources for research on plant-pathogen interactions; however, integrating data from different studies can be challenging due to experimental variation. In this study, we aimed to identify the core genes that defend against the pathogenic fungi Colletotrichum higginsianum and Botrytis cinerea in Arabidopsis thaliana. Using a custom framework to control batch effects and construct Gene Co-expression Networks in publicly available RNA-seq dataset from infected A. thaliana plants, we successfully identified a gene module that was responsive to both pathogens. We also performed gene annotation to reveal the roles of previously unknown protein-coding genes in plant defenses against fungal infections. This research demonstrates the potential of publicly available RNA-seq data for identifying the core genes involved in defending against multiple fungal pathogens.
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Affiliation(s)
- Cynthia Soto-Cardinault
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida 97205, Mexico;
| | - Kevin L. Childs
- Plant Biology Department, Michigan State University, East Lansing, MI 48824, USA;
| | - Elsa Góngora-Castillo
- CONAHCYT-Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida 97205, Mexico
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13
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Bai Y, Wang H, Zhu K, Cheng ZM. The dynamic arms race during the early invasion of woodland strawberry by Botrytis cinerea revealed by dual dense high-resolution RNA-seq analyses. HORTICULTURE RESEARCH 2023; 10:uhad225. [PMID: 38143486 PMCID: PMC10745266 DOI: 10.1093/hr/uhad225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 10/29/2023] [Indexed: 12/26/2023]
Abstract
Necrotrophic pathogens replicate massively upon colonizing plants, causing large-scale wilting and death of plant tissues. Understanding both mechanisms of pathogen invasion and host response processes prior to symptom appearance and their key regulatory networks is therefore important for defense against pathogen attack. Here, we investigated the mechanisms of interaction between woodland strawberry (Fragaria vesca) leaves and gray mold pathogen (Botrytis cinerea) at 14 infection time points during the first 12 hours of the infection period using a dense, high-resolution time series dual transcriptomic analysis, characterizing the arms race between strawberry F. vesca and B. cinerea before the appearance of localized lesions. Strawberry leaves rapidly initiated strong systemic defenses at the first sign of external stimulation and showed lower levels of transcriptomic change later in the infection process. Unlike the host plants, B. cinerea showed larger-scale transcriptomic changes that persisted throughout the infection process. Weighted gene co-expression network analysis identified highly correlated genes in 32 gene expression modules between B. cinerea and strawberry. Yeast two-hybrid and bimolecular fluorescence complementation assays revealed that the disease response protein FvRLP2 from woodland strawberry interacted with the cell death inducing proteins BcXYG1 and BcPG3 from B. cinerea. Overexpression of FvRLP2 in both strawberry and Arabidopsis inhibited B. cinerea infection, confirming these genes' respective functions. These findings shed light on the arms race process by which B. cinerea invades host plants and strawberry to defend against pathogen infection.
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Affiliation(s)
- Yibo Bai
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture; Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Haibin Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Kaikai Zhu
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Zong-Ming Cheng
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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14
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López-Bucio J, Ortiz-Castro R, Magaña-Dueñas V, García-Cárdenas E, Jiménez-Vázquez KR, Raya-González J, Pelagio-Flores R, Ibarra-Laclette E, Herrera-Estrella L. Pseudomonas aeruginosa LasI-dependent plant growth promotion requires the host nitrate transceptor AtNRT1.1/CHL1 and the nitrate reductases NIA1 and NIA2. PLANTA 2023; 258:80. [PMID: 37715847 DOI: 10.1007/s00425-023-04236-7] [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: 01/18/2023] [Accepted: 09/04/2023] [Indexed: 09/18/2023]
Abstract
MAIN CONCLUSION In P. aeruginosa, mutation of the gene encoding N-acyl-L-homoserine lactone synthase LasI drives defense and plant growth promotion, and this latter trait requires adequate nitrate nutrition. Cross-kingdom communication with bacteria is crucial for plant growth and productivity. Here, we show a strong induction of genes for nitrate uptake and assimilation in Arabidopsis seedlings co-cultivated with P. aeruginosa WT (PAO1) or ΔlasI mutants defective on the synthesis of the quorum-sensing signaling molecule N-(3-oxododecanoyl)-L-homoserine lactone. Along with differential induction of defense-related genes, the change from plant growth repression to growth promotion upon bacterial QS disruption, correlated with upregulation of the dual-affinity nitrate transceptor CHL1/AtNRT1/NPF6.3 and the nitrate reductases NIA1 and NIA2. CHL1-GUS was induced in Arabidopsis primary root tips after transfer onto P. aeruginosa ΔlasI streaks at low and high N availability, whereas this bacterium required high concentrations of nitrogen to potentiate root and shoot biomass production and to improve root branching. Arabidopsis chl1-5 and chl1-12 mutants and double mutants in NIA1 and NIA2 nitrate reductases showed compromised growth under low nitrogen availability and failed to mount an effective growth promotion and root branching response even at high NH4NO3. WT P. aeruginosa PAO1 and P. aeruginosa ΔlasI mutant promoted the accumulation of nitric oxide (NO) in roots of both the WT and nia1nia2 double mutants, whereas NO donors SNP or SNAP did not improve growth or root branching in nia1nia2 double mutants with or without bacterial cocultivation. Thus, inoculation of Arabidopsis roots with P. aeruginosa drives gene expression for improved nitrogen acquisition and this macronutrient is critical for the plant growth-promoting effects upon disruption of the LasI quorum-sensing system.
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Affiliation(s)
- José López-Bucio
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B3, Ciudad Universitaria, 58030, Morelia, Michoacán, Mexico.
| | - Randy Ortiz-Castro
- Red de estudios moleculares avanzados, Instituto de Ecología A. C., Carretera Antigua a Coatepec 351, El Haya, 91070, Xalapa, Veracruz, Mexico
| | - Viridiana Magaña-Dueñas
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B3, Ciudad Universitaria, 58030, Morelia, Michoacán, Mexico
| | - Elizabeth García-Cárdenas
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B3, Ciudad Universitaria, 58030, Morelia, Michoacán, Mexico
| | - Kirán Rubí Jiménez-Vázquez
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B3, Ciudad Universitaria, 58030, Morelia, Michoacán, Mexico
| | - Javier Raya-González
- Facultad de Químico Farmacobiología, Universidad Michoacana de San Nicolás de Hidalgo, Avenida Tzintzunzan 173, Col. Matamoros, 58240, Morelia, Michoacán, Mexico
| | - Ramón Pelagio-Flores
- Facultad de Químico Farmacobiología, Universidad Michoacana de San Nicolás de Hidalgo, Avenida Tzintzunzan 173, Col. Matamoros, 58240, Morelia, Michoacán, Mexico
| | - Enrique Ibarra-Laclette
- Red de estudios moleculares avanzados, Instituto de Ecología A. C., Carretera Antigua a Coatepec 351, El Haya, 91070, Xalapa, Veracruz, Mexico
| | - Luis Herrera-Estrella
- Centro de Investigación y de Estudios Avanzados del IPN, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Campus Irapuato, Km. 9.6 Libramiento Norte Carretera Irapuato-León, 36821, Irapuato, Guanajuato, Mexico
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15
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Kumar A, Sichov N, Bucki P, Miyara SB. SlWRKY16 and SlWRKY31 of tomato, negative regulators of plant defense, involved in susceptibility activation following root-knot nematode Meloidogyne javanica infection. Sci Rep 2023; 13:14592. [PMID: 37669955 PMCID: PMC10480479 DOI: 10.1038/s41598-023-40557-z] [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: 05/22/2023] [Accepted: 08/12/2023] [Indexed: 09/07/2023] Open
Abstract
The involvement of WRKY transcription factors in plant-nematode interactions, and in particular, how these WRKYs participate in regulating the complex morphological and physiological changes occurring after nematode infection, are the topic of active research. We characterized the functional role of the unstudied tomato WRKY genes SlWRKY16 and SlWRKY31 in regulating tomato roots' response to infection by the root-knot nematode Meloidogyne javanica. Using promoter-GUS reporter gene fusions and qRT-PCR, we show that both SlWRKYs are predominantly expressed during the first half of the parasitic life stages, when feeding-site induction and construction occur. Expression of SlWRKY16 increased sharply 15 days after inoculation, whereas SlWRKY31 was already induced earlier, but reached its maximum expression at this time. Both genes were downregulated at the mature female stage. To determine biological function, we produced transgenic lines overexpressing SlWRKY16 and SlWRKY31 in tomato hairy roots. Overexpression of both genes resulted in enhanced M. javanica infection, reflected by increased galling occurrence and reproduction. Expression profiling of marker genes responsive to defense-associated phytohormones indicated reductions in salicylic acid defense-related PR-1 and jasmonic acid defense-related PI in inoculated roots overexpressing SlWRK16 and SlWRKY31, respectively. Our results suggest that SlWRKY16 and SlWRKY31 function as negative regulators of plant immunity induced upon nematode infection.
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Affiliation(s)
- Anil Kumar
- Department of Entomology, Nematology and Chemistry Units, Agricultural Research Organization (ARO), Volcani Center, 50250, Bet Dagan, Israel
| | - Natalia Sichov
- Department of Entomology, Nematology and Chemistry Units, Agricultural Research Organization (ARO), Volcani Center, 50250, Bet Dagan, Israel
| | - Patricia Bucki
- Department of Entomology, Nematology and Chemistry Units, Agricultural Research Organization (ARO), Volcani Center, 50250, Bet Dagan, Israel
| | - Sigal Brown Miyara
- Department of Entomology, Nematology and Chemistry Units, Agricultural Research Organization (ARO), Volcani Center, 50250, Bet Dagan, Israel.
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16
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Scholz P, Chapman KD, Ischebeck T, Guzha A. Quantification of Botrytis cinerea Growth in Arabidopsis thaliana. Bio Protoc 2023; 13:e4740. [PMID: 37638304 PMCID: PMC10450733 DOI: 10.21769/bioprotoc.4740] [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: 01/15/2023] [Revised: 03/06/2023] [Accepted: 06/19/2023] [Indexed: 08/29/2023] Open
Abstract
Yield losses attributed to plant pathogens pose a serious threat to plant productivity and food security. Botrytis cinerea is one of the most devastating plant pathogens, infecting a wide array of plant species; it has also been established as a model organism to study plant-pathogen interactions. In this context, development of different assays to follow the relative success of B. cinerea infections is required. Here, we describe two methods to quantify B. cinerea development in Arabidopsis thaliana genotypes through measurements of lesion development and quantification of fungal genomic DNA in infected tissues. This provides two independent techniques that are useful in assessing the susceptibility or tolerance of different Arabidopsis genotypes to B. cinerea. Key features Protocol for the propagation of the necrotrophic plant pathogen fungus Botrytis cinerea and spore production. Two methods of Arabidopsis thaliana infection with the pathogen using droplet and spray inoculation. Two readouts, either by measuring lesion size or by the quantification of fungal DNA using quantitative PCR. The two methods are applicable across plant species susceptible the B. cinerea. Graphical overview A simplified overview of the droplet and spray infection methods used for the determination of B. cinerea growth in different Arabidopsis genotypes.
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Affiliation(s)
- Patricia Scholz
- University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Department for Plant Biochemistry, Goettingen, Germany
| | - Kent D Chapman
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Till Ischebeck
- Institute of Plant Biology and Biotechnology (IBBP), Green Biotechnology, University of Münster, Münster, Germany
| | - Athanas Guzha
- University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Department for Plant Biochemistry, Goettingen, Germany
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17
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Tian S, Liu B, Shen Y, Cao S, Lai Y, Lu G, Wang Z, Wang A. Unraveling the Molecular Mechanisms of Tomatoes' Defense against Botrytis cinerea: Insights from Transcriptome Analysis of Micro-Tom and Regular Tomato Varieties. PLANTS (BASEL, SWITZERLAND) 2023; 12:2965. [PMID: 37631176 PMCID: PMC10459989 DOI: 10.3390/plants12162965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/13/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023]
Abstract
Botrytis cinerea is a devastating fungal pathogen that causes severe economic losses in global tomato cultivation. Understanding the molecular mechanisms driving tomatoes' response to this pathogen is crucial for developing effective strategies to counter it. Although the Micro-Tom (MT) cultivar has been used as a model, its stage-specific response to B. cinerea remains poorly understood. In this study, we examined the response of the MT and Ailsa Craig (AC) cultivars to B. cinerea at different time points (12-48 h post-infection (hpi)). Our results indicated that MT exhibited a stronger resistant phenotype at 18-24 hpi but became more susceptible to B. cinerea later (26-48 hpi) compared to AC. Transcriptome analysis revealed differential gene expression between MT at 24 hpi and AC at 22 hpi, with MT showing a greater number of differentially expressed genes (DEGs). Pathway and functional annotation analysis revealed significant differential gene expression in processes related to metabolism, biological regulation, detoxification, photosynthesis, and carbon metabolism, as well as some immune system-related genes. MT demonstrated an increased reliance on Ca2+ pathway-related proteins, such as CNGCs, CDPKs, and CaMCMLs, to resist B. cinerea invasion. B. cinerea infection induced the activation of PTI, ETI, and SA signaling pathways, involving the modulation of various genes such as FLS2, BAK1, CERK1, RPM, SGT1, and EDS1. Furthermore, transcription factors such as WRKY, MYB, NAC, and AUX/IAA families played crucial regulatory roles in tomatoes' defense against B. cinerea. These findings provide valuable insights into the molecular mechanisms underlying tomatoes' defense against B. cinerea and offer potential strategies to enhance plant resistance.
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Affiliation(s)
- Shifu Tian
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.T.); (Y.S.); (S.C.); (Y.L.); (G.L.)
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Bojing Liu
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Yanan Shen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.T.); (Y.S.); (S.C.); (Y.L.); (G.L.)
| | - Shasha Cao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.T.); (Y.S.); (S.C.); (Y.L.); (G.L.)
| | - Yinyan Lai
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.T.); (Y.S.); (S.C.); (Y.L.); (G.L.)
| | - Guodong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.T.); (Y.S.); (S.C.); (Y.L.); (G.L.)
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.T.); (Y.S.); (S.C.); (Y.L.); (G.L.)
- Institute of Oceanography, Minjiang University, Fuzhou 350108, China
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou 350003, China
| | - Airong Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.T.); (Y.S.); (S.C.); (Y.L.); (G.L.)
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou 350003, China
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18
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Krishnan P, Caseys C, Soltis N, Zhang W, Burow M, Kliebenstein DJ. Polygenic pathogen networks influence transcriptional plasticity in the Arabidopsis-Botrytis pathosystem. Genetics 2023; 224:iyad099. [PMID: 37216906 PMCID: PMC10789313 DOI: 10.1093/genetics/iyad099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 03/30/2023] [Accepted: 05/16/2023] [Indexed: 05/24/2023] Open
Abstract
Bidirectional flow of information shapes the outcome of the host-pathogen interactions and depends on the genetics of each organism. Recent work has begun to use co-transcriptomic studies to shed light on this bidirectional flow, but it is unclear how plastic the co-transcriptome is in response to genetic variation in both the host and pathogen. To study co-transcriptome plasticity, we conducted transcriptomics using natural genetic variation in the pathogen, Botrytis cinerea, and large-effect genetic variation abolishing defense signaling pathways within the host, Arabidopsis thaliana. We show that genetic variation in the pathogen has a greater influence on the co-transcriptome than mutations that abolish defense signaling pathways in the host. Genome-wide association mapping using the pathogens' genetic variation and both organisms' transcriptomes allowed an assessment of how the pathogen modulates plasticity in response to the host. This showed that the differences in both organism's responses were linked to trans-expression quantitative trait loci (eQTL) hotspots within the pathogen's genome. These hotspots control gene sets in either the host or pathogen and show differential allele sensitivity to the host's genetic variation rather than qualitative host specificity. Interestingly, nearly all the trans-eQTL hotspots were unique to the host or pathogen transcriptomes. In this system of differential plasticity, the pathogen mediates the shift in the co-transcriptome more than the host.
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Affiliation(s)
- Parvathy Krishnan
- DynaMo Center of Excellence, University of Copenhagen, Copenhagen DL-1165Denmark
| | - Celine Caseys
- Department of Plant Sciences, University of California Davis, Davis, CA 95616USA
| | - Nik Soltis
- Department of Plant Sciences, University of California Davis, Davis, CA 95616USA
| | - Wei Zhang
- Department of Botany & Plant Sciences, Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Meike Burow
- DynaMo Center of Excellence, University of Copenhagen, Copenhagen DL-1165Denmark
| | - Daniel J Kliebenstein
- DynaMo Center of Excellence, University of Copenhagen, Copenhagen DL-1165Denmark
- Department of Plant Sciences, University of California Davis, Davis, CA 95616USA
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19
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Miao W, Yang Y, Wu M, Huang G, Ge L, Liu Y, Guan Z, Chen S, Fang W, Chen F, Zhao S. Potential pathways and genes expressed in Chrysanthemum in response to early fusarium oxysporum infection. BMC PLANT BIOLOGY 2023; 23:312. [PMID: 37308810 DOI: 10.1186/s12870-023-04331-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 06/05/2023] [Indexed: 06/14/2023]
Abstract
BACKGROUND Chrysanthemum Fusarium wilt is a common fungal disease caused by Fusarium oxysporum, which causes continuous cropping obstacles and huge losses to the chrysanthemum industry. The defense mechanism of chrysanthemum against F. oxysporum remains unclear, especially during the early stages of the disease. Therefore, in the present study, we analyzed chrysanthemum 'Jinba' samples inoculated with F. oxysporum at 0, 3, and 72 h using RNA-seq. RESULTS The results revealed that 7985 differentially expressed genes (DEGs) were co-expressed at 3 and 72 h after F. oxysporum infection. We analyzed the identified DEGs using Kyoto Encyclopedia of Genes and Genomes and Gene Ontology. The DEGs were primarily enriched in "Plant pathogen interaction", "MAPK signaling pathway", "Starch and sucrose metabolism", and "Biosynthesis of secondary metabolites". Genes related to the synthesis of secondary metabolites were upregulated in chrysanthemum early during the inoculation period. Furthermore, peroxidase, polyphenol oxidase, and phenylalanine ammonia-lyase enzymes were consistently produced to accumulate large amounts of phenolic compounds to resist F. oxysporum infection. Additionally, genes related to the proline metabolic pathway were upregulated, and proline levels accumulated within 72 h, regulating osmotic balance in chrysanthemum. Notably, the soluble sugar content in chrysanthemum decreased early during the inoculation period; we speculate that this is a self-protective mechanism of chrysanthemums for inhibiting fungal reproduction by reducing the sugar content in vivo. In the meantime, we screened for transcription factors that respond to F. oxysporum at an early stage and analyzed the relationship between WRKY and DEGs in the "Plant-pathogen interaction" pathway. We screened a key WRKY as a research target for subsequent experiments. CONCLUSION This study revealed the relevant physiological responses and gene expression changes in chrysanthemum in response to F. oxysporum infection, and provided a relevant candidate gene pool for subsequent studies on chrysanthemum Fusarium wilt.
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Affiliation(s)
- Weihao Miao
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Key laboratory of landscaping, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, PR China
| | - Yanrong Yang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Key laboratory of landscaping, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, PR China
| | - Mengtong Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Key laboratory of landscaping, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, PR China
| | - Gan Huang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Key laboratory of landscaping, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, PR China
| | - Lijiao Ge
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Key laboratory of landscaping, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, PR China
| | - Ye Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Key laboratory of landscaping, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, PR China
| | - Zhiyong Guan
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Key laboratory of landscaping, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, PR China
| | - Sumei Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Key laboratory of landscaping, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, PR China
| | - Weimin Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Key laboratory of landscaping, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, PR China
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Key laboratory of landscaping, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, PR China
| | - Shuang Zhao
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
- Key laboratory of landscaping, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China.
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, PR China.
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20
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Breeze E, Vale V, McLellan H, Pecrix Y, Godiard L, Grant M, Frigerio L. A tell tail sign: a conserved C-terminal tail-anchor domain targets a subset of pathogen effectors to the plant endoplasmic reticulum. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:3188-3202. [PMID: 36860200 DOI: 10.1093/jxb/erad075] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 02/27/2023] [Indexed: 05/21/2023]
Abstract
The endoplasmic reticulum (ER) is the entry point to the secretory pathway and, as such, is critical for adaptive responses to biotic stress, when the demand for de novo synthesis of immunity-related proteins and signalling components increases significantly. Successful phytopathogens have evolved an arsenal of small effector proteins which collectively reconfigure multiple host components and signalling pathways to promote virulence; a small, but important, subset of which are targeted to the endomembrane system including the ER. We identified and validated a conserved C-terminal tail-anchor motif in a set of pathogen effectors known to localize to the ER from the oomycetes Hyaloperonospora arabidopsidis and Plasmopara halstedii (downy mildew of Arabidopsis and sunflower, respectively) and used this protein topology to develop a bioinformatic pipeline to identify putative ER-localized effectors within the effectorome of the related oomycete, Phytophthora infestans, the causal agent of potato late blight. Many of the identified P. infestans tail-anchor effectors converged on ER-localized NAC transcription factors, indicating that this family is a critical host target for multiple pathogens.
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Affiliation(s)
- Emily Breeze
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Victoria Vale
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Hazel McLellan
- Division of Plant Science, University of Dundee (at JHI), Invergowrie, Dundee DD2 5DA, UK
| | - Yann Pecrix
- CIRAD, UMR PVBMT, Peuplements Végétaux et Bioagresseurs en Milieu Tropical (UMR C53), Ligne Paradis, 97410 St Pierre, La Réunion, France
| | - Laurence Godiard
- Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Castanet-Tolosan, France
| | - Murray Grant
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Lorenzo Frigerio
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
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21
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Pérez-Lara G, Olivares-Yañez C, van Bakel H, Larrondo LF, Canessa P. Genome-Wide Characterization of Light-Regulated Gene Expression in Botrytis cinerea Reveals Underlying Complex Photobiology. Int J Mol Sci 2023; 24:8705. [PMID: 37240051 PMCID: PMC10218500 DOI: 10.3390/ijms24108705] [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: 04/10/2023] [Revised: 05/06/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Botrytis cinerea is a necrotrophic fungus characterized mainly by its wide host range of infected plants. The deletion of the white-collar-1 gene (bcwcl1), which encodes for a blue-light receptor/transcription factor, causes a decrease in virulence, particularly when assays are conducted in the presence of light or photocycles. However, despite ample characterization, the extent of the light-modulated transcriptional responses regulated by BcWCL1 remains unknown. In this study, pathogen and pathogen:host RNA-seq analyses, conducted during non-infective in vitro plate growth and when infecting Arabidopsis thaliana leaves, respectively, informed on the global gene expression patterns after a 60 min light pulse on the wild-type B05.10 or ∆bcwcl1 B. cinerea strains. The results revealed a complex fungal photobiology, where the mutant did not react to the light pulse during its interaction with the plant. Indeed, when infecting Arabidopsis, no photoreceptor-encoding genes were upregulated upon the light pulse in the ∆bcwcl1 mutant. Differentially expressed genes (DEGs) in B. cinerea under non-infecting conditions were predominantly related to decreased energy production in response to the light pulse. In contrast, DEGs during infection significantly differ in the B05.10 strain and the ∆bcwcl1 mutant. Upon illumination at 24 h post-infection in planta, a decrease in the B. cinerea virulence-associated transcripts was observed. Accordingly, after a light pulse, biological functions associated with plant defense appear enriched among light-repressed genes in fungus-infected plants. Taken together, our results show the main transcriptomic differences between wild-type B. cinerea B05.10 and ∆bcwcl1 after a 60 min light pulse when growing saprophytically on a Petri dish and necrotrophically over A. thaliana.
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Affiliation(s)
- Gabriel Pérez-Lara
- Centro de Biotecnologia Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370186, Chile
- ANID–Millennium Science Initiative–Millennium Institute for Integrative Biology (iBIO), Santiago 7500565, Chile
| | - Consuelo Olivares-Yañez
- Centro de Biotecnologia Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370186, Chile
- ANID–Millennium Science Initiative–Millennium Institute for Integrative Biology (iBIO), Santiago 7500565, Chile
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Luis F. Larrondo
- ANID–Millennium Science Initiative–Millennium Institute for Integrative Biology (iBIO), Santiago 7500565, Chile
- Departamento de Genetica Molecular y Microbiologia, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Santiago 8331150, Chile
| | - Paulo Canessa
- Centro de Biotecnologia Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370186, Chile
- ANID–Millennium Science Initiative–Millennium Institute for Integrative Biology (iBIO), Santiago 7500565, Chile
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22
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Dreischhoff S, Das IS, Häffner F, Wolf AM, Polle A, Kasper KH. Fast and easy bioassay for the necrotizing fungus Botrytis cinerea on poplar leaves. PLANT METHODS 2023; 19:32. [PMID: 36991511 PMCID: PMC10061990 DOI: 10.1186/s13007-023-01011-3] [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: 12/05/2022] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Necrotizing pathogens pose an immense economic and ecological threat to trees and forests, but the molecular analysis of these pathogens is still in its infancy because of lacking model systems. To close this gap, we developed a reliable bioassay for the widespread necrotic pathogen Botrytis cinerea on poplars (Populus sp.), which are established model organisms to study tree molecular biology. RESULTS Botrytis cinerea was isolated from Populus x canescens leaves. We developed an infection system using fungal agar plugs, which are easy to handle. The method does not require costly machinery and results in very high infection success and significant fungal proliferation within four days. We successfully tested the fungal plug infection on 18 poplar species from five different sections. Emerging necroses were phenotypically and anatomically examined in Populus x canescens leaves. We adapted methods for image analyses of necrotic areas. We calibrated B. cinerea DNA against Ct-values obtained by quantitative real-time polymerase chain reaction and measured the amounts of fungal DNA in infected leaves. Increases in necrotic area and fungal DNA were strictly correlated within the first four days after inoculation. Methyl jasmonate pretreatment of poplar leaves decreased the spreading of the infection. CONCLUSIONS We provide a simple and rapid protocol to study the effects of a necrotizing pathogen on poplar leaves. The bioassay and fungal DNA quantification for Botrytis cinerea set the stage for in-depth molecular studies of immunity and resistance to a generalist necrotic pathogen in trees.
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Affiliation(s)
- Steven Dreischhoff
- Forest Botany and Tree Physiology, University of Goettingen, 37077, Göttingen, Germany
| | - Ishani Shankar Das
- Forest Botany and Tree Physiology, University of Goettingen, 37077, Göttingen, Germany
| | - Felix Häffner
- Department Aquatic Ecosystem Analysis, Helmholtz Center for Environmental Research-UFZ, Magdeburg, Germany
| | | | - Andrea Polle
- Forest Botany and Tree Physiology, University of Goettingen, 37077, Göttingen, Germany
| | - Karl Henrik Kasper
- Forest Botany and Tree Physiology, University of Goettingen, 37077, Göttingen, Germany.
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23
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Macioszek VK, Jęcz T, Ciereszko I, Kononowicz AK. Jasmonic Acid as a Mediator in Plant Response to Necrotrophic Fungi. Cells 2023; 12:cells12071027. [PMID: 37048100 PMCID: PMC10093439 DOI: 10.3390/cells12071027] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
Jasmonic acid (JA) and its derivatives, all named jasmonates, are the simplest phytohormones which regulate multifarious plant physiological processes including development, growth and defense responses to various abiotic and biotic stress factors. Moreover, jasmonate plays an important mediator’s role during plant interactions with necrotrophic oomycetes and fungi. Over the last 20 years of research on physiology and genetics of plant JA-dependent responses to pathogens and herbivorous insects, beginning from the discovery of the JA co-receptor CORONATINE INSENSITIVE1 (COI1), research has speeded up in gathering new knowledge on the complexity of plant innate immunity signaling. It has been observed that biosynthesis and accumulation of jasmonates are induced specifically in plants resistant to necrotrophic fungi (and also hemibiotrophs) such as mostly investigated model ones, i.e., Botrytis cinerea, Alternaria brassicicola or Sclerotinia sclerotiorum. However, it has to be emphasized that the activation of JA-dependent responses takes place also during susceptible interactions of plants with necrotrophic fungi. Nevertheless, many steps of JA function and signaling in plant resistance and susceptibility to necrotrophs still remain obscure. The purpose of this review is to highlight and summarize the main findings on selected steps of JA biosynthesis, perception and regulation in the context of plant defense responses to necrotrophic fungal pathogens.
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24
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Lacrampe N, Colombié S, Dumont D, Nicot P, Lecompte F, Lugan R. Nitrogen-mediated metabolic patterns of susceptibility to Botrytis cinerea infection in tomato (Solanum lycopersicum) stems. PLANTA 2023; 257:41. [PMID: 36680621 PMCID: PMC9867679 DOI: 10.1007/s00425-022-04065-0] [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: 09/16/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
Severe N stress allows an accumulation of C-based compounds but impedes that of N-based compounds required to lower the susceptibility of tomato stem to Botrytis cinerea. Botrytis cinerea, a necrotrophic filamentous fungus, forms potentially lethal lesions on the stems of infected plants. Contrasted levels of susceptibility to B. cinerea were obtained in a tomato cultivar grown on a range of nitrate concentration: low N supply resulted in high susceptibility while high N supply conferred a strong resistance. Metabolic deviations and physiological traits resulting from both infection and nitrogen limitation were investigated in the symptomless stem tissue surrounding the necrotic lesion. Prior to infection, nitrogen-deficient plants showed reduced levels of nitrogen-based compounds such as amino acids, proteins, and glutathione and elevated levels of carbon-based and defence compounds such as α-tomatine and chlorogenic acid. After B. cinerea inoculation, all plants displayed a few common responses, mainly alanine accumulation and galactinol depletion. The metabolome of resistant plants grown under high N supply showed no significant change after inoculation. On the contrary, the metabolome of susceptible plants grown under low N supply showed massive metabolic adjustments, including changes in central metabolism around glutamate and respiratory pathways, suggesting active resource mobilization and production of energy and reducing power. Redox and defence metabolisms were also stimulated by the infection in plants grown under low N supply; glutathione and chlorogenic acid accumulated, as well as metabolites with more controversial defensive roles, such as polyamines, GABA, branched-chain amino acids and phytosterols. Taken together, the results showed that nitrogen deficiency, although leading to an increase in secondary metabolites even before the pathogen attack, must have compromised the constitutive levels of defence proteins and delayed or attenuated the induced responses. The involvement of galactinol, alanine, cycloartenol and citramalate in the tomato stem response to B. cinerea is reported here for the first time.
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Affiliation(s)
- Nathalie Lacrampe
- PSH Unit, INRAE, 84914 Avignon, France
- UMR Qualisud, Avignon Université, 84916 Avignon, France
| | - Sophie Colombié
- UMR 1332 BFP, INRAE, Univ Bordeaux, 33883 Villenave d’Ornon, France
| | | | | | | | - Raphaël Lugan
- UMR Qualisud, Avignon Université, 84916 Avignon, France
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25
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Huang H, Mehta A, Kalmanovich J, Anand A, Bejarano MC, Garg T, Khan N, Tonpouwo GK, Shkodina AD, Bardhan M. Immunological and inflammatory effects of infectious diseases in circadian rhythm disruption and future therapeutic directions. Mol Biol Rep 2023; 50:3739-3753. [PMID: 36656437 PMCID: PMC9851103 DOI: 10.1007/s11033-023-08276-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 01/11/2023] [Indexed: 01/20/2023]
Abstract
BACKGROUND Circadian rhythm is characterised by daily variations in biological activity to align with the light and dark cycle. These diurnal variations, in turn, influence physiological functions such as blood pressure, temperature, and sleep-wake cycle. Though it is well established that the circadian pathway is linked to pro-inflammatory responses and circulating immune cells, its association with infectious diseases is widely unknown. OBJECTIVE This comprehensive review aims to describe the association between circadian rhythm and host immune response to various kinds of infection. METHODS We conducted a literature search in databases Pubmed/Medline and Science direct. Our paper includes a comprehensive analysis of findings from articles in English which was related to our hypothesis. FINDINGS Molecular clocks determine circadian rhythm disruption in response to infection, influencing the host's response toward infection. Moreover, there is a complex interplay with intrinsic oscillators of pathogens and the influence of specific infectious processes on the CLOCK: BMAL1 pathway. Such mechanisms vary for bacterial and viral infections, both well studied in the literature. However, less is known about the association of parasitic infections and fungal pathogens with circadian rhythm modulation. CONCLUSION It is shown that bidirectional relationships exist between circadian rhythm disruption and infectious process, which contains interplay between the host's and pathogens' circadian oscillator, immune response, and the influence of specific infectious. Further studies exploring the modulations of circadian rhythm and immunity can offer novel explanations of different susceptibilities to infection and can lead to therapeutic avenues in circadian immune modulation of infectious diseases.
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Affiliation(s)
- Helen Huang
- Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland
| | - Aashna Mehta
- Faculty of Medicine, University of Debrecen, Debrecen, 4032 Hungary
| | | | - Ayush Anand
- B. P. Koirala Institute of Health Sciences, Dharan, Nepal
| | - Maria Chilo Bejarano
- Facultad de Ciencias de la Salud Humana, Universidad Autónoma Gabriel René Moreno, Santa Cruz de la Sierra, Bolivia
| | - Tulika Garg
- Government Medical College and Hospital, Chandigarh, India
| | - Nida Khan
- Jinnah Sindh Medical University, Karachi, Pakistan
| | - Gauvain Kankeu Tonpouwo
- Faculté de Médecine, Université de Lubumbashi, Plaine Tshombé, Lubumbashi, Democratic Republic of the Congo
| | | | - Mainak Bardhan
- ICMR-National Institute of Cholera and Enteric Diseases (NICED), Kolkata, India
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26
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Badmi R, Tengs T, Brurberg MB, Elameen A, Zhang Y, Haugland LK, Fossdal CG, Hytönen T, Krokene P, Thorstensen T. Transcriptional profiling of defense responses to Botrytis cinerea infection in leaves of Fragaria vesca plants soil-drenched with β-aminobutyric acid. FRONTIERS IN PLANT SCIENCE 2022; 13:1025422. [PMID: 36570914 PMCID: PMC9772985 DOI: 10.3389/fpls.2022.1025422] [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: 08/22/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Grey mold caused by the necrotrophic fungal pathogen Botrytis cinerea can affect leaves, flowers, and berries of strawberry, causing severe pre- and postharvest damage. The defense elicitor β-aminobutyric acid (BABA) is reported to induce resistance against B. cinerea and many other pathogens in several crop plants. Surprisingly, BABA soil drench of woodland strawberry (Fragaria vesca) plants two days before B. cinerea inoculation caused increased infection in leaf tissues, suggesting that BABA induce systemic susceptibility in F. vesca. To understand the molecular mechanisms involved in B. cinerea susceptibility in leaves of F. vesca plants soil drenched with BABA, we used RNA sequencing to characterize the transcriptional reprogramming 24 h post-inoculation. The number of differentially expressed genes (DEGs) in infected vs. uninfected leaf tissue in BABA-treated plants was 5205 (2237 upregulated and 2968 downregulated). Upregulated genes were involved in pathogen recognition, defense response signaling, and biosynthesis of secondary metabolites (terpenoid and phenylpropanoid pathways), while downregulated genes were involved in photosynthesis and response to auxin. In control plants not treated with BABA, we found a total of 5300 DEGs (2461 upregulated and 2839 downregulated) after infection. Most of these corresponded to those in infected leaves of BABA-treated plants but a small subset of DEGs, including genes involved in 'response to biologic stimulus', 'photosynthesis' and 'chlorophyll biosynthesis and metabolism', differed significantly between treatments and could play a role in the induced susceptibility of BABA-treated plants.
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Affiliation(s)
- Raghuram Badmi
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Torstein Tengs
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - May Bente Brurberg
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, Ås, Norway
- Department of Plant Sciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Abdelhameed Elameen
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Yupeng Zhang
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Lisa Karine Haugland
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Carl Gunnar Fossdal
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Timo Hytönen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Department of Genetics, Genomics and Breeding, National Institute of Agricultural Botany- East Malling Research Station, East Malling, United Kingdom
| | - Paal Krokene
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Tage Thorstensen
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, Ås, Norway
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Kumar A, Kanak KR, Arunachalam A, Dass RS, Lakshmi PTV. Comparative transcriptome profiling and weighted gene co-expression network analysis to identify core genes in maize ( Zea mays L.) silks infected by multiple fungi. FRONTIERS IN PLANT SCIENCE 2022; 13:985396. [PMID: 36388593 PMCID: PMC9647128 DOI: 10.3389/fpls.2022.985396] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Maize (Zea mays L.) is the third most popular Poaceae crop after wheat and rice and used in feed and pharmaceutical sectors. The maize silk contains bioactive components explored by traditional Chinese herbal medicine for various pharmacological activities. However, Fusarium graminearum, Fusarium verticillioides, Trichoderma atroviride, and Ustilago maydis can infect the maize, produce mycotoxins, hamper the quantity and quality of silk production, and further harm the primary consumer's health. However, the defense mechanism is not fully understood in multiple fungal infections in the silk of Z. mays. In this study, we applied bioinformatics approaches to use the publicly available transcriptome data of Z. mays silk affected by multiple fungal flora to identify core genes involved in combatting disease response. Differentially expressed genes (DEGs) were identified among intra- and inter-transcriptome data sets of control versus infected Z. mays silks. Upon further comparison between up- and downregulated genes within the control of datasets, 4,519 upregulated and 5,125 downregulated genes were found. The DEGs have been compared with genes in the modules of weighted gene co-expression network analysis to relevant specific traits towards identifying core genes. The expression pattern of transcription factors, carbohydrate-active enzymes (CAZyme), and resistance genes was analyzed. The present investigation is supportive of our findings that the gene ontology, immunity stimulus, and resistance genes are upregulated, but physical and metabolic processes such as cell wall organizations and pectin synthesis were downregulated respectively. Our results are indicative that terpene synthase TPS6 and TPS11 are involved in the defense mechanism against fungal infections in maize silk.
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Affiliation(s)
- Amrendra Kumar
- Phytomatics Lab, Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Kanak Raj Kanak
- Fungal Genetics and Mycotoxicology Laboratory, Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Annamalai Arunachalam
- Postgraduate and Research Department of Botany, Arignar Anna Government Arts College, Villupuram, Tamil Nadu, India
| | - Regina Sharmila Dass
- Fungal Genetics and Mycotoxicology Laboratory, Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - P. T. V. Lakshmi
- Phytomatics Lab, Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
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Orf I, Tenenboim H, Omranian N, Nikoloski Z, Fernie AR, Lisec J, Brotman Y, Bromke MA. Transcriptomic and Metabolomic Analysis of a Pseudomonas-Resistant versus a Susceptible Arabidopsis Accession. Int J Mol Sci 2022; 23:ijms232012087. [PMID: 36292941 PMCID: PMC9603445 DOI: 10.3390/ijms232012087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/06/2022] [Accepted: 10/08/2022] [Indexed: 11/24/2022] Open
Abstract
Accessions of one plant species may show significantly different levels of susceptibility to stresses. The Arabidopsis thaliana accessions Col-0 and C24 differ significantly in their resistance to the pathogen Pseudomonas syringae pv. tomato (Pst). To help unravel the underlying mechanisms contributing to this naturally occurring variance in resistance to Pst, we analyzed changes in transcripts and compounds from primary and secondary metabolism of Col-0 and C24 at different time points after infection with Pst. Our results show that the differences in the resistance of Col-0 and C24 mainly involve mechanisms of salicylic-acid-dependent systemic acquired resistance, while responses of jasmonic-acid-dependent mechanisms are shared between the two accessions. In addition, arginine metabolism and differential activity of the biosynthesis pathways of aliphatic glucosinolates and indole glucosinolates may also contribute to the resistance. Thus, this study highlights the difference in the defense response strategies utilized by different genotypes.
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Affiliation(s)
- Isabel Orf
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Hezi Tenenboim
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Nooshin Omranian
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Zoran Nikoloski
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Alisdair R. Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Jan Lisec
- Department of Analytical Chemistry, Federal Institute for Materials Research and Testing, Richard-Willstätter-Straße 11, 12489 Berlin, Germany
| | - Yariv Brotman
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- Correspondence: (Y.B.); (M.A.B.)
| | - Mariusz A. Bromke
- Department of Biochemistry and Immunochemistry, Wroclaw Medical University, ul. Chałubińskiego 10, 50-367 Wrocław, Poland
- Correspondence: (Y.B.); (M.A.B.)
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Reboledo G, Agorio A, Vignale L, Alvarez A, Ponce De León I. The moss-specific transcription factor PpERF24 positively modulates immunity against fungal pathogens in Physcomitrium patens. FRONTIERS IN PLANT SCIENCE 2022; 13:908682. [PMID: 36186018 PMCID: PMC9520294 DOI: 10.3389/fpls.2022.908682] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
APETALA2/ethylene response factors (AP2/ERFs) transcription factors (TFs) have greatly expanded in land plants compared to algae. In angiosperms, AP2/ERFs play important regulatory functions in plant defenses against pathogens and abiotic stress by controlling the expression of target genes. In the moss Physcomitrium patens, a high number of members of the ERF family are induced during pathogen infection, suggesting that they are important regulators in bryophyte immunity. In the current study, we analyzed a P. patens pathogen-inducible ERF family member designated as PpERF24. Orthologs of PpERF24 were only found in other mosses, while they were absent in the bryophytes Marchantia polymorpha and Anthoceros agrestis, the vascular plant Selaginella moellendorffii, and angiosperms. We show that PpERF24 belongs to a moss-specific clade with distinctive amino acids features in the AP2 domain that binds to the DNA. Interestingly, all P. patens members of the PpERF24 subclade are induced by fungal pathogens. The function of PpERF24 during plant immunity was assessed by an overexpression approach and transcriptomic analysis. Overexpressing lines showed increased defenses to infection by the fungal pathogens Botrytis cinerea and Colletotrichum gloeosporioides evidenced by reduced cellular damage and fungal biomass compared to wild-type plants. Transcriptomic and RT-qPCR analysis revealed that PpERF24 positively regulates the expression levels of defense genes involved in transcriptional regulation, phenylpropanoid and jasmonate pathways, oxidative burst and pathogenesis-related (PR) genes. These findings give novel insights into potential mechanism by which PpERF24 increases plant defenses against several pathogens by regulating important players in plant immunity.
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Affiliation(s)
- Guillermo Reboledo
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Astrid Agorio
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Lucía Vignale
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Alfonso Alvarez
- Laboratorio de Fisiología Vegetal, Facultad de Ciencias, Centro de Investigaciones Nucleares, Universidad de la República, Montevideo, Uruguay
| | - Inés Ponce De León
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
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Stroud EA, Jayaraman J, Templeton MD, Rikkerink EHA. Comparison of the pathway structures influencing the temporal response of salicylate and jasmonate defence hormones in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2022; 13:952301. [PMID: 36160984 PMCID: PMC9504473 DOI: 10.3389/fpls.2022.952301] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/01/2022] [Indexed: 06/16/2023]
Abstract
Defence phytohormone pathways evolved to recognize and counter multiple stressors within the environment. Salicylic acid responsive pathways regulate the defence response to biotrophic pathogens whilst responses to necrotrophic pathogens, herbivory, and wounding are regulated via jasmonic acid pathways. Despite their contrasting roles in planta, the salicylic acid and jasmonic acid defence networks share a common architecture, progressing from stages of biosynthesis, to modification, regulation, and response. The unique structure, components, and regulation of each stage of the defence networks likely contributes, in part, to the speed, establishment, and longevity of the salicylic acid and jasmonic acid signaling pathways in response to hormone treatment and various biotic stressors. Recent advancements in the understanding of the Arabidopsis thaliana salicylic acid and jasmonic acid signaling pathways are reviewed here, with a focus on how the structure of the pathways may be influencing the temporal regulation of the defence responses, and how biotic stressors and the many roles of salicylic acid and jasmonic acid in planta may have shaped the evolution of the signaling networks.
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Affiliation(s)
- Erin A. Stroud
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Jay Jayaraman
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
- Bioprotection Aotearoa, Lincoln, New Zealand
| | - Matthew D. Templeton
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Bioprotection Aotearoa, Lincoln, New Zealand
| | - Erik H. A. Rikkerink
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
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Sasi JM, Gupta S, Singh A, Kujur A, Agarwal M, Katiyar-Agarwal S. Know when and how to die: gaining insights into the molecular regulation of leaf senescence. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:1515-1534. [PMID: 36389097 PMCID: PMC9530073 DOI: 10.1007/s12298-022-01224-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 08/17/2022] [Accepted: 08/21/2022] [Indexed: 06/16/2023]
Abstract
Senescence is the ultimate phase in the life cycle of leaves which is crucial for recycling of nutrients to maintain plant fitness and reproductive success. The earliest visible manifestation of leaf senescence is their yellowing, which usually commences with the breakdown of chlorophyll. The degradation process involves a gradual and highly coordinated disassembly of macromolecules resulting in the accumulation of nutrients, which are subsequently mobilized from the senescing leaves to the developing organs. Leaf senescence progresses under overly tight genetic and molecular control involving a well-orchestrated and intricate network of regulators that coordinate spatio-temporally with the influence of both internal and external cues. Owing to the advancements in omics technologies, the availability of mutant resources, scalability of molecular analyses methodologies and the advanced capacity to integrate multidimensional data, our understanding of the genetic and molecular basis of leaf ageing has greatly expanded. The review provides a compilation of the multitier regulation of senescence process and the interrelation between the environment and the terminal phase of leaf development. The knowledge gained would benefit in devising the strategies for manipulation of leaf senescence process to improve crop quality and productivity.
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Affiliation(s)
- Jyothish Madambikattil Sasi
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
| | - Shitij Gupta
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
| | - Apurva Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
| | - Alice Kujur
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
- USDA-ARS Plant Genetics Research Unit, The Donald Danforth Plant Science Center, St. Louis, MO 63132 USA
- Centre of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana 502324 India
| | - Manu Agarwal
- Department of Botany, University of Delhi North Campus, Delhi, 110007 India
| | - Surekha Katiyar-Agarwal
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
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Pink H, Talbot A, Graceson A, Graham J, Higgins G, Taylor A, Jackson AC, Truco M, Michelmore R, Yao C, Gawthrop F, Pink D, Hand P, Clarkson JP, Denby K. Identification of genetic loci in lettuce mediating quantitative resistance to fungal pathogens. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2481-2500. [PMID: 35674778 PMCID: PMC9271113 DOI: 10.1007/s00122-022-04129-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
KEY MESSAGE We demonstrate genetic variation for quantitative resistance against important fungal pathogens in lettuce and its wild relatives, map loci conferring resistance and predict key molecular mechanisms using transcriptome profiling. Lactuca sativa L. (lettuce) is an important leafy vegetable crop grown and consumed globally. Chemicals are routinely used to control major pathogens, including the causal agents of grey mould (Botrytis cinerea) and lettuce drop (Sclerotinia sclerotiorum). With increasing prevalence of pathogen resistance to fungicides and environmental concerns, there is an urgent need to identify sources of genetic resistance to B. cinerea and S. sclerotiorum in lettuce. We demonstrated genetic variation for quantitative resistance to B. cinerea and S. sclerotiorum in a set of 97 diverse lettuce and wild relative accessions, and between the parents of lettuce mapping populations. Transcriptome profiling across multiple lettuce accessions enabled us to identify genes with expression correlated with resistance, predicting the importance of post-transcriptional gene regulation in the lettuce defence response. We identified five genetic loci influencing quantitative resistance in a F6 mapping population derived from a Lactuca serriola (wild relative) × lettuce cross, which each explained 5-10% of the variation. Differential gene expression analysis between the parent lines, and integration of data on correlation of gene expression and resistance in the diversity set, highlighted potential causal genes underlying the quantitative trait loci.
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Affiliation(s)
- Harry Pink
- Biology Department, Centre for Novel Agricultural Products (CNAP), University of York, Wentworth Way, York, YO10 5DD, UK
| | - Adam Talbot
- Biology Department, Centre for Novel Agricultural Products (CNAP), University of York, Wentworth Way, York, YO10 5DD, UK
| | - Abi Graceson
- Department of Agriculture and Environment, Harper Adams University, Newport, Shropshire, TF10 8NB, UK
| | - Juliane Graham
- Department of Agriculture and Environment, Harper Adams University, Newport, Shropshire, TF10 8NB, UK
| | - Gill Higgins
- Biology Department, Centre for Novel Agricultural Products (CNAP), University of York, Wentworth Way, York, YO10 5DD, UK
| | - Andrew Taylor
- School of Life Sciences, University of Warwick, Wellesbourne Campus, Warwick, CV35 9EF, UK
| | - Alison C Jackson
- School of Life Sciences, University of Warwick, Wellesbourne Campus, Warwick, CV35 9EF, UK
| | - Maria Truco
- Genome Center, University of California Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Richard Michelmore
- Genome Center, University of California Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Chenyi Yao
- A. L. Tozer Ltd., Pyports, Downside Road, Cobham, Surrey, KT11 3EH, UK
| | - Frances Gawthrop
- A. L. Tozer Ltd., Pyports, Downside Road, Cobham, Surrey, KT11 3EH, UK
| | - David Pink
- Department of Agriculture and Environment, Harper Adams University, Newport, Shropshire, TF10 8NB, UK
| | - Paul Hand
- Department of Agriculture and Environment, Harper Adams University, Newport, Shropshire, TF10 8NB, UK
| | - John P Clarkson
- School of Life Sciences, University of Warwick, Wellesbourne Campus, Warwick, CV35 9EF, UK
| | - Katherine Denby
- Biology Department, Centre for Novel Agricultural Products (CNAP), University of York, Wentworth Way, York, YO10 5DD, UK.
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Foo M, Dony L, He F. Data-driven dynamical modelling of a pathogen-infected plant gene regulatory network: A comparative analysis. Biosystems 2022; 219:104732. [PMID: 35781035 DOI: 10.1016/j.biosystems.2022.104732] [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: 02/25/2022] [Revised: 05/30/2022] [Accepted: 06/22/2022] [Indexed: 11/02/2022]
Abstract
Recent advances in synthetic biology have enabled the design of genetic feedback control circuits that could be implemented to build resilient plants against pathogen attacks. To facilitate the proper design of these genetic feedback control circuits, an accurate model that is able to capture the vital dynamical behaviour of the pathogen-infected plant is required. In this study, using a data-driven modelling approach, we develop and compare four dynamical models (i.e. linear, Michaelis-Menten with Hill coefficient (Hill Function), standard S-System and extended S-System) of a pathogen-infected plant gene regulatory network (GRN). These models are then assessed across several criteria, i.e. ease of identifying the type of gene regulation, the predictive capability, Akaike Information Criterion (AIC) and the robustness to parameter uncertainty to determine its viability of balancing between biological complexity and accuracy when modelling the pathogen-infected plant GRN. Using our defined ranking score, we obtain the following insights to the modelling of GRN. Our analyses show that despite commonly used and provide biological relevance, the Hill Function model ranks the lowest while the extended S-System model ranks highest in the overall comparison. Interestingly, the performance of the linear model is more consistent throughout the comparison, making it the preferred model for this pathogen-infected plant GRN when considering data-driven modelling approach.
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Affiliation(s)
- Mathias Foo
- School of Engineering, University of Warwick, CV4 7AL, Coventry, UK.
| | - Leander Dony
- Institute of Computational Biology, Helmholtz Munich, 85764, Neuherberg, Germany; Department of Translational Psychiatry, Max Planck Institute of Psychiatry, International Max Planck Research School for Translational Psychiatry (IMPRS-TP), 80804, Munich, Germany; TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany.
| | - Fei He
- Centre for Computational Science and Mathematical Modelling, Coventry University, CV1 2JH, Coventry, UK.
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Transcriptional regulation of plant innate immunity. Essays Biochem 2022; 66:607-620. [PMID: 35726519 PMCID: PMC9528082 DOI: 10.1042/ebc20210100] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 12/20/2022]
Abstract
Transcriptional reprogramming is an integral part of plant immunity. Tight regulation of the immune transcriptome is essential for a proper response of plants to different types of pathogens. Consequently, transcriptional regulators are proven targets of pathogens to enhance their virulence. The plant immune transcriptome is regulated by many different, interconnected mechanisms that can determine the rate at which genes are transcribed. These include intracellular calcium signaling, modulation of the redox state, post-translational modifications of transcriptional regulators, histone modifications, DNA methylation, modulation of RNA polymerases, alternative transcription inititation, the Mediator complex and regulation by non-coding RNAs. In addition, on their journey from transcription to translation, mRNAs are further modulated through mechanisms such as nuclear RNA retention, storage of mRNA in stress granules and P-bodies, and post-transcriptional gene silencing. In this review, we highlight the latest insights into these mechanisms. Furthermore, we discuss some emerging technologies that promise to greatly enhance our understanding of the regulation of the plant immune transcriptome in the future.
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Xiao G, Zhang Q, Zeng X, Chen X, Liu S, Han Y. Deciphering the Molecular Signatures Associated With Resistance to Botrytis cinerea in Strawberry Flower by Comparative and Dynamic Transcriptome Analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:888939. [PMID: 35720571 PMCID: PMC9198642 DOI: 10.3389/fpls.2022.888939] [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: 03/03/2022] [Accepted: 04/19/2022] [Indexed: 06/15/2023]
Abstract
Gray mold caused by Botrytis cinerea, which is considered to be the second most destructive necrotrophic fungus, leads to major economic losses in strawberry (Fragaria × ananassa) production. B. cinerea preferentially infects strawberry flowers and fruits, leading to flower blight and fruit rot. Compared with those of the fruit, the mechanisms of flower defense against B. cinerea remain largely unexplored. Therefore, in this study, we aimed to unveil the resistance mechanisms of strawberry flower through dynamic and comparative transcriptome analysis with resistant and susceptible strawberry cultivars. Our experimental data suggest that resistance to B. cinerea in the strawberry flower is probably regulated at the transcriptome level during the early stages of infection and strawberry flower has highly complex and dynamic regulatory networks controlling a multi-layered defense response to B. cinerea. First of all, the higher expression of disease-resistance genes but lower expression of cell wall degrading enzymes and peroxidases leads to higher resistance to B. cinerea in the resistant cultivar. Interestingly, CPKs, RBOHDs, CNGCs, and CMLs comprised a calcium signaling pathway especially play a crucial role in enhancing resistance by increasing their expression. Besides, six types of phytohormones forming a complex regulatory network mediated flower resistance, especially JA and auxin. Finally, the genes involved in the phenylpropanoid and amino acids biosynthesis pathways were gene sets specially expressed or different expression genes, both of them contribute to the flower resistance to B. cinerea. These data provide the foundation for a better understanding of strawberry gray mold, along with detailed genetic information and resistant materials to enable genetic improvement of strawberry plant resistance to gray mold.
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Naets M, Van Hemelrijck W, Gruyters W, Verboven P, Nicolaï B, Keulemans W, De Coninck B, Geeraerd AH. Time Is of the Essence—Early Activation of the Mevalonate Pathway in Apple Challenged With Gray Mold Correlates With Reduced Susceptibility During Postharvest Storage. Front Microbiol 2022; 13:797234. [PMID: 35633666 PMCID: PMC9133740 DOI: 10.3389/fmicb.2022.797234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 02/14/2022] [Indexed: 12/02/2022] Open
Abstract
Apple is typically stored under low temperature and controlled atmospheric conditions to ensure a year round supply of high quality fruit for the consumer. During storage, losses in quality and quantity occur due to spoilage by postharvest pathogens. One important postharvest pathogen of apple is Botrytis cinerea. The fungus is a broad host necrotroph with a large arsenal of infection strategies able to infect over 1,400 different plant species. We studied the apple-B. cinerea interaction to get a better understanding of the defense response in apple. We conducted an RNAseq experiment in which the transcriptome of inoculated and non-inoculated (control and mock) apples was analyzed at 0, 1, 12, and 28 h post inoculation. Our results show extensive reprogramming of the apple’s transcriptome with about 28.9% of expressed genes exhibiting significant differential regulation in the inoculated samples. We demonstrate the transcriptional activation of pathogen-triggered immunity and a reprogramming of the fruit’s metabolism. We demonstrate a clear transcriptional activation of secondary metabolism and a correlation between the early transcriptional activation of the mevalonate pathway and reduced susceptibility, expressed as a reduction in resulting lesion diameters. This pathway produces the building blocks for terpenoids, a large class of compounds with diverging functions including defense. 1-MCP and hot water dip treatment are used to further evidence the key role of terpenoids in the defense and demonstrate that ethylene modulates this response.
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Affiliation(s)
- Matthias Naets
- Division of MeBioS, Department of Biosystems (BIOSYST), KU Leuven, Leuven, Belgium
| | - Wendy Van Hemelrijck
- Research Station for Fruit Cultivation, Department of Mycology, Sint-Truiden, Belgium
| | - Willem Gruyters
- Division of MeBioS, Department of Biosystems (BIOSYST), KU Leuven, Leuven, Belgium
| | - Pieter Verboven
- Division of MeBioS, Department of Biosystems (BIOSYST), KU Leuven, Leuven, Belgium
| | - Bart Nicolaï
- Division of MeBioS, Department of Biosystems (BIOSYST), KU Leuven, Leuven, Belgium
- Flanders Centre of Postharvest Technology (VCBT), Leuven, Belgium
| | - Wannes Keulemans
- Division of Crop Biotechnics, Department of Biosystems (BIOSYST), KU Leuven, Leuven, Belgium
| | - Barbara De Coninck
- Division of Crop Biotechnics, Department of Biosystems (BIOSYST), KU Leuven, Leuven, Belgium
| | - Annemie H. Geeraerd
- Division of MeBioS, Department of Biosystems (BIOSYST), KU Leuven, Leuven, Belgium
- *Correspondence: Annemie H. Geeraerd,
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Chen H, Zhang S, He S, A R, Wang M, Liu S. The necrotroph Botrytis cinerea promotes disease development in Panax ginseng by manipulating plant defense signals and antifungal metabolites degradation. J Ginseng Res 2022; 46:790-800. [PMID: 36312732 PMCID: PMC9597437 DOI: 10.1016/j.jgr.2022.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 03/21/2022] [Accepted: 03/29/2022] [Indexed: 01/04/2023] Open
Abstract
Background Panax ginseng Meyer is one of the most valuable medicinal plants which is enriched in anti-microbe secondary metabolites and widely used in traditional medicine. Botrytis cinerea is a necrotrophic fungus that causes gray mold disease in a broad range of hosts. B. cinerea could overcome the ginseng defense and cause serious leaf and root diseases with unknown mechanism. Methods We conducted simultaneous transcriptomic and metabolomic analysis of the host to investigate the defense response of ginseng affected by B. cinerea. The gene deletion and replacement were then performed to study the pathogenic gene in B. cinerea during ginseng - fungi interaction. Results Upon B. cinerea infection, ginseng defense responses were switched from the activation to repression, thus the expression of many defense genes decreased and the biosynthesis of antifungal metabolites were reduced. Particularly, ginseng metabolites like kaempferol, quercetin and luteolin which could inhibit fungi growth were decreased after B. cinerea infection. B. cinerea quercetin dioxygenase (Qdo) involved in catalyzing flavonoids degradation and △BcQdo mutants showed increased substrates accumulation and reduced disease development. Conclusion This work indicates the flavonoids play a role in ginseng defense and BcQdo involves in B. cinerea virulence towards the P. ginseng. B. cinerea promotes disease development in ginseng by suppressing of defense related genes expression and reduction of antifungal metabolites biosynthesis.
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Affiliation(s)
| | | | | | | | | | - Shouan Liu
- Corresponding author. Laboratory of Tea and Medicinal Plant Pathology, Jilin University, Changchun, 130062, China.
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Blayney J, Geary J, Chrisp R, Violet J, Barratt L, Tavukçu L, Paine K, Vaistij FE, Graham IA, Denby KJ, White RJ. Impact on Arabidopsis growth and stress resistance of depleting the Maf1 repressor of RNA polymerase III. Gene 2022; 815:146130. [PMID: 35017035 DOI: 10.1016/j.gene.2021.146130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 12/07/2021] [Accepted: 12/15/2021] [Indexed: 11/30/2022]
Abstract
Maf1 is a transcription factor that is conserved in sequence and structure between yeasts, animals and plants. Its principal molecular function is also well conserved, being to bind and repress RNA polymerase (pol) III, thereby inhibiting synthesis of tRNAs and other noncoding RNAs. Restrictions on tRNA production and hence protein synthesis can provide a mechanism to preserve resources under conditions that are suboptimal for growth. Accordingly, Maf1 is found in some organisms to influence growth and/or stress survival. Because of their sessile nature, plants are especially vulnerable to environmental changes and molecular adaptations that enhance growth under benign circumstances can increase sensitivity to external challenges. We tested if Maf1 depletion in the model plant Arabidopsis affects growth, pathogen resistance and tolerance of drought or soil salinity, a common physiological challenge that imposes both osmotic and ionic stress. We find that disruption of the Maf1 gene or RNAi-mediated depletion of its transcript is well-tolerated and confers a modest growth advantage without compromising resistance to common biotic and abiotic challenges.
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Affiliation(s)
- Joseph Blayney
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - James Geary
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Ruby Chrisp
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Joseph Violet
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Liam Barratt
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Laçin Tavukçu
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Katherine Paine
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Fabián E Vaistij
- Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Ian A Graham
- Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Katherine J Denby
- Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Robert J White
- Department of Biology, University of York, Heslington, York YO10 5DD, UK.
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Topcu H, Degirmenci I, Sonmez DA, Paizila A, Karci H, Kafkas S, Kafkas E, Ercisli S, Alatawi A. Sugar, Invertase Enzyme Activities and Invertase Gene Expression in Different Developmental Stages of Strawberry Fruits. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11040509. [PMID: 35214842 PMCID: PMC8877310 DOI: 10.3390/plants11040509] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 02/08/2022] [Accepted: 02/11/2022] [Indexed: 05/26/2023]
Abstract
The cultivated strawberry (Fragaria × ananassa) is octoploid (2n = 8x = 56) and has been the focused fruit species of which an increasing number of molecular and genetic research has been conducted in recent years. The aim of this study is to identify the relationships between sucrose metabolism, invertase enzyme activity and gene expression in four different fruit development periods (red, pink, green and white) of two commercially important strawberry varieties 'Rubygem' and 'Fortuna'. The metabolite profiles (glucose, fructose, sucrose and total sugar content) of two varieties were discovered to be extremely similar. The highest amount of total sugar was found in red fruits, while the lowest was obtained from green fruits. Invertase represents one of the key enzymes in sucrose metabolism. The lowest invertase activity was obtained from the green fruits in 'Rubygem' and 'Fortuna' during four developmental periods. In these varieties, the amount of sucrose was found to be close to glucose and fructose and the lowest amount was detected in green period, while invertase activity was relatively high during red and pink periods and invertase gene expression was determined at high levels in both primers (St-4 and St-6) in the green period. The results of the study indicated that sugar content and invertase activity were positively correlated while enzyme activity and gene expression were negatively correlated.
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Affiliation(s)
- Hayat Topcu
- Department of Agricultural Biotechnology, Faculty of Agriculture, Namik Kemal University, Tekirdag 59030, Turkey
| | - Ipek Degirmenci
- Department of Horticulture, Faculty of Agriculture, Cukurova University, Adana 01330, Turkey; (I.D.); (H.K.); (S.K.); (E.K.)
| | - Duygu Ayvaz Sonmez
- Yaltir Agricultural Products Inc., Sarihuglar, Algida 51-1, Adana 01355, Turkey;
| | - Aibibula Paizila
- Department of Laboratory Technologies, Imamoglu Vocational School, Cukurova University, Adana 01330, Turkey;
| | - Harun Karci
- Department of Horticulture, Faculty of Agriculture, Cukurova University, Adana 01330, Turkey; (I.D.); (H.K.); (S.K.); (E.K.)
| | - Salih Kafkas
- Department of Horticulture, Faculty of Agriculture, Cukurova University, Adana 01330, Turkey; (I.D.); (H.K.); (S.K.); (E.K.)
| | - Ebru Kafkas
- Department of Horticulture, Faculty of Agriculture, Cukurova University, Adana 01330, Turkey; (I.D.); (H.K.); (S.K.); (E.K.)
| | - Sezai Ercisli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum 25240, Turkey
| | - Aishah Alatawi
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71421, Saudi Arabia;
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Shiels D, Prestwich BD, Koo O, Kanchiswamy CN, O'Halloran R, Badmi R. Hemp Genome Editing—Challenges and Opportunities. Front Genome Ed 2022; 4:823486. [PMID: 35187530 PMCID: PMC8847435 DOI: 10.3389/fgeed.2022.823486] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 01/05/2022] [Indexed: 11/13/2022] Open
Abstract
Hemp (Cannabis sativa L.) is a multipurpose crop with many important uses including medicine, fibre, food and biocomposites. This plant is currently gaining prominence and acceptance for its valuable applications. Hemp is grown as a cash crop for its novel cannabinoids which are estimated to be a multibillion-dollar downstream market. Hemp cultivation can play a major role in carbon sequestration with good CO2 to biomass conversion in low input systems and can also improve soil health and promote phytoremediation. The recent advent of genome editing tools to produce non-transgenic genome-edited crops with no trace of foreign genetic material has the potential to overcome regulatory hurdles faced by genetically modified crops. The use of Artificial Intelligence - mediated trait discovery platforms are revolutionizing the agricultural industry to produce desirable crops with unprecedented accuracy and speed. However, genome editing tools to improve the beneficial properties of hemp have not yet been deployed. Recent availability of high-quality Cannabis genome sequences from several strains (cannabidiol and tetrahydrocannabinol balanced and CBD/THC rich strains) have paved the way for improving the production of valuable bioactive molecules for the welfare of humankind and the environment. In this context, the article focuses on exploiting advanced genome editing tools to produce non-transgenic hemp to improve the most industrially desirable traits. The challenges, opportunities and interdisciplinary approaches that can be adopted from existing technologies in other plant species are highlighted.
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Affiliation(s)
- Donal Shiels
- School of Biological Earth and Environmental Sciences, Environmental Research Institute, University College Cork, Cork, Ireland
| | - Barbara Doyle Prestwich
- School of Biological Earth and Environmental Sciences, Environmental Research Institute, University College Cork, Cork, Ireland
| | | | | | - Roisin O'Halloran
- School of Biological Earth and Environmental Sciences, Environmental Research Institute, University College Cork, Cork, Ireland
| | - Raghuram Badmi
- School of Biological Earth and Environmental Sciences, Environmental Research Institute, University College Cork, Cork, Ireland
- Plantedit Pvt Ltd, Cork, Ireland
- *Correspondence: Raghuram Badmi,
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He T, Ren Z, Muhae-Ud-Din G, Guo Q, Liu T, Chen W, Gao L. Transcriptomics Analysis of Wheat Tassel Response to Tilletia laevis Kühn, Which Causes Common Bunt of Wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:823907. [PMID: 35273625 PMCID: PMC8902468 DOI: 10.3389/fpls.2022.823907] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 01/10/2022] [Indexed: 05/20/2023]
Abstract
Tilletia laevis Kühn [synonym T. foetida (Wallr.) Liro] can lead to a wheat common bunt, which is one of the most serious diseases affecting kernels, a serious reduction in grain yield, and losses can reach up to 80% in favorable environments. To understand how wheat tassels respond to T. laevis, based on an RNA-Seq technology, we analyzed a host transcript accumulation on healthy wheat tassels and on tassels infected by the pathogen. Our results showed that 7,767 out of 15,658 genes were upregulated and 7,891 out of 15,658 genes were downregulated in wheat tassels. Subsequent gene ontology (GO) showed that differentially expressed genes (DEGs) are predominantly involved in biological processes, cellular components, and molecular functions. Additionally, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that 20 pathways were expressed significantly during the infection of wheat with T. laevis, while biosynthesis of amino acids, carbon metabolism, and starch and sucrose metabolism pathways were more highly expressed. Our findings also demonstrated that genes involved in defense mechanisms and myeloblastosis (MYB) transcription factor families were mostly upregulated, and the RNA-seq results were validated by quantitative real-time polymerase chain reaction (qRT-PCR). This is the first report on transcriptomics analysis of wheat tassels in response to T. laevis, which will contribute to understanding the interaction of T. laevis and wheat, and may provide higher efficiency control strategies, including developing new methods to increase the resistance of wheat crops to T. laevis-caused wheat common bunt.
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Affiliation(s)
- Ting He
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Agricultural Integrated Pest Management, Qinghai University, Xining, China
| | - Zhaoyu Ren
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ghulam Muhae-Ud-Din
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qingyun Guo
- Key Laboratory of Agricultural Integrated Pest Management, Qinghai University, Xining, China
| | - Taiguo Liu
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Li Gao
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Li Gao,
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Yang YN, Kim Y, Kim H, Kim SJ, Cho KM, Kim Y, Lee DS, Lee MH, Kim SY, Hong JC, Kwon SJ, Choi J, Park OK. The transcription factor ORA59 exhibits dual DNA binding specificity that differentially regulates ethylene- and jasmonic acid-induced genes in plant immunity. PLANT PHYSIOLOGY 2021; 187:2763-2784. [PMID: 34890461 PMCID: PMC8644270 DOI: 10.1093/plphys/kiab437] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Jasmonic acid (JA) and ethylene (ET) signaling modulate plant defense against necrotrophic pathogens in a synergistic and interdependent manner, while JA and ET also have independent roles in certain processes, e.g. in responses to wounding and flooding, respectively. These hormone pathways lead to transcriptional reprogramming, which is a major part of plant immunity and requires the roles of transcription factors. ET response factors are responsible for the transcriptional regulation of JA/ET-responsive defense genes, of which ORA59 functions as a key regulator of this process and has been implicated in the JA-ET crosstalk. We previously demonstrated that Arabidopsis (Arabidopsis thaliana) GDSL LIPASE 1 (GLIP1) depends on ET for gene expression and pathogen resistance. Here, promoter analysis of GLIP1 revealed ERELEE4 as the critical cis-element for ET-responsive GLIP1 expression. In a yeast one-hybrid screening, ORA59 was isolated as a specific transcription factor that binds to the ERELEE4 element, in addition to the well-characterized GCC box. We found that ORA59 regulates JA/ET-responsive genes through direct binding to these elements in gene promoters. Notably, ORA59 exhibited a differential preference for GCC box and ERELEE4, depending on whether ORA59 activation is achieved by JA and ET, respectively. JA and ET induced ORA59 phosphorylation, which was required for both activity and specificity of ORA59. Furthermore, RNA-seq and virus-induced gene silencing analyses led to the identification of ORA59 target genes of distinct functional categories in JA and ET pathways. Our results provide insights into how ORA59 can generate specific patterns of gene expression dynamics through JA and ET hormone pathways.
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Affiliation(s)
- Young Nam Yang
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Youngsung Kim
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Hyeri Kim
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Su Jin Kim
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Kwang-Moon Cho
- Molecular Diagnosis Division, AccuGene, Incheon 22006, Korea
| | - Yerin Kim
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
| | - Dong Sook Lee
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Myoung-Hoon Lee
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Soo Young Kim
- Department of Biotechnology and Kumho Life Science Laboratory, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea
| | - Jong Chan Hong
- Division of Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
| | - Sun Jae Kwon
- Molecular Diagnosis Division, AccuGene, Incheon 22006, Korea
| | - Jungmin Choi
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
| | - Ohkmae K Park
- Department of Life Sciences, Korea University, Seoul 02841, Korea
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Comparative Transcriptomics and Gene Knockout Reveal Virulence Factors of Arthrinium phaeospermum in Bambusa pervariabilis × Dendrocalamopsis grandis. J Fungi (Basel) 2021; 7:jof7121001. [PMID: 34946984 PMCID: PMC8705590 DOI: 10.3390/jof7121001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/19/2021] [Accepted: 11/19/2021] [Indexed: 11/17/2022] Open
Abstract
Arthrinium phaeospermum can cause branch wilting of Bambusa pervariabilis × Dendrocalamopsis grandis, causing great economic losses and ecological damage. A. phaeospermum was sequenced in sterile deionized water (CK), rice tissue (T1) and B. pervariabilis × D. grandis (T2) fluid by RNA-Seq, and the function of Ctf1β 1 and Ctf1β 2 was verified by gene knockout. There were 424, 471 and 396 differentially expressed genes between the T2 and CK, T2 and T1, and CK and T1 groups, respectively. Thirty DEGs had verified the change in expression by fluorescent quantitative PCR. Twenty-nine DEGs were the same as the expression level in RNA-Seq. In addition, ΔApCtf1β 1 and ΔApCtf1β 2 showed weaker virulence by gene knockout, and the complementary strains Ctf1β 1 and Ctf1β 2 showed the same virulence as the wild-type strains. Relative growth inhibition of ΔApCtf1β 1 and ΔApCtf1β was significantly decreased by 21.4% and 19.2%, respectively, by adding H2O2 compared to the estimates from the wild-type strain and decreased by 25% and 19.4%, respectively, by adding Congo red. The disease index of B. pervariabilis × D. grandis infected by two mutants was significantly lower than that of wild type. This suggested that Ctf1β genes are required for the stress response and virulence of A. phaeospermum.
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Courbier S, Snoek BL, Kajala K, Li L, van Wees SCM, Pierik R. Mechanisms of far-red light-mediated dampening of defense against Botrytis cinerea in tomato leaves. PLANT PHYSIOLOGY 2021; 187:1250-1266. [PMID: 34618050 PMCID: PMC8566310 DOI: 10.1093/plphys/kiab354] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
Plants detect neighboring competitors through a decrease in the ratio between red and far-red light (R:FR). This decreased R:FR is perceived by phytochrome photoreceptors and triggers shade avoidance responses such as shoot elongation and upward leaf movement (hyponasty). In addition to promoting elongation growth, low R:FR perception enhances plant susceptibility to pathogens: the growth-defense tradeoff. Although increased susceptibility in low R:FR has been studied for over a decade, the associated timing of molecular events is still unknown. Here, we studied the chronology of FR-induced susceptibility events in tomato (Solanum lycopersicum) plants pre-exposed to either white light (WL) or WL supplemented with FR light (WL+FR) prior to inoculation with the necrotrophic fungus Botrytis cinerea (B.c.). We monitored the leaf transcriptional changes over a 30-h time course upon infection and followed up with functional studies to identify mechanisms. We found that FR-induced susceptibility in tomato is linked to a general dampening of B.c.-responsive gene expression, and a delay in both pathogen recognition and jasmonic acid-mediated defense gene expression. In addition, we found that the supplemental FR-induced ethylene emissions affected plant immune responses under the WL+FR condition. This study improves our understanding of the growth-immunity tradeoff, while simultaneously providing leads to improve tomato resistance against pathogens in dense cropping systems.
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Affiliation(s)
- Sarah Courbier
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, The Netherlands
| | - Basten L Snoek
- Theoretical Biology and Bioinformatics, Institute of Biodynamics and Biocomplexity, Utrecht University, The Netherlands
| | - Kaisa Kajala
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, The Netherlands
| | - Linge Li
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, The Netherlands
| | - Saskia C M van Wees
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, The Netherlands
| | - Ronald Pierik
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, The Netherlands
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Muñoz A, Santamaria ME, Fernández-Bautista N, Mangano S, Toribio R, Martínez M, Berrocal-Lobo M, Diaz I, Castellano MM. The co-chaperone HOP3 participates in jasmonic acid signaling by regulating CORONATINE-INSENSITIVE 1 activity. PLANT PHYSIOLOGY 2021; 187:1679-1689. [PMID: 34618051 PMCID: PMC8566277 DOI: 10.1093/plphys/kiab334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 06/21/2021] [Indexed: 05/25/2023]
Abstract
HOPs (HSP70-HSP90 organizing proteins) are a highly conserved family of HSP70 and HSP90 co-chaperones whose role in assisting the folding of various hormonal receptors has been extensively studied in mammals. In plants, HOPs are mainly associated with stress response, but their potential involvement in hormonal networks remains completely unexplored. In this article we describe that a member of the HOP family, HOP3, is involved in the jasmonic acid (JA) pathway and is linked to plant defense responses not only to pathogens, but also to a generalist herbivore. The JA pathway regulates responses to Botrytis cinerea infection and to Tetranychus urticae feeding; our data demonstrate that the Arabidopsis (Arabidopsis thaliana) hop3-1 mutant shows an increased susceptibility to both. The hop3-1 mutant exhibits reduced sensitivity to JA derivatives in root growth assays and downregulation of different JA-responsive genes in response to methyl jasmonate, further revealing the relevance of HOP3 in the JA pathway. Interestingly, yeast two-hybrid assays and in planta co-immunoprecipitation assays found that HOP3 interacts with COI1, suggesting that COI1 is a target of HOP3. Consistent with this observation, COI1 activity is reduced in the hop3-1 mutant. All these data strongly suggest that, specifically among HOPs, HOP3 plays a relevant role in the JA pathway by regulating COI1 activity in response to JA and, consequently, participating in defense signaling to biotic stresses.
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Affiliation(s)
- Alfonso Muñoz
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
- Departamento de Botánica, Ecología y Fisiología Vegetal, Campus de Rabanales, Edificio Severo Ochoa, Universidad de Córdoba, Córdoba 14071, Spain
| | - M Estrella Santamaria
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
| | - Nuria Fernández-Bautista
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
| | - Silvina Mangano
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBA, CONICET), Av. Patricias Argentinas 435, Buenos Aires, C1405BWE, Argentina
| | - René Toribio
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
| | - Manuel Martínez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM 28040, Madrid, Spain
| | - Marta Berrocal-Lobo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
- Departamento de Sistemas y Recursos Naturales, E.T.S.I. Montes, Forestal y del Medio Natural, Ciudad Universitaria s/n, 28040, Madrid, Spain
| | - Isabel Diaz
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM 28040, Madrid, Spain
| | - M Mar Castellano
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
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Reboledo G, Agorio AD, Vignale L, Batista-García RA, Ponce De León I. Transcriptional profiling reveals conserved and species-specific plant defense responses during the interaction of Physcomitrium patens with Botrytis cinerea. PLANT MOLECULAR BIOLOGY 2021; 107:365-385. [PMID: 33521880 DOI: 10.1007/s11103-021-01116-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 01/03/2021] [Indexed: 06/12/2023]
Abstract
Evolutionary conserved defense mechanisms present in extant bryophytes and angiosperms, as well as moss-specific defenses are part of the immune response of Physcomitrium patens. Bryophytes and tracheophytes are descendants of early land plants that evolved adaptation mechanisms to cope with different kinds of terrestrial stresses, including drought, variations in temperature and UV radiation, as well as defense mechanisms against microorganisms present in the air and soil. Although great advances have been made on pathogen perception and subsequent defense activation in angiosperms, limited information is available in bryophytes. In this study, a transcriptomic approach uncovered the molecular mechanisms underlying the defense response of the bryophyte Physcomitrium patens (previously Physcomitrella patens) against the important plant pathogen Botrytis cinerea. A total of 3.072 differentially expressed genes were significantly affected during B. cinerea infection, including genes encoding proteins with known functions in angiosperm immunity and involved in pathogen perception, signaling, transcription, hormonal signaling, metabolic pathways such as shikimate and phenylpropanoid, and proteins with diverse role in defense against biotic stress. Similarly as in other plants, B. cinerea infection leads to downregulation of genes involved in photosynthesis and cell cycle progression. These results highlight the existence of evolutionary conserved defense responses to pathogens throughout the green plant lineage, suggesting that they were probably present in the common ancestors of land plants. Moreover, several genes acquired by horizontal transfer from prokaryotes and fungi, and a high number of P. patens-specific orphan genes were differentially expressed during B. cinerea infection, suggesting that they are important players in the moss immune response.
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Affiliation(s)
- Guillermo Reboledo
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Astri D Agorio
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Lucía Vignale
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | | | - Inés Ponce De León
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay.
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Chen L, Xiao J, Song Y, Li Y, Liu J, Cai H, Wang HB, Liu B. The Zygotic Division Regulator ZAR1 Plays a Negative Role in Defense Against Botrytis cinerea in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2021; 12:736560. [PMID: 34764967 PMCID: PMC8575783 DOI: 10.3389/fpls.2021.736560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/29/2021] [Indexed: 06/13/2023]
Abstract
A phosphorylation/dephosphorylation cycle at tyrosine 428 of CHITIN ELICITOR RECEPTOR KINASE 1 (CERK1) plays an essential role in chitin triggered immunity in Arabidopsis thaliana. In this study, we used a differential peptide pull-down (PPD) assay to identify factors that could participate downstream of this cycle. We identified ZYGOTIC ARREST 1 (ZAR1) and showed that it interacts with CERK1 specifically when the tyrosine 428 (Y428) residue of CERK1 is dephosphorylated. ZAR1 was originally characterized as an integrator for calmodulin and G-protein signals to regulate zygotic division in Arabidopsis. Our current results established that ZAR1 also negatively contributed to defense against the fungus Botrytis cinerea and played a redundant role with its homolog ZAR2 in this process. The zar1-3 zar2-1 double mutant exhibited stronger resistance to B. cinerea compared with zar1-3 single mutant, zar2-1 single mutant, and wild-type plants. Moreover, the inducible expression of numerous defense response genes upon B. cinerea infection was increased in the zar1-3zar2-1 double mutant, consistent with a repressive role for ZAR proteins in the defense response. Therefore, our findings provided insight into the function of ZAR1 in multiple defenses and developmental regulation pathways.
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Affiliation(s)
- Lijuan Chen
- Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jiahui Xiao
- Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuxiao Song
- Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - You Li
- Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jun Liu
- Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Huiren Cai
- Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Hong-Bin Wang
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Bing Liu
- Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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48
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Development of Molecular Markers Associated with Resistance to Gray Mold Disease in Onion (Allium cepa L.) through RAPD-PCR and Transcriptome Analysis. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7110436] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Onions (Allium cepa L.) are one of the most consumed vegetable crops worldwide and are damaged by several fungal diseases in the field or during storage. Gray mold disease caused by the necrotrophic pathogens Botrytis cinerea and Botrytis squamosa is a disease that reduces the productivity and storage life in onions. However, it is difficult to control gray mold disease in onions by using physical and chemical methods. Breeding resistant onions against gray mold disease can reduce the damage caused by pathogens, reduce the labor required for control, and reduce environmental pollution caused by fungicides. However, onions have a large genome size (16Gb), making them difficult to analyze, and have a biennial cycle, resulting in a very long breeding period. Therefore, in this study, markers were developed to shorten the onion breeding period. First, random amplified polymorphic DNA (RAPD) was performed to confirm the genetic relationship between the gray mold disease-resistant and -susceptible lines through a dendrogram. In addition, the sequence characterized amplified region (SCAR)-OPAN1 marker to select resistant lines was developed using a polymorphic RAPD fragment. Second, the RNA-seq of the gray mold-resistant and -susceptible onion lines were analyzed using NGS technology. Using the RNA-seq results and DEG and GO analyses were performed, and the variants, such as SNPs and indels, were analyzed to develop a selectable marker for the resistant line. This study developed the SNP-3 HRM marker for selecting gray mold disease-resistant lines by using the SNPs present in the aldo-keto reductase (AKR) gene with high expression levels in these lines. The SCAR-OPAN1 and SNP-3 HRM markers developed in this study could be used to select gray mold disease-resistant onions in breeding programs to reduce the damage caused by gray mold disease.
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Experimental Design for Time-Series RNA-Seq Analysis of Gene Expression and Alternative Splicing. Methods Mol Biol 2021. [PMID: 34674176 DOI: 10.1007/978-1-0716-1912-4_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2023]
Abstract
RNA-sequencing (RNA-seq) is currently the method of choice for analysis of differential gene expression. To fully exploit the wealth of data generated from genome-wide transcriptomic approaches, the initial design of the experiment is of paramount importance. Biological rhythms in nature are pervasive and are driven by endogenous gene networks collectively known as circadian clocks. Measuring circadian gene expression requires time-course experiments which take into account time-of-day factors influencing variability in expression levels. We describe here an approach for characterizing diurnal changes in expression and alternative splicing for plants undergoing cooling. The method uses inexpensive everyday laboratory equipment and utilizes an RNA-seq application (3D RNA-seq) that can handle complex experimental designs and requires little or no prior bioinformatics expertise.
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Coexpression of Fungal Cell Wall-Modifying Enzymes Reveals Their Additive Impact on Arabidopsis Resistance to the Fungal Pathogen, Botrytis cinerea. BIOLOGY 2021; 10:biology10101070. [PMID: 34681168 PMCID: PMC8533531 DOI: 10.3390/biology10101070] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 01/04/2023]
Abstract
Simple Summary In the present study, we created transgenic Arabidopsis plants overexpressing two fungal acetylesterases and a fungal feruloylesterase that acts on cell wall polysaccharides and studied their possible complementary additive effects on host defense reactions against the fungal pathogen, Botrytis cinerea. Our results showed that the Arabidopsis plants overexpressing two acetylesterases together contributed significantly higher resistance to B. cinerea in comparison with single protein expression. Conversely, coexpression of either of the acetyl esterases together with feruloylesterase compensates the latter’s negative impact on plant resistance. The results also provided evidence that combinatorial coexpression of some cell wall polysaccharide-modifying enzymes might exert an additive effect on plant immune response by constitutively priming plant defense pathways even before pathogen invasion. These findings have potential uses in protecting valuable crops against pathogens. Abstract The plant cell wall (CW) is an outer cell skeleton that plays an important role in plant growth and protection against both biotic and abiotic stresses. Signals and molecules produced during host–pathogen interactions have been proven to be involved in plant stress responses initiating signal pathways. Based on our previous research findings, the present study explored the possibility of additively or synergistically increasing plant stress resistance by stacking beneficial genes. In order to prove our hypothesis, we generated transgenic Arabidopsis plants constitutively overexpressing three different Aspergillus nidulans CW-modifying enzymes: a xylan acetylesterase, a rhamnogalacturonan acetylesterase and a feruloylesterase. The two acetylesterases were expressed either together or in combination with the feruloylesterase to study the effect of CW polysaccharide deacetylation and deferuloylation on Arabidopsis defense reactions against a fungal pathogen, Botrytis cinerea. The transgenic Arabidopsis plants expressing two acetylesterases together showed higher CW deacetylation and increased resistance to B. cinerea in comparison to wild-type (WT) Col-0 and plants expressing single acetylesterases. While the expression of feruloylesterase alone compromised plant resistance, coexpression of feruloylesterase together with either one of the two acetylesterases restored plant resistance to the pathogen. These CW modifications induced several defense-related genes in uninfected healthy plants, confirming their impact on plant resistance. These results demonstrated that coexpression of complementary CW-modifying enzymes in different combinations have an additive effect on plant stress response by constitutively priming the plant defense pathways. These findings might be useful for generating valuable crops with higher protections against biotic stresses.
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