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Fernandes P, Pimentel D, Ramiro RS, Silva MDC, Fevereiro P, Costa RL. Dual transcriptomic analysis reveals early induced Castanea defense-related genes and Phytophthora cinnamomi effectors. FRONTIERS IN PLANT SCIENCE 2024; 15:1439380. [PMID: 39188543 PMCID: PMC11345161 DOI: 10.3389/fpls.2024.1439380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 07/05/2024] [Indexed: 08/28/2024]
Abstract
Phytophthora cinnamomi Rands devastates forest species worldwide, causing significant ecological and economic impacts. The European chestnut (Castanea sativa) is susceptible to this hemibiotrophic oomycete, whereas the Asian chestnuts (Castanea crenata and Castanea mollissima) are resistant and have been successfully used as resistance donors in breeding programs. The molecular mechanisms underlying the different disease outcomes among chestnut species are a key foundation for developing science-based control strategies. However, these are still poorly understood. Dual RNA sequencing was performed in C. sativa and C. crenata roots inoculated with P. cinnamomi. The studied time points represent the pathogen's hemibiotrophic lifestyle previously described at the cellular level. Phytophthora cinnamomi expressed several genes related to pathogenicity in both chestnut species, such as cell wall-degrading enzymes, host nutrient uptake transporters, and effectors. However, the expression of effectors related to the modulation of host programmed cell death (elicitins and NLPs) and sporulation-related genes was higher in the susceptible chestnut. After pathogen inoculation, 1,556 and 488 genes were differentially expressed by C. crenata and C. sativa, respectively. The most significant transcriptional changes occur at 2 h after inoculation (hai) in C. sativa and 48 hai in C. crenata. Nevertheless, C. crenata induced more defense-related genes, indicating that the resistant response to P. cinnamomi is controlled by multiple loci, including several pattern recognition receptors, genes involved in the phenylpropanoid, salicylic acid and ethylene/jasmonic acid pathways, and antifungal genes. Importantly, these results validate previously observed cellular responses for C. crenata. Collectively, this study provides a comprehensive time-resolved description of the chestnut-P. cinnamomi dynamic, revealing new insights into susceptible and resistant host responses and important pathogen strategies involved in disease development.
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Affiliation(s)
- Patrícia Fernandes
- Department of Environmental Biology, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States
| | - Diana Pimentel
- InnovPlantProtect Collaborative Laboratory, Elvas, Portugal
| | | | - Maria do Céu Silva
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
- Linking Landscape, Environment, Agriculture and Food, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Pedro Fevereiro
- InnovPlantProtect Collaborative Laboratory, Elvas, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB, Green-It Unit), Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Rita Lourenço Costa
- Instituto Nacional de Investigação Agrária e Veterinária I.P., Oeiras, Portugal
- Centro de Estudos Florestais, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
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2
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Safdar A, He F, Shen D, Hamid MI, Khan SA, Tahir HAS, Dou D. PcLRR-RK3, an LRR receptor kinase is required for growth and in-planta infection processes in Phytophthora capsici. Mycology 2024; 15:471-484. [PMID: 39247892 PMCID: PMC11376283 DOI: 10.1080/21501203.2024.2305720] [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: 08/29/2023] [Accepted: 01/10/2024] [Indexed: 09/10/2024] Open
Abstract
Receptor protein kinases (RPKs) critically provide the basic infrastructure to sense, perceive, and conduct the signalling events at the cell surface of organisms. The importance of LRR-RLKs has been well studied in plants, but much less information has been reported in oomycetes. In this work, we have silenced the PcLRR-RK3 and characterised its functional importance in Phytophthora capsici. PcLRR-RK3 was predicted to encode signal peptides, leucine-rich repeats, transmembrane, and kinase domains. PcLRR-RK3-silenced transformants showed impaired colony growth, decreased deformed sporangia, and reduced zoospores count. The mycelium of silenced transformants did not penetrate within the host tissues and showed defects in the pathogenicity of P. capsici. Interestingly, gene silencing also weakens the ability of zoospores germination and penetration into host tissues and fails to produce necrotic lesions. Furthermore, PcLRR-RK3 localisation was found to be the plasma membrane of the cell. Altogether, our results revealed that PcLRR-RK3 was required for the regulation of vegetative growth, zoospores penetration, and establishment into host leaf tissues.
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Affiliation(s)
- Asma Safdar
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Department of Plant Pathology, College of Agriculture, University of Sargodha, Sargodha, Pakistan
| | - Feng He
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Danyu Shen
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Muhammad Imran Hamid
- Department of Plant Pathology, College of Agriculture, University of Sargodha, Sargodha, Pakistan
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Sajid Aleem Khan
- Department of Plant Pathology, University of Agriculture, Faisalabad, Pakistan
| | - Hafiz Abdul Samad Tahir
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Daolong Dou
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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3
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Situ J, Xi P, Lin L, Huang W, Song Y, Jiang Z, Kong G. Signal and regulatory mechanisms involved in spore development of Phytophthora and Peronophythora. Front Microbiol 2022; 13:984672. [PMID: 36160220 PMCID: PMC9500583 DOI: 10.3389/fmicb.2022.984672] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/23/2022] [Indexed: 11/13/2022] Open
Abstract
Oomycetes cause hundreds of destructive plant diseases, threatening agricultural production and food security. These fungus-like eukaryotes show multiple sporulation pattern including the production of sporangium, zoospore, chlamydospore and oospore, which are critical for their survival, dispersal and infection on hosts. Recently, genomic and genetic technologies have greatly promoted the study of molecular mechanism of sporulation in the genus Phytophthora and Peronophythora. In this paper, we characterize the types of asexual and sexual spores and review latest progress of these two genera. We summarize the genes encoding G protein, mitogen-activated protein kinase (MAPK) cascade, transcription factors, RNA-binding protein, autophagy-related proteins and so on, which function in the processes of sporangium production and cleavage, zoospore behaviors and oospore formation. Meanwhile, various molecular, chemical and electrical stimuli in zoospore behaviors are also discussed. Finally, with the molecular mechanism of sporulation in Phytophthora and Peronophythora is gradually being revealed, we propose some thoughts for the further research and provide the alternative strategy for plant protection against phytopathogenic oomycetes.
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Affiliation(s)
- Junjian Situ
- Department of Plant Pathology, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Pinggen Xi
- Department of Plant Pathology, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Long Lin
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Weixiong Huang
- Department of Plant Pathology, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Yu Song
- Department of Plant Pathology, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Zide Jiang
- Department of Plant Pathology, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Guanghui Kong
- Department of Plant Pathology, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
- *Correspondence: Guanghui Kong,
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Balotf S, Wilson R, Tegg RS, Nichols DS, Wilson CR. In Planta Transcriptome and Proteome Profiles of Spongospora subterranea in Resistant and Susceptible Host Environments Illuminates Regulatory Principles Underlying Host-Pathogen Interaction. BIOLOGY 2021; 10:biology10090840. [PMID: 34571717 PMCID: PMC8471823 DOI: 10.3390/biology10090840] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 01/13/2023]
Abstract
Simple Summary Infections of potato tubers and roots by Spongospora subterranea result in powdery scab and root diseases. Losses due to infections with S. subterranea are substantial in most potato-growing regions of the world with no fully effective treatments available. Understanding the gene regulation of pathogens in their host is dependent on multidimensional datasets. In this study, we profiled the transcriptome and proteome of S. subterranea within the susceptible and resistant host. Enzyme activity and nucleic acid metabolism appear to be important to the virulence of S. subterranea. Our results provide a good resource for future functional studies of powdery scab and might be useful in S. subterranea inoculum management. Abstract Spongospora subterranea is an obligate biotrophic pathogen, causing substantial economic loss to potato industries globally. Currently, there are no fully effective management strategies for the control of potato diseases caused by S. subterranea. To further our understanding of S. subterranea biology during infection, we characterized the transcriptome and proteome of the pathogen during the invasion of roots of a susceptible and a resistant potato cultivar. A total of 7650 transcripts from S. subterranea were identified in the transcriptome analysis in which 1377 transcripts were differentially expressed between two cultivars. In proteome analysis, we identified 117 proteins with 42 proteins significantly changed in comparisons between resistant and susceptible cultivars. The functional annotation of transcriptome data indicated that the gene ontology terms related to the transportation and actin processes were induced in the resistant cultivar. The downregulation of enzyme activity and nucleic acid metabolism in the resistant cultivar suggests a probable influence of these processes in the virulence of S. subterranea. The protein analysis results indicated that the majority of differentially expressed proteins were related to the metabolic processes and transporter activity. The present study provides a comprehensive molecular insight into the multiple layers of gene regulation that contribute to S. subterranea infection and development in planta and illuminates the role of host immunity in affecting pathogen responses.
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Affiliation(s)
- Sadegh Balotf
- Tasmanian Institute of Agriculture, New Town Research Laboratories, University of Tasmania, New Town, TAS 7008, Australia; (S.B.); (R.S.T.)
| | - Richard Wilson
- Central Science Laboratory, University of Tasmania, Hobart, TAS 7001, Australia; (R.W.); (D.S.N.)
| | - Robert S. Tegg
- Tasmanian Institute of Agriculture, New Town Research Laboratories, University of Tasmania, New Town, TAS 7008, Australia; (S.B.); (R.S.T.)
| | - David S. Nichols
- Central Science Laboratory, University of Tasmania, Hobart, TAS 7001, Australia; (R.W.); (D.S.N.)
| | - Calum R. Wilson
- Tasmanian Institute of Agriculture, New Town Research Laboratories, University of Tasmania, New Town, TAS 7008, Australia; (S.B.); (R.S.T.)
- Correspondence:
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Sharma S, Sundaresha S, Bhardwaj V. Biotechnological approaches in management of oomycetes diseases. 3 Biotech 2021; 11:274. [PMID: 34040923 DOI: 10.1007/s13205-021-02810-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/24/2021] [Indexed: 11/26/2022] Open
Abstract
Plant pathogenic oomycetes cause significant impact on agriculture and, therefore, their management is utmost important. Though conventional methods to combat these pathogens (resistance breeding and use of fungicides) are available but these are limited by the availability of resistant cultivars due to evolution of new pathogenic races, development of resistance in the pathogens against agrochemicals and their potential hazardous effects on the environment and human health. This has fuelled a continual search for novel and alternate strategies for management of phytopathogens. The recent advances in oomycetes genome (Phytophthora infestans, P. ramorum, P. sojae, Pythium ultimum, Albugo candida etc.) would further help in understanding host-pathogen interactions essentially needed for designing effective management strategies. In the present communication the novel and alternate strategies for the management of oomycetes diseases are discussed.
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Affiliation(s)
- Sanjeev Sharma
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171001 India
| | - S Sundaresha
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171001 India
| | - Vinay Bhardwaj
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171001 India
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6
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RNA Interference Strategies for Future Management of Plant Pathogenic Fungi: Prospects and Challenges. PLANTS 2021; 10:plants10040650. [PMID: 33805521 PMCID: PMC8067263 DOI: 10.3390/plants10040650] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 12/11/2022]
Abstract
Plant pathogenic fungi are the largest group of disease-causing agents on crop plants and represent a persistent and significant threat to agriculture worldwide. Conventional approaches based on the use of pesticides raise social concern for the impact on the environment and human health and alternative control methods are urgently needed. The rapid improvement and extensive implementation of RNA interference (RNAi) technology for various model and non-model organisms has provided the initial framework to adapt this post-transcriptional gene silencing technology for the management of fungal pathogens. Recent studies showed that the exogenous application of double-stranded RNA (dsRNA) molecules on plants targeting fungal growth and virulence-related genes provided disease attenuation of pathogens like Botrytis cinerea, Sclerotinia sclerotiorum and Fusarium graminearum in different hosts. Such results highlight that the exogenous RNAi holds great potential for RNAi-mediated plant pathogenic fungal disease control. Production of dsRNA can be possible by using either in-vitro or in-vivo synthesis. In this review, we describe exogenous RNAi involved in plant pathogenic fungi and discuss dsRNA production, formulation, and RNAi delivery methods. Potential challenges that are faced while developing a RNAi strategy for fungal pathogens, such as off-target and epigenetic effects, with their possible solutions are also discussed.
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7
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Howard JM, Beech PL, Callahan DL. Detection of Endogenous Phosphatidylinositol 4,5-bisphosphate in Phytophthora cinnamomi. Lipids 2018; 53:835-839. [PMID: 30334270 DOI: 10.1002/lipd.12093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 09/17/2018] [Accepted: 09/19/2018] [Indexed: 11/07/2022]
Abstract
Plant diseases caused by Phytophthora species are serious threats to agriculture and the natural environment. Genome sequencing has revealed the lack of a gene for canonical phospholipase C (PLC), an enzyme that was hitherto thought to be ubiquitous in eukaryotes. PLC acts in the hydrolysis of phosphatidylinositol 4,5-bisphosphate (PtdIns-4,5-P2 ), a membrane-bound phospholipid critical for signal initiation in many cellular processes. Previous studies have not provided evidence of endogenous PtdIns-4,5-P2 in Phytophthora and, in the absence of canonical PLC, argued for redundancy or loss in the PLC pathway in Phytophthora. Using liquid chromatography mass spectrometry, we have detected endogenous PtdIns-4,5-P2 in Phytophthora cinnamomi. This is the first identification of the phospholipid in the genus, and is significant because it indicates that the signal transduction pathway of the PLC product, inositol 1,4,5-trisphosphate (IP3 ), may have been retained in Phytophthora incorporating an as-yet unidentified homolog or analog of PLC.
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Affiliation(s)
- Jeff M Howard
- School of Life and Environmental Sciences, Deakin University, 221 Burwood Highway, Burwood, VIC, 3125, Australia
| | - Peter L Beech
- School of Life and Environmental Sciences, Deakin University, 221 Burwood Highway, Burwood, VIC, 3125, Australia
| | - Damien L Callahan
- School of Life and Environmental Sciences, Deakin University, 221 Burwood Highway, Burwood, VIC, 3125, Australia
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8
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An LRR receptor kinase regulates growth, development and pathogenesis in Phytophthora capsici. Microbiol Res 2017; 198:8-15. [DOI: 10.1016/j.micres.2017.01.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 11/27/2016] [Accepted: 01/23/2017] [Indexed: 11/20/2022]
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9
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Zhu C, Yang X, Lv R, Li Z, Ding X, Tyler BM, Zhang X. Phytophthora capsici homologue of the cell cycle regulator SDA1 is required for sporangial morphology, mycelial growth and plant infection. MOLECULAR PLANT PATHOLOGY 2016; 17:369-87. [PMID: 26095317 PMCID: PMC6638425 DOI: 10.1111/mpp.12285] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
SDA1 encodes a highly conserved protein that is widely distributed in eukaryotic organisms. SDA1 is essential for cell cycle progression and organization of the actin cytoskeleton in yeasts and humans. In this study, we identified a Phytophthora capsici orthologue of yeast SDA1, named PcSDA1. In P. capsici, PcSDA1 is strongly expressed in three asexual developmental states (mycelium, sporangia and germinating cysts), as well as late in infection. Silencing or overexpression of PcSDA1 in P. capsici transformants affected the growth of hyphae and sporangiophores, sporangial development, cyst germination and zoospore release. Phalloidin staining confirmed that PcSDA1 is required for organization of the actin cytoskeleton. Moreover, 4',6-diamidino-2-phenylindole (DAPI) staining and PcSDA1-green fluorescent protein (GFP) fusions revealed that PcSDA1 is involved in the regulation of nuclear distribution in hyphae and sporangia. Both silenced and overexpression transformants showed severely diminished virulence. Thus, our results suggest that PcSDA1 plays a similar role in the regulation of the actin cytoskeleton and nuclear division in this filamentous organism as in non-filamentous yeasts and human cells.
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Affiliation(s)
- Chunyuan Zhu
- Department of Plant Pathology, Shandong Agricultural University, 61, Daizong Street, Tai'an, Shandong, 271018, China
| | - Xiaoyan Yang
- Department of Plant Pathology, Shandong Agricultural University, 61, Daizong Street, Tai'an, Shandong, 271018, China
| | - Rongfei Lv
- Department of Plant Pathology, Shandong Agricultural University, 61, Daizong Street, Tai'an, Shandong, 271018, China
| | - Zhuang Li
- Department of Plant Pathology, Shandong Agricultural University, 61, Daizong Street, Tai'an, Shandong, 271018, China
| | - Xiaomeng Ding
- Department of Plant Pathology, Shandong Agricultural University, 61, Daizong Street, Tai'an, Shandong, 271018, China
| | - Brett M Tyler
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA
| | - Xiuguo Zhang
- Department of Plant Pathology, Shandong Agricultural University, 61, Daizong Street, Tai'an, Shandong, 271018, China
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10
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Saraiva M, de Bruijn I, Grenville-Briggs L, McLaggan D, Willems A, Bulone V, van West P. Functional characterization of a tyrosinase gene from the oomycete Saprolegnia parasitica by RNAi silencing. Fungal Biol 2014; 118:621-9. [PMID: 25088076 PMCID: PMC4152626 DOI: 10.1016/j.funbio.2014.01.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 01/17/2014] [Accepted: 01/24/2014] [Indexed: 02/04/2023]
Abstract
Here we describe the first application of transient gene silencing in Saprolegnia parasitica, a pathogenic oomycete that infects a wide range of fish, amphibians, and crustaceans. A gene encoding a putative tyrosinase from S. parasitica, SpTyr, was selected to investigate the suitability of RNA-interference (RNAi) to functionally characterize genes of this economically important pathogen. Tyrosinase is a mono-oxygenase enzyme that catalyses the O-hydroxylation of monophenols and subsequent oxidation of O-diphenols to quinines. These enzymes are widely distributed in nature, and are involved in the melanin biosynthesis. Gene silencing was obtained by delivering in vitro synthesized SpTyr dsRNA into protoplasts. Expression analysis, tyrosinase activity measurements, and melanin content analysis confirmed silencing in individual lines. Silencing of SpTyr resulted in a decrease of tyrosinase activity between 38 % and 60 %, dependent on the level of SpTyr-expression achieved. The SpTyr-silenced lines displayed less pigmentation in developing sporangia and occasionally an altered morphology. Moreover, developing sporangia from individual silenced lines possessed a less electron dense cell wall when compared to control lines, treated with GFP-dsRNA. In conclusion, the tyrosinase gene of S. parasitica is required for melanin formation and transient gene silencing can be used to functionally characterize genes in S. parasitica. Successful transient gene silencing in Saprolegnia parasitica through RNAi. Silencing a tyrosinase in S. parasitica results in reduced melanin formation. Silencing a tyrosinase in S. parasitica results in aberrant sporangia formation.
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Affiliation(s)
- Marcia Saraiva
- Aberdeen Oomycete Laboratory, University of Aberdeen, Foresterhill, AB25 2ZD Aberdeen, UK
| | - Irene de Bruijn
- Aberdeen Oomycete Laboratory, University of Aberdeen, Foresterhill, AB25 2ZD Aberdeen, UK
| | - Laura Grenville-Briggs
- Aberdeen Oomycete Laboratory, University of Aberdeen, Foresterhill, AB25 2ZD Aberdeen, UK; Division of Glycoscience, School of Biotechnology, KTH - Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Debbie McLaggan
- Aberdeen Oomycete Laboratory, University of Aberdeen, Foresterhill, AB25 2ZD Aberdeen, UK
| | - Ariane Willems
- Aberdeen Oomycete Laboratory, University of Aberdeen, Foresterhill, AB25 2ZD Aberdeen, UK
| | - Vincent Bulone
- Division of Glycoscience, School of Biotechnology, KTH - Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Pieter van West
- Aberdeen Oomycete Laboratory, University of Aberdeen, Foresterhill, AB25 2ZD Aberdeen, UK.
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Fahlgren N, Bollmann SR, Kasschau KD, Cuperus JT, Press CM, Sullivan CM, Chapman EJ, Hoyer JS, Gilbert KB, Grünwald NJ, Carrington JC. Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs. PLoS One 2013; 8:e77181. [PMID: 24204767 PMCID: PMC3804510 DOI: 10.1371/journal.pone.0077181] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Accepted: 09/06/2013] [Indexed: 12/21/2022] Open
Abstract
In eukaryotes, RNA silencing pathways utilize 20-30-nucleotide small RNAs to regulate gene expression, specify and maintain chromatin structure, and repress viruses and mobile genetic elements. RNA silencing was likely present in the common ancestor of modern eukaryotes, but most research has focused on plant and animal RNA silencing systems. Phytophthora species belong to a phylogenetically distinct group of economically important plant pathogens that cause billions of dollars in yield losses annually as well as ecologically devastating outbreaks. We analyzed the small RNA-generating components of the genomes of P. infestans, P. sojae and P. ramorum using bioinformatics, genetic, phylogenetic and high-throughput sequencing-based methods. Each species produces two distinct populations of small RNAs that are predominantly 21- or 25-nucleotides long. The 25-nucleotide small RNAs were primarily derived from loci encoding transposable elements and we propose that these small RNAs define a pathway of short-interfering RNAs that silence repetitive genetic elements. The 21-nucleotide small RNAs were primarily derived from inverted repeats, including a novel microRNA family that is conserved among the three species, and several gene families, including Crinkler effectors and type III fibronectins. The Phytophthora microRNA is predicted to target a family of amino acid/auxin permeases, and we propose that 21-nucleotide small RNAs function at the post-transcriptional level. The functional significance of microRNA-guided regulation of amino acid/auxin permeases and the association of 21-nucleotide small RNAs with Crinkler effectors remains unclear, but this work provides a framework for testing the role of small RNAs in Phytophthora biology and pathogenesis in future work.
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Affiliation(s)
- Noah Fahlgren
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Stephanie R. Bollmann
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, Oregon, United States of America
| | - Kristin D. Kasschau
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Josh T. Cuperus
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Caroline M. Press
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, Oregon, United States of America
| | - Christopher M. Sullivan
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Elisabeth J. Chapman
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - J. Steen Hoyer
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Kerrigan B. Gilbert
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Niklaus J. Grünwald
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, Oregon, United States of America
- * E-mail: (NJG); (JCC)
| | - James C. Carrington
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail: (NJG); (JCC)
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Zhang M, Meng Y, Wang Q, Liu D, Quan J, Hardham AR, Shan W. PnPMA1, an atypical plasma membrane H(+)-ATPase, is required for zoospore development in Phytophthora parasitica. Fungal Biol 2012; 116:1013-23. [PMID: 22954344 DOI: 10.1016/j.funbio.2012.07.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 07/15/2012] [Accepted: 07/17/2012] [Indexed: 10/28/2022]
Abstract
Biflagellate zoospores are the major infective agents that initiate plant infection for most Phytophthora species. Once released from sporangia, zoospores swim and use a number of tactic responses to actively target host tissues. However, the molecular mechanisms controlling zoospore development and behaviour are largely unknown. Previous studies have shown that the PnPMA1 gene is highly expressed in zoospores and germinated cysts of Phytophthora parasitica and encodes an atypical plasma membrane H(+)-ATPase containing an insertion of ~155 amino acid residues at the C terminus. Using topology determination we now show that the C-terminal insertion loop in the PnPMA1 protein is located in the extracellular space. To elucidate the biological function of PnPMA1, PnPMA1-deficient transformants were generated by homology-dependent gene silencing and were confirmed by quantitative PCR of PnPMA1 transcripts and detection of associated small interfering RNAs (siRNAs). High levels of PnPMA1 silencing in P. parasitica resulted in production of nonflagellate and large aberrant zoospores, rapid transition from zoospores to cysts, and a decreased germination rate of cysts. These results indicate that PnPMA1 plays important roles in zoospore development.
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Affiliation(s)
- Meixiang Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
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13
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Nunes CC, Dean RA. Host-induced gene silencing: a tool for understanding fungal host interaction and for developing novel disease control strategies. MOLECULAR PLANT PATHOLOGY 2012; 13:519-29. [PMID: 22111693 PMCID: PMC6638818 DOI: 10.1111/j.1364-3703.2011.00766.x] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Recent discoveries regarding small RNAs and the mechanisms of gene silencing are providing new opportunities to explore fungal pathogen-host interactions and potential strategies for novel disease control. Plant pathogenic fungi are a constant and major threat to global food security; they represent the largest group of disease-causing agents on crop plants on the planet. An initial understanding of RNA silencing mechanisms and small RNAs was derived from model fungi. Now, new knowledge with practical implications for RNA silencing is beginning to emerge from the study of plant-fungus interactions. Recent studies have shown that the expression of silencing constructs in plants designed on fungal genes can specifically silence their targets in invading pathogenic fungi, such as Fusarium verticillioides, Blumeria graminis and Puccinia striiformis f.sp. tritici. Here, we highlight the important general aspects of RNA silencing mechanisms and emphasize recent findings from plant pathogenic fungi. Strategies to employ RNA silencing to investigate the basis of fungal pathogenesis are discussed. Finally, we address important aspects for the development of fungal-derived resistance through the expression of silencing constructs in host plants as a powerful strategy to control fungal disease.
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Affiliation(s)
- Cristiano C Nunes
- Department of Plant Pathology, Fungal Genomics Laboratory, Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC 27606, USA
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Zhao W, Yang X, Dong S, Sheng Y, Wang Y, Zheng X. Transient silencing mediated by in vitro synthesized double-stranded RNA indicates that PsCdc14 is required for sporangial development in a soybean root rot pathogen. SCIENCE CHINA. LIFE SCIENCES 2011; 54:1143-50. [PMID: 22227907 DOI: 10.1007/s11427-011-4250-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2011] [Accepted: 10/18/2011] [Indexed: 11/27/2022]
Abstract
In many eukaryotic organisms, Cdc14 phosphatase regulates multiple biological events during anaphase and is essential for mitosis. It has been shown that Cdc14 is required for sporulation in the potato blight pathogen Phytophthora infestans; however, the role that the Cdc14 homolog (PsCdc14) plays in the soil-borne soybean root rot pathogen P. sojae remains ambiguous. PsCdc14 is highly expressed in sporulation, zoospore, and cyst life stages, but not in vegetative mycelia and infection stages, suggesting that it contributes to asexual reproduction and thus the spread of the disease. Double-stranded RNA (dsRNA) mediates gene silencing, a post-transcriptional and highly conserved process in eukaryotes, involving specific gene silencing through degradation of target mRNA. We combined in vitro dsRNA synthesis and a polyethylene glycol-mediated transformation system to construct a dsRNA-mediated transient gene silencing system; and then performed a functional analysis of PsCdc14 in P. sojae. PsCdc14 mRNA was dramatically reduced in transformants after protoplasts were exposed in in vitro synthesized PsCdc14 dsRNA, resulting in low sporangial production and abnormal development in P. sojae silencing lines. Furthermore, dsRNA-mediated transient gene silencing could enable elucidation of P. sojae rapid gene function, facilitating our understanding of the development and pathogenicity mechanisms of this oomycete fungus.
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Affiliation(s)
- Wei Zhao
- College of Plant Protection, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China
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15
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Zhang M, Wang Q, Xu K, Meng Y, Quan J, Shan W. Production of dsRNA sequences in the host plant is not sufficient to initiate gene silencing in the colonizing oomycete pathogen Phytophthora parasitica. PLoS One 2011; 6:e28114. [PMID: 22140518 PMCID: PMC3223229 DOI: 10.1371/journal.pone.0028114] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 11/01/2011] [Indexed: 11/19/2022] Open
Abstract
Species of the oomycete genus Phytophthora are destructive pathogens, causing extensive losses in agricultural crops and natural ecosystems. A potential disease control approach is the application of RNA silencing technology which has proven to be effective in improving plant resistance against a wide range of pests including parasitic plants, nematodes, insects and fungi. In this study, we tested the potential application of RNA silencing in improving plant disease resistance against oomycete pathogens. The endogenous P. parasitica gene PnPMA1 and the reporter gene GFP were used to evaluate the potential application of host induced gene silencing (HIGS). The GFP-expressing P. parasitica efficiently colonized Arabidopsis thaliana lines stably expressing GFP dsRNA and showed no obvious decrease in GFP signal intensity. Quantitative RT-PCR analyses showed no significant reductions in the abundance of GFP and PnPMA1 transcripts in P. parasitica during colonization of A. thaliana lines stably expressing GFP and PnPMA1 dsRNAs, respectively. Neither GFP siRNAs nor PnPMA1 siRNAs produced by transgenic plants were detected in P. parasitica re-isolated from infected tissues by Northern blot analyses. Phenotypic characterization of zoospores released from infected plant roots expressing PnPMA1 dsRNA showed no motility changes compared with those from wild-type plants. Similar results were obtained by analysis of zoospores released from sporulating hyphae of P. parasitica re-isolated from PnPMA1 dsRNA-expressing plant roots. Thus, the ectopic expression of dsRNA sequences in the host plant is not sufficient to initiate silencing of homologous genes in the colonizing oomycete pathogen, and this may be due to a number of different reasons including the absence of genetic machinery required for uptake of silencing signals in particular dsRNAs which are essential for environmental RNA silencing.
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Affiliation(s)
- Meixiang Zhang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Qinhu Wang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Ke Xu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Yuling Meng
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Junli Quan
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Weixing Shan
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
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Vetukuri RR, Avrova AO, Grenville-Briggs LJ, Van West P, Söderbom F, Savenkov EI, Whisson SC, Dixelius C. Evidence for involvement of Dicer-like, Argonaute and histone deacetylase proteins in gene silencing in Phytophthora infestans. MOLECULAR PLANT PATHOLOGY 2011; 12:772-85. [PMID: 21726377 PMCID: PMC6640358 DOI: 10.1111/j.1364-3703.2011.00710.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Gene silencing may have a direct or indirect impact on many biological processes in eukaryotic cells, and is a useful tool for the determination of the roles of specific genes. In this article, we report silencing in Phytophthora infestans, an oomycete pathogen of potato and tomato. Gene silencing is known to occur in P. infestans, but its genetic basis has yet to be determined. Genes encoding the major components of the RNA interference (RNAi) pathway, Dicer-like (Pidcl1), Argonaute (Piago1-5) and RNA-directed RNA polymerase (Pirdr1), were identified in the P. infestans genome by comparative genomics, together with families of other genes potentially involved in gene silencing, such as histone deacetylases, histone methyltransferases, DEAD helicases, chromodomain proteins and a class 1 RNaseIII. Real-time reverse transcription-polymerase chain reaction demonstrated transcript accumulation for all candidate genes throughout the asexual lifecycle and plant infection, but at different levels of mRNA abundance. A functional assay was developed in which silencing of the sporulation-associated Picdc14 gene was released by the treatment of protoplasts with in vitro-synthesized double-stranded RNAs homologous to Pidcl1, Piago1/2 and histone deacetylase Pihda1. These results suggest that the components of gene silencing, namely Dicer-like, Argonaute and histone deacetylase, are functional in P. infestans. Our data demonstrate that this oomycete possesses canonical gene silencing pathways similar to those of other eukaryotes.
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Affiliation(s)
- Ramesh R Vetukuri
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, SLU, 750 07 Uppsala, Sweden.
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Franklin S, Zhang MJ, Chen H, Paulsson AK, Mitchell-Jordan SA, Li Y, Ping P, Vondriska TM. Specialized compartments of cardiac nuclei exhibit distinct proteomic anatomy. Mol Cell Proteomics 2010; 10:M110.000703. [PMID: 20807835 DOI: 10.1074/mcp.m110.000703] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
As host to the genome, the nucleus plays a critical role as modulator of cellular phenotype. To understand the totality of proteins that regulate this organelle, we used proteomics to characterize the components of the cardiac nucleus. Following purification, cardiac nuclei were fractionated into biologically relevant fractions including acid-soluble proteins, chromatin-bound molecules and nucleoplasmic proteins. These distinct subproteomes were characterized by liquid chromatography-tandem MS. We report a cardiac nuclear proteome of 1048 proteins--only 146 of which are shared between the distinct subcompartments of this organelle. Analysis of genomic loci encoding these molecules gives insights into local hotspots for nuclear protein regulation. High mass accuracy and complementary analytical techniques allowed the discrimination of distinct protein isoforms, including 54 total histone variants, 17 of which were distinguished by unique peptide sequences and four of which have never been detected at the protein level. These studies are the first unbiased analysis of cardiac nuclear subcompartments and provide a foundation for exploration of this organelle's proteomes during disease.
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Affiliation(s)
- Sarah Franklin
- Department of Anesthesiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
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18
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Li A, Wang Y, Tao K, Dong S, Huang Q, Dai T, Zheng X, Wang Y. PsSAK1, a stress-activated MAP kinase of Phytophthora sojae, is required for zoospore viability and infection of soybean. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2010; 23:1022-31. [PMID: 20615113 DOI: 10.1094/mpmi-23-8-1022] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Mitogen-activated protein kinase (MAPK) pathways are universal and evolutionarily conserved signal transduction modules in all eukaryotic cells. In this study, PsSAK1, which encodes a stress-activated MAPK of Phytophthora sojae, was identified. PsSAK1 is highly conserved in oomycetes, and it represents a novel group of MAPK due to its pleckstrin homology domain. Reverse-transcription polymerase chain reaction analysis showed that PsSAK1 expression was upregulated in zoospores and cysts and during early infection. In addition, its expression was induced by osmotic and oxidative stress mediated by NaCl and H(2)O(2), respectively. To elucidate the function, the expression of PsSAK1 was silenced using stable transformation of P. sojae. The silencing of PsSAK1 did not impair hyphal growth, sporulation, or oospore production but severely hindered zoospore development, in that the silenced strains showed quicker encystment and a lower germination ratio than the wild type. PsSAK1-silenced mutants produced much longer germ tubes and could not colonize either wounded or unwounded soybean leaves. Our results indicate that PsSAK1 is an important regulator of zoospore development and pathogenicity in P. sojae.
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Affiliation(s)
- Aining Li
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
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19
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Wang Y, Dou D, Wang X, Li A, Sheng Y, Hua C, Cheng B, Chen X, Zheng X, Wang Y. The PsCZF1 gene encoding a C2H2 zinc finger protein is required for growth, development and pathogenesis in Phytophthora sojae. Microb Pathog 2009; 47:78-86. [PMID: 19447167 DOI: 10.1016/j.micpath.2009.04.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2008] [Revised: 04/09/2009] [Accepted: 04/29/2009] [Indexed: 01/01/2023]
Abstract
The C(2)H(2) zinc finger proteins form one of the largest families of transcriptional regulators in eukaryotes. We identified a Phytophthora sojae C(2)H(2) zinc finger (PsCZF1), that is highly conserved in sequenced oomycete pathogens. In transformants of P. sojae containing the PsCZF1 promoter fused to the beta-glucuronidase (GUS) reporter gene, GUS activity was highly induced in the P. sojae oospore stage and upregulated after infection. To elucidate the function of PsCZF1, its expression was silenced by introducing anti-sense constructs into P sojae. PsCZF1-silenced transformants did not exhibit altered cell size or morphology of sporangia and hyphae; however, hyphal growth rate was reduced by around 50% in the mutants. PsCZF1-deficient mutants were also impaired in production of oospores, swimming zoospores and germinating cysts, indicating that the gene is involved in various stages of the life cycle. Furthermore, we found that PsCZF1-deficient mutants lost virulence on host soybean cultivars. Our results suggest that this oomycete-specific C(2)H(2)-type zinc finger protein plays an important role in growth, development, and pathogenesis; therefore, PsCZF1 might be an attractive oomycete-specific target for chemical fungicide screening.
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Affiliation(s)
- Yonglin Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
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Gene expression changes during asexual sporulation by the late blight agent Phytophthora infestans occur in discrete temporal stages. Mol Genet Genomics 2008; 281:193-206. [DOI: 10.1007/s00438-008-0407-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2008] [Accepted: 11/15/2008] [Indexed: 10/21/2022]
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21
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Avrova AO, Boevink PC, Young V, Grenville-Briggs LJ, van West P, Birch PRJ, Whisson SC. A novel Phytophthora infestans haustorium-specific membrane protein is required for infection of potato. Cell Microbiol 2008; 10:2271-84. [PMID: 18637942 DOI: 10.1111/j.1462-5822.2008.01206.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phytophthora infestans causes late-blight, a devastating and re-emerging disease of potato crops. During the early stages of infection, P. infestans differentiates infection-specific structures such as appressoria for host epidermal cell penetration, followed by infection vesicles, and haustoria to establish a biotrophic phase of interaction. Here we report the cloning, from a suppression subtractive hybridization library, of a P. infestans gene called Pihmp1 encoding a putative glycosylated protein with four closely spaced trans-membrane helices. Pihmp1 expression is upregulated in germinating cysts and in germinating cysts with appressoria, and significantly upregulated throughout infection of potato. Transient gene silencing of Pihmp1 led to loss of pathogenicity and indicated involvement of this gene in the penetration and early infection processes of P. infestans. P. infestans transformants expressing a Pihmp1::monomeric red fluorescent protein (mRFP) fusion demonstrated that Pihmp1 was translated in germinating sporangia, germinating cysts and appressoria, accumulated in the appressorium, and was located at the haustorial membrane during infection. Furthermore, we discovered that haustorial structures are formed over a 3 h period, maturing for up to 12 h, and that their formation is initiated only at sites on the surface of intercellular hyphae where Pihmp1::mRFP is localized. We propose that Pihmp1 is an integral membrane protein that provides physical stability to the plasma membrane of P. infestans infection structures. We have provided the first evidence that the surface of oomycete haustoria possess proteins specific to these biotrophic structures, and that formation of biotrophic structures (infection vesicles and haustoria) is essential to successful host colonization by P. infestans.
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Affiliation(s)
- Anna O Avrova
- Plant Pathology Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD25DA, UK.
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