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Myo-D-inositol Trisphosphate Signalling in Oomycetes. Microorganisms 2022; 10:microorganisms10112157. [DOI: 10.3390/microorganisms10112157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/21/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022] Open
Abstract
Oomycetes are pathogens of plants and animals, which cause billions of dollars of global losses to the agriculture, aquaculture and forestry sectors each year. These organisms superficially resemble fungi, with an archetype being Phytophthora infestans, the cause of late blight of tomatoes and potatoes. Comparison of the physiology of oomycetes with that of other organisms, such as plants and animals, may provide new routes to selectively combat these pathogens. In most eukaryotes, myo-inositol 1,4,5 trisphosphate is a key second messenger that links extracellular stimuli to increases in cytoplasmic Ca2+, to regulate cellular activities. In the work presented in this study, investigation of the molecular components of myo-inositol 1,4,5 trisphosphate signaling in oomycetes has unveiled similarities and differences with that in other eukaryotes. Most striking is that several oomycete species lack detectable phosphoinositide-selective phospholipase C homologues, the enzyme family that generates this second messenger, but still possess relatives of myo-inositol 1,4,5 trisphosphate-gated Ca2+-channels.
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2
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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: 3] [Impact Index Per Article: 1.5] [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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3
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Nekrakalaya B, Arefian M, Kotimoole CN, Krishna RM, Palliyath GK, Najar MA, Behera SK, Kasaragod S, Santhappan P, Hegde V, Prasad TSK. Towards Phytopathogen Diagnostics? Coconut Bud Rot Pathogen Phytophthora palmivora Mycelial Proteome Analysis Informs Genome Annotation. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:189-203. [PMID: 35353641 DOI: 10.1089/omi.2021.0208] [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: 06/14/2023]
Abstract
Planetary agriculture stands to benefit immensely from phytopathogen diagnostics, which would enable early detection of pathogens with harmful effects on crops. For example, Phytophthora palmivora is one of the most destructive phytopathogens affecting many economically important tropical crops such as coconut. P. palmivora causes diseases in over 200 host plants, and notably, the bud rot disease in coconut and oil palm, which is often lethal because it is usually detected at advanced stages of infection. Limited availability of large-scale omics datasets for P. palmivora is an important barrier for progress toward phytopathogen diagnostics. We report here the mycelial proteome of P. palmivora using high-resolution mass spectrometry analysis. We identified 8073 proteins in the mycelium. Gene Ontology-based functional classification of detected proteins revealed 4884, 4981, and 3044 proteins, respectively, with roles in biological processes, molecular functions, and cellular components. Proteins such as P-loop, NTPase, and WD40 domains with key roles in signal transduction pathways were identified. KEGG pathway analysis annotated 2467 proteins to various signaling pathways, such as phosphatidylinositol, Ca2+, and mitogen-activated protein kinase, and autophagy and cell cycle. These molecular substrates might possess vital roles in filamentous growth, sporangia formation, degradation of damaged cellular content, and recycling of nutrients in P. palmivora. This large-scale proteomics data and analyses pave the way for new insights on biology, genome annotation, and vegetative growth of the important plant pathogen P. palmivora. They also can help accelerate research on future phytopathogen diagnostics and preventive interventions.
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Affiliation(s)
- Bhagya Nekrakalaya
- Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Mohammad Arefian
- Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Chinmaya Narayana Kotimoole
- Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | | | | | - Mohammad Altaf Najar
- Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Santosh Kumar Behera
- Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Sandeep Kasaragod
- Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | | | - Vinayaka Hegde
- ICAR-Central Plantation Crops Research Institute, Kasaragod, India
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Sundaresha S, Bairwa A, Tomar M, Kumar R, Venkatasalam EP, Sagar V, Bhardwaj V, Sharma S. In Vitro Method for Synthesis of Large-Scale dsRNA Molecule as a Novel Plant Protection Strategy. Methods Mol Biol 2022; 2408:211-226. [PMID: 35325425 DOI: 10.1007/978-1-0716-1875-2_14] [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] [Indexed: 06/14/2023]
Abstract
Double-stranded RNA (dsRNAs) molecules are the precursors and effective triggers of RNAi in most organisms. RNAi can be induced by the direct introduction of dsRNAs in plants, fungi, insects, and nematodes. Until now RNAi is usually established by transformation of the plant with a construct that produces hairpin RNAs. Alternatively, advances in RNA biology demonstrated efficiently the in vitro method of large-scale synthesis of dsRNA molecule. Here we describe the de novo synthesis of dsRNA molecule targeting the specific gene of interest for functional application. Selection of off-target effective siRNA regions, flanking of T7 promoter sequences, T7 polymerase reaction, and maintenance of the stability of dsRNA molecules are the main criteria of this method to obtain pure and effective yield for functional applications. IPTG (isopropyl-β-D-thiogalactopyranoside) induced, T7 express E. coli cells, could be used for large scale synthesis of dsRNA molecule are also described in this method.
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Affiliation(s)
| | - Aarti Bairwa
- Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Maharishi Tomar
- Central Potato Research Institute, Shimla, Himachal Pradesh, India
- ICAR-Indian Grassland and Fodder Research Institute, Jhansi, UP, India
| | - Ravinder Kumar
- Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - E P Venkatasalam
- Central Potato Research Institute, Shimla, Himachal Pradesh, India
- Central Potato Research Station, Udhagamandalam, India
| | - Vinay Sagar
- Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Vinay Bhardwaj
- Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Sanjeev Sharma
- Central Potato Research Institute, Shimla, Himachal Pradesh, India
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Yuan XL, Zhang CS, Kong FY, Zhang ZF, Wang FL. Genome Analysis of Phytophthora nicotianae JM01 Provides Insights into Its Pathogenicity Mechanisms. PLANTS 2021; 10:plants10081620. [PMID: 34451665 PMCID: PMC8400872 DOI: 10.3390/plants10081620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/01/2021] [Accepted: 08/04/2021] [Indexed: 12/21/2022]
Abstract
Phytophthora nicotianae is a widely distributed plant pathogen that can cause serious disease and cause significant economic losses to various crops, including tomatoes, tobacco, onions, and strawberries. To understand its pathogenic mechanisms and explore strategies for controlling diseases caused by this pathogen, we sequenced and analyzed the whole genome of Ph. nicotianae JM01. The Ph. nicotianae JM01 genome was assembled using a combination of approaches including shotgun sequencing, single-molecule sequencing, and the Hi-C technique. The assembled Ph. nicotianae JM01 genome is about 95.32 Mb, with contig and scaffold N50 54.23 kb and 113.15 kb, respectively. The average GC content of the whole-genome is about 49.02%, encoding 23,275 genes. In addition, we identified 19.15% of interspersed elements and 0.95% of tandem elements in the whole genome. A genome-wide phylogenetic tree indicated that Phytophthora diverged from Pythium approximately 156.32 Ma. Meanwhile, we found that 252 and 285 gene families showed expansion and contraction in Phytophthora when compared to gene families in Pythium. To determine the pathogenic mechanisms Ph. nicotianae JM01, we analyzed a suite of proteins involved in plant-pathogen interactions. The results revealed that gene duplication contributed to the expansion of Cell Wall Degrading Enzymes (CWDEs) such as glycoside hydrolases, and effectors such as Arg-Xaa-Leu-Arg (RXLR) effectors. In addition, transient expression was performed on Nicotiana benthamiana by infiltrating with Agrobacterium tumefaciens cells containing a cysteine-rich (SCR) protein. The results indicated that SCR can cause symptoms of hypersensitive response. Moreover, we also conducted comparative genome analysis among four Ph. nicotianae genomes. The completion of the Ph. nicotianae JM01 genome can not only help us understand its genomic characteristics, but also help us discover genes involved in infection and then help us understand its pathogenic mechanisms.
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Affiliation(s)
- Xiao-Long Yuan
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (X.-L.Y.); (F.-Y.K.); (Z.-F.Z.)
- Special Crops Research Center of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Cheng-Sheng Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (X.-L.Y.); (F.-Y.K.); (Z.-F.Z.)
- Special Crops Research Center of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
- Correspondence: (C.-S.Z.); (F.-L.W.); Tel.: +86-532-88701035 (C.-S.Z. & F.-L.W.)
| | - Fan-Yu Kong
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (X.-L.Y.); (F.-Y.K.); (Z.-F.Z.)
- Special Crops Research Center of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Zhong-Feng Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (X.-L.Y.); (F.-Y.K.); (Z.-F.Z.)
- Special Crops Research Center of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Feng-Long Wang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (X.-L.Y.); (F.-Y.K.); (Z.-F.Z.)
- Special Crops Research Center of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
- Correspondence: (C.-S.Z.); (F.-L.W.); Tel.: +86-532-88701035 (C.-S.Z. & F.-L.W.)
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Estevez-Fregoso E, Farfán-García ED, García-Coronel IH, Martínez-Herrera E, Alatorre A, Scorei RI, Soriano-Ursúa MA. Effects of boron-containing compounds in the fungal kingdom. J Trace Elem Med Biol 2021; 65:126714. [PMID: 33453473 DOI: 10.1016/j.jtemb.2021.126714] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/10/2020] [Accepted: 01/04/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND The number of known boron-containing compounds (BCCs) is increasing due to their identification in nature and innovative synthesis procedures. Their effects on the fungal kingdom are interesting, and some of their mechanisms of action have recently been elucidated. METHODS In this review, scientific reports from relevant chemistry and biomedical databases were collected and analyzed. RESULTS It is notable that several BCC actions in fungi induce social and economic benefits for humans. In fact, boric acid was traditionally used for multiple purposes, but some novel synthetic BCCs are effective antifungal agents, particularly in their action against pathogen species, and some were recently approved for use in humans. Moreover, most reports testing BCCs in fungal species suggest a limiting effect of these compounds on some vital reactions. CONCLUSIONS New BCCs have been synthesized and tested for innovative technological and biomedical emerging applications, and new interest is developing for discovering new strategic compounds that can act as environmental or wood protectors, as well as antimycotic agents that let us improve food acquisition and control some human infections.
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Affiliation(s)
- Elizabeth Estevez-Fregoso
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, 11340, Mexico
| | - Eunice D Farfán-García
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, 11340, Mexico.
| | - Itzel H García-Coronel
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, 11340, Mexico; Unidad de Investigación, Hospital Regional de Alta Especialidad Ixtapaluca, Carretera Federal México-Puebla km 34.5, C.P. 56530, Ixtapaluca, State of Mexico, Mexico
| | - Erick Martínez-Herrera
- Unidad de Investigación, Hospital Regional de Alta Especialidad Ixtapaluca, Carretera Federal México-Puebla km 34.5, C.P. 56530, Ixtapaluca, State of Mexico, Mexico
| | - Alberto Alatorre
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, 11340, Mexico
| | - Romulus I Scorei
- BioBoron Research Institute, Dunarii 31B Street, 207465, Podari, Romania
| | - Marvin A Soriano-Ursúa
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, 11340, Mexico.
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7
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Tani S, Nishio N, Kai K, Hagiwara D, Ogata Y, Tojo M, Sumitani JI, Judelson HS, Kawaguchi T. Chemical genetic approach using β-rubromycin reveals that a RIO kinase-like protein is involved in morphological development in Phytophthora infestans. Sci Rep 2020; 10:22326. [PMID: 33339950 PMCID: PMC7749174 DOI: 10.1038/s41598-020-79326-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 12/08/2020] [Indexed: 11/10/2022] Open
Abstract
To characterize the molecular mechanisms underlying life-stage transitions in Phytophthora infestans, we initiated a chemical genetics approach by screening for a stage-specific inhibitor of morphological development from microbial culture extracts prepared mostly from actinomycetes from soil in Japan. Of the more than 700 extracts, one consistently inhibited Ph. infestans cyst germination. Purification and identification of the active compound by ESI–MS, 1H-NMR, and 13C-NMR identified β-rubromycin as the inhibitor of cyst germination (IC50 = 19.8 μg/L); β-rubromycin did not inhibit growth on rye media, sporangium formation, zoospore release, cyst formation, or appressorium formation in Ph. infestans. Further analyses revealed that β-rubromycin inhibited the germination of cysts and oospores in Pythium aphanidermatum. A chemical genetic approach revealed that β-rubromycin stimulated the expression of RIO kinase-like gene (PITG_04584) by 60-fold in Ph. infestans. Genetic analyses revealed that PITG_04584, which lacks close non-oomycete relatives, was involved in zoosporogenesis, cyst germination, and appressorium formation in Ph. infestans. These data imply that further functional analyses of PITG_04584 may contribute to new methods to suppress diseases caused by oomycetes.
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Affiliation(s)
- Shuji Tani
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, 599-8531, Japan.
| | - Naotaka Nishio
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, 599-8531, Japan
| | - Kenji Kai
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, 599-8531, Japan
| | - Daisuke Hagiwara
- Medical Mycology Research Center, Chiba University, Chiba, Japan.,Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yoshiyuki Ogata
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, 599-8531, Japan
| | - Motoaki Tojo
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, 599-8531, Japan
| | - Jun-Ichi Sumitani
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, 599-8531, Japan
| | - Howard S Judelson
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, USA
| | - Takashi Kawaguchi
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, 599-8531, Japan
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Zheng L, Prestwich BD, Harrison PT, Mackrill JJ. Polycystic Kidney Disease Ryanodine Receptor Domain (PKDRR) Proteins in Oomycetes. Pathogens 2020; 9:pathogens9070577. [PMID: 32708691 PMCID: PMC7399828 DOI: 10.3390/pathogens9070577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 11/16/2022] Open
Abstract
In eukaryotes, two sources of Ca2+ are accessed to allow rapid changes in the cytosolic levels of this second messenger: the extracellular medium and intracellular Ca2+ stores, such as the endoplasmic reticulum. One class of channel that permits Ca2+ entry is the transient receptor potential (TRP) superfamily, including the polycystic kidney disease (PKD) proteins, or polycystins. Channels that release Ca2+ from intracellular stores include the inositol 1,4,5-trisphosphate/ryanodine receptor (ITPR/RyR) superfamily. Here, we characterise a family of proteins that are only encoded by oomycete genomes, that we have named PKDRR, since they share domains with both PKD and RyR channels. We provide evidence that these proteins belong to the TRP superfamily and are distinct from the ITPR/RyR superfamily in terms of their evolutionary relationships, protein domain architectures and predicted ion channel structures. We also demonstrate that a hypothetical PKDRR protein from Phytophthora infestans is produced by this organism, is located in the cell-surface membrane and forms multimeric protein complexes. Efforts to functionally characterise this protein in a heterologous expression system were unsuccessful but support a cell-surface localisation. These PKDRR proteins represent potential targets for the development of new "fungicides", since they are of a distinctive structure that is only found in oomycetes and not in any other cellular organisms.
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Affiliation(s)
- Limian Zheng
- Department of Physiology, School of Medicine, University College Cork, T12 XF62 Cork, Ireland; (L.Z.); (P.T.H.)
| | - Barbara Doyle Prestwich
- School of Biological, Earth and Environmental Sciences, University College Cork, T23 TK30 Cork, Ireland;
| | - Patrick T. Harrison
- Department of Physiology, School of Medicine, University College Cork, T12 XF62 Cork, Ireland; (L.Z.); (P.T.H.)
| | - John J. Mackrill
- Department of Physiology, School of Medicine, University College Cork, T12 XF62 Cork, Ireland; (L.Z.); (P.T.H.)
- Correspondence:
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Dellero Y, Maës C, Morabito C, Schuler M, Bournaud C, Aiese Cigliano R, Maréchal E, Amato A, Rébeillé F. The zoospores of the thraustochytridAurantiochytrium limacinum: Transcriptional reprogramming and lipid metabolism associated to their specific functions. Environ Microbiol 2020; 22:1901-1916. [DOI: 10.1111/1462-2920.14978] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 03/04/2020] [Accepted: 03/05/2020] [Indexed: 12/26/2022]
Affiliation(s)
- Younès Dellero
- Laboratoire de Physiologie Cellulaire VégétaleUniversité Grenoble Alpes, CEA, CNRS, INRA, IRIG‐LPCV 38054 Grenoble Cedex 9 France
| | - Cécile Maës
- Laboratoire de Physiologie Cellulaire VégétaleUniversité Grenoble Alpes, CEA, CNRS, INRA, IRIG‐LPCV 38054 Grenoble Cedex 9 France
| | - Christian Morabito
- INRAE Metagenopolis Unit, Domaine de Vilvert Bât. 325. 78 352 Jouy‐en‐Josas France
| | - Martin Schuler
- Laboratoire de Physiologie Cellulaire VégétaleUniversité Grenoble Alpes, CEA, CNRS, INRA, IRIG‐LPCV 38054 Grenoble Cedex 9 France
| | - Caroline Bournaud
- Laboratoire de Physiologie Cellulaire VégétaleUniversité Grenoble Alpes, CEA, CNRS, INRA, IRIG‐LPCV 38054 Grenoble Cedex 9 France
| | - Riccardo Aiese Cigliano
- Sequentia Biotech Campus UAB, Edifici Eureka Av. de Can Domènech s/n 08193 Bellaterra (Cerdanyola del Vallès) Spain
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire VégétaleUniversité Grenoble Alpes, CEA, CNRS, INRA, IRIG‐LPCV 38054 Grenoble Cedex 9 France
| | - Alberto Amato
- Laboratoire de Physiologie Cellulaire VégétaleUniversité Grenoble Alpes, CEA, CNRS, INRA, IRIG‐LPCV 38054 Grenoble Cedex 9 France
| | - Fabrice Rébeillé
- Laboratoire de Physiologie Cellulaire VégétaleUniversité Grenoble Alpes, CEA, CNRS, INRA, IRIG‐LPCV 38054 Grenoble Cedex 9 France
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10
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Leesutthiphonchai W, Judelson HS. Phytophthora infestans Sporangia Produced in Artificial Media and Plant Lesions Have Subtly Divergent Transcription Profiles but Equivalent Infection Potential and Aggressiveness. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1077-1087. [PMID: 30908943 DOI: 10.1094/mpmi-12-18-0349-ta] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Sporangia of the potato late blight agent Phytophthora infestans are often used in studies of pathogen biology and plant responses to infection. Investigations of spore biology can be challenging in oomycetes because their sporangia are physiologically active and change in response to environmental factors and aging. Whether sporangia from artificial media and plant lesions are functionally equivalent has been a topic of debate. To address these issues, we compared the transcriptomes and infection ability of sporangia from rye-sucrose media, potato and tomato leaflets, and potato tubers. Small differences were observed between the mRNA profiles of sporangia from all sources, including variation in genes encoding metabolic enzymes, cell-wall-degrading enzymes, and ABC transporters. Small differences in sporangia age also resulted in variation in the transcriptome. Taking care to use sporangia of similar maturity, we observed that those sourced from media or plant lesions had similar rates of zoospore release and cyst germination. There were also no differences in infection rates or aggressiveness on leaflets, based on single-spore inoculation assays. Such results are discordant with those of a recent publication in this journal. Nevertheless, we conclude that sporangia from plant and media cultures are functionally similar and emphasize the importance of using "best practices" in experiments with sporangia to obtain reliable results.
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Affiliation(s)
| | - Howard S Judelson
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, U.S.A
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11
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Fry WE, Patev SP, Myers KL, Bao K, Fei Z. Phytophthora infestans Sporangia Produced in Culture and on Tomato Leaflet Lesions Show Marked Differences in Indirect Germination Rates, Aggressiveness, and Global Transcription Profiles. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:515-526. [PMID: 30480479 DOI: 10.1094/mpmi-09-18-0255-ta] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Sporangia of Phytophthora infestans from pure cultures on agar plates are typically used in lab studies, whereas sporangia from leaflet lesions drive natural infections and epidemics. Multiple assays were performed to determine if sporangia from these two sources are equivalent. Sporangia from plate cultures showed much lower rates of indirect germination and produced much less disease in field and moist-chamber tests. This difference in aggressiveness was observed whether the sporangia had been previously incubated at 4°C (to induce indirect germination) or at 21°C (to prevent indirect germination). Furthermore, lesions caused by sporangia from plates produced much less sporulation. RNA-Seq analysis revealed that thousands of the >17,000 P. infestans genes with a RPKM (reads per kilobase of exon model per million mapped reads) >1 were differentially expressed in sporangia obtained from plate cultures of two independent field isolates compared with sporangia of those isolates from leaflet lesions. Among the significant differentially expressed genes (DEGs), putative RxLR effectors were overrepresented, with almost half of the 355 effectors with RPKM >1 being up- or downregulated. DEGs of both isolates include nine flagellar-associated genes, and all were down-regulated in plate sporangia. Ten elicitin genes were also detected as DEGs in both isolates, and nine (including INF1) were up-regulated in plate sporangia. These results corroborate previous observations that sporangia produced from plates and leaflets sometimes yield different experimental results and suggest hypotheses for potential mechanisms. We caution that use of plate sporangia in assays may not always produce results reflective of natural infections and epidemics.
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Affiliation(s)
- William E Fry
- 1 Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
| | - Sean P Patev
- 1 Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
| | - Kevin L Myers
- 1 Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
| | - Kan Bao
- 2 Boyce Thompson Institute, Cornell University
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12
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Asatryan A, Boussiba S, Zarka A. Stimulation and Isolation of Paraphysoderma sedebokerense (Blastocladiomycota) Propagules and Their Infection Capacity Toward Their Host Under Different Physiological and Environmental Conditions. Front Cell Infect Microbiol 2019; 9:72. [PMID: 30972306 PMCID: PMC6446968 DOI: 10.3389/fcimb.2019.00072] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 03/05/2019] [Indexed: 11/15/2022] Open
Abstract
Paraphysoderma sedebokerense (P. sedebokerense) (Blastocladiomycota) is a facultative pathogenic chytrid that causes irreversible damage to some green microalgae. Specific attacks leading to culture collapse under different conditions have only been described in the lucrative microalga Haematococcus pluvialis (H. pluvialis), while generating biomass for ketocarotenoid astaxanthin production, both indoors and outdoors. In order to manage the infection, parasite propagules (zoospores/amoeboid swarmers), the initiators of the disease, must be studied. Until now, no report on isolated P. sedebokerense propagules has been published. Here, we report on a reproducible method for the stimulation of P. sedebokerense propagule release and their isolation from fungal cultures in synthetic media and infected H. pluvialis cultures, and we further studied their development under different conditions. The isolated propagules featured different spore morphotypes, with coatless spherical spores and amoeboid swarmers being the most dominant in the first pulse of propagule release in both cultures. Inoculating the pure propagules with the host, in both the presence and absence of nitrogen, resulted in epidemic development in both green and red cells; however, in red cells, the epidemic developed more quickly in the presence of nitrogen. Biologically non-active autoclaved host cells were used to distinguish the initial stages of recognition from more progressive stages of the epidemics; on these cells, propagules encysted but did not develop further. These results prove the existence of heat-stable recognition sites on the host and an obligatory signal transduction from the host to support fungal cyst development. The propagule isolation method described herein is a breakthrough that will enable researchers to study the influence of different substances on the propagules, specifically as the initiators of the infection, and thus assist in the management of chytrid diseases. Moreover, it will be useful in studying host-parasite recognition and, therefore, will increase our understanding of the multiple chytrid infections found in nature.
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Affiliation(s)
- Armine Asatryan
- Microalgal Biotechnology Laboratory, French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Sammy Boussiba
- Microalgal Biotechnology Laboratory, French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Aliza Zarka
- Microalgal Biotechnology Laboratory, French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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13
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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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14
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Kagda MS, Vu AL, Ah-Fong AMV, Judelson HS. Phosphagen kinase function in flagellated spores of the oomycete Phytophthora infestans integrates transcriptional regulation, metabolic dynamics and protein retargeting. Mol Microbiol 2018; 110:296-308. [PMID: 30137656 DOI: 10.1111/mmi.14108] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2018] [Indexed: 11/30/2022]
Abstract
Flagellated spores play important roles in the infection of plants and animals by many eukaryotic microbes. The oomycete Phytophthora infestans, which causes potato blight, expresses two phosphagen kinases (PKs). These enzymes store energy in taurocyamine, and are hypothesized to resolve spatial and temporal imbalances between rates of ATP creation and use in zoospores. A dimeric PK is found at low levels in vegetative mycelia, but high levels in ungerminated sporangia and zoospores. In contrast, a monomeric PK protein is at similar levels in all tissues, although is transcribed primarily in mycelia. Subcellular localization studies indicate that the monomeric PK is mitochondrial. In contrast, the dimeric PK is cytoplasmic in mycelia and sporangia but is retargeted to flagellar axonemes during zoosporogenesis. This supports a model in which PKs shuttle energy from mitochondria to and through flagella. Metabolite analysis indicates that deployment of the flagellar PK is coordinated with a large increase in taurocyamine, synthesized by sporulation-induced enzymes that were lost during the evolution of zoospore-lacking oomycetes. Thus, PK function is enabled by coordination of the transcriptional, metabolic and protein targeting machinery during the life cycle. Since plants lack PKs, the enzymes may be useful targets for inhibitors of oomycete plant pathogens.
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Affiliation(s)
- Meenakshi S Kagda
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Andrea L Vu
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Audrey M V Ah-Fong
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Howard S Judelson
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
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15
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Wang Y, Jin X, Rui H, Liu T, Hou J. Cold Temperature Regulation of Zoospore Release in Phytophthora sojae: The Genes That Differentially Expressed by Cold Temperature. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418060133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Hardham AR, Blackman LM. Phytophthora cinnamomi. MOLECULAR PLANT PATHOLOGY 2018; 19:260-285. [PMID: 28519717 PMCID: PMC6637996 DOI: 10.1111/mpp.12568] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 04/20/2017] [Accepted: 05/11/2017] [Indexed: 05/12/2023]
Abstract
Phytophthora cinnamomi is one of the most devastating plant pathogens in the world. It infects close to 5000 species of plants, including many of importance in agriculture, forestry and horticulture. The inadvertent introduction of P. cinnamomi into natural ecosystems, including a number of recognized Global Biodiversity Hotspots, has had disastrous consequences for the environment and the biodiversity of flora and fauna. The genus Phytophthora belongs to the Class Oomycetes, a group of fungus-like organisms that initiate plant disease through the production of motile zoospores. Disease control is difficult in agricultural and forestry situations and even more challenging in natural ecosystems as a result of the scale of the problem and the limited range of effective chemical inhibitors. The development of sustainable control measures for the future management of P. cinnamomi requires a comprehensive understanding of the cellular and molecular basis of pathogen development and pathogenicity. The application of next-generation sequencing technologies to generate genomic and transcriptomic data promises to underpin a new era in P. cinnamomi research and discovery. The aim of this review is to integrate bioinformatic analyses of P. cinnamomi sequence data with current knowledge of the cellular and molecular basis of P. cinnamomi growth, development and plant infection. The goal is to provide a framework for future research by highlighting potential pathogenicity genes, shedding light on their possible functions and identifying suitable targets for future control measures. TAXONOMY Phytophthora cinnamomi Rands; Kingdom Chromista; Phylum Oomycota or Pseudofungi; Class Oomycetes; Order Peronosporales; Family Peronosporaceae; genus Phytophthora. HOST RANGE Infects about 5000 species of plants, including 4000 Australian native species. Host plants important for agriculture and forestry include avocado, chestnut, macadamia, oak, peach and pineapple. DISEASE SYMPTOMS A root pathogen which causes rotting of fine and fibrous roots, but which can also cause stem cankers. Root damage may inhibit water movement from roots to shoots, leading to dieback of young shoots. USEFUL WEBSITES: http://fungidb.org/fungidb/; http://genome.jgi.doe.gov/Phyci1/Phyci1.home.html; http://www.ncbi.nlm.nih.gov/assembly/GCA_001314365.1; http://www.ncbi.nlm.nih.gov/assembly/GCA_001314505.1.
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Affiliation(s)
- Adrienne R. Hardham
- Plant Science Division, Research School of Biology, College of Medicine, Biology and EnvironmentThe Australian National UniversityCanberraACT 2601Australia
| | - Leila M. Blackman
- Plant Science Division, Research School of Biology, College of Medicine, Biology and EnvironmentThe Australian National UniversityCanberraACT 2601Australia
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17
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Abstract
The eukaryotic microbes called oomycetes include many important saprophytes and pathogens, with the latter exhibiting necrotrophy, biotrophy, or obligate biotrophy. Understanding oomycete metabolism is fundamental to understanding these lifestyles. Genome mining and biochemical studies have shown that oomycetes, which belong to the kingdom Stramenopila, secrete suites of carbohydrate- and protein-degrading enzymes adapted to their environmental niches and produce unusual lipids and energy storage compounds. Despite having limited secondary metabolism, many oomycetes make chemicals for communicating within their species or with their hosts. Horizontal and endosymbiotic gene transfer events have diversified oomycete metabolism, resulting in biochemical pathways that often depart from standard textbook descriptions by amalgamating enzymes from multiple sources. Gene fusions and duplications have further shaped the composition and expression of the enzymes. Current research is helping us learn how oomycetes interact with host and environment, understand eukaryotic diversity and evolution, and identify targets for drugs and crop protection chemicals.
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Affiliation(s)
- Howard S Judelson
- Department of Plant Pathology and Microbiology, University of California, Riverside, California 92521;
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18
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Hwu FY, Lai MW, Liou RF. PpMID1 Plays a Role in the Asexual Development and Virulence of Phytophthora parasitica. Front Microbiol 2017; 8:610. [PMID: 28469602 PMCID: PMC5395580 DOI: 10.3389/fmicb.2017.00610] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 03/27/2017] [Indexed: 01/01/2023] Open
Abstract
Phytophthora parasitica is a notorious oomycete pathogen that causes severe disease in a wide variety of crop species. Infection of plants involves mainly its asexual life stage, including papillate sporangia and biflagellated zoospores, which are the primary dispersal and infection agents of this pathogen. Calcium signaling has been thought as the key regulator for sporangium formation and zoospore differentiation. However, not much is known about the molecular players involved in these processes. In Saccharomyces cerevisiae, mating pheromone-induced death 1 (MID1) encodes a component of a putative calcium channel. Here, we identified and characterized the function of PpMID1, an MID1 homolog from P. parasitica. The expression of PpMID1 was high in sporangia. Gene silencing of PpMID1 resulted in the formation of sporangia that lacked papilla and showed a tendency for direct germination. Notably, in response to cold shock to induce zoospore formation, these sporangia showed no sign of cytoplasmic cleavage and thereby failed to form zoospores. Nonetheless, the addition of CaCl2 or MgCl2 partially recovered the silenced sporangia phenotype, with the formation of papillate sporangia similar to those of the wild type and the release of zoospores upon cold shock. As well, virulence toward Nicotiana benthamiana was reduced in the PpMID1-silenced transformants. These results indicate a role of PpMID1 in the asexual development and virulence of P. parasitica.
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Affiliation(s)
- Fang-Yu Hwu
- Department of Plant Pathology and Microbiology, National Taiwan UniversityTaipei, Taiwan
| | - Ming-Wei Lai
- Department of Plant Pathology and Microbiology, National Taiwan UniversityTaipei, Taiwan
| | - Ruey-Fen Liou
- Department of Plant Pathology and Microbiology, National Taiwan UniversityTaipei, Taiwan
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19
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Ah-Fong AMV, Kim KS, Judelson HS. RNA-seq of life stages of the oomycete Phytophthora infestans reveals dynamic changes in metabolic, signal transduction, and pathogenesis genes and a major role for calcium signaling in development. BMC Genomics 2017; 18:198. [PMID: 28228125 PMCID: PMC5322657 DOI: 10.1186/s12864-017-3585-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 02/13/2017] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The oomycete Phytophthora infestans causes the devastating late blight diseases of potato and tomato. P. infestans uses spores for dissemination and infection, like many other filamentous eukaryotic plant pathogens. The expression of a subset of its genes during spore formation and germination were studied previously, but comprehensive genome-wide data have not been available. RESULTS RNA-seq was used to profile hyphae, sporangia, sporangia undergoing zoosporogenesis, motile zoospores, and germinated cysts of P. infestans. Parallel studies of two isolates generated robust expression calls for 16,000 of 17,797 predicted genes, with about 250 transcribed in one isolate but not the other. The largest changes occurred in the transition from hyphae to sporangia, when >4200 genes were up-regulated. More than 1350 of these were induced >100-fold, accounting for 26% of total mRNA. Genes encoding calcium-binding proteins, cation channels, signaling proteins, and flagellar proteins were over-represented in genes up-regulated in sporangia. Proteins associated with pathogenicity were transcribed in waves with subclasses induced during zoosporogenesis, in zoospores, or in germinated cysts. Genes involved in most metabolic pathways were down-regulated upon sporulation and reactivated during cyst germination, although there were exceptions such as DNA replication, where transcripts peaked in zoospores. Inhibitor studies indicated that the transcription of two-thirds of genes induced during zoosporogenesis relied on calcium signaling. A sporulation-induced protein kinase was shown to bind a constitutive Gβ-like protein, which contributed to fitness based on knock-down analysis. CONCLUSIONS Spore formation and germination involves the staged expression of a large subset of the transcriptome, commensurate with the importance of spores in the life cycle. A comparison of the RNA-seq results with the older microarray data indicated that information is now available for about twice the number of genes than before. Analyses based on function revealed dynamic changes in genes involved in pathogenicity, metabolism, and signaling, with diversity in expression observed within members of multigene families and between isolates. The effects of calcium signaling, a spore-induced protein kinase, and an interacting Gβ-like protein were also demonstrated experimentally. The results reveal aspects of oomycete biology that underly their success as pathogens and potential targets for crop protection chemicals.
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Affiliation(s)
- Audrey M. V. Ah-Fong
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521 USA
| | - Kyoung Su Kim
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521 USA
- Present address: Department of Applied Biology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Korea
| | - Howard S. Judelson
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521 USA
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20
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Zheng L, Mackrill JJ. Calcium Signaling in Oomycetes: An Evolutionary Perspective. Front Physiol 2016; 7:123. [PMID: 27092083 PMCID: PMC4820453 DOI: 10.3389/fphys.2016.00123] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/21/2016] [Indexed: 01/06/2023] Open
Abstract
Oomycetes are a family of eukaryotic microbes that superficially resemble fungi, but which are phylogenetically distinct from them. These organisms cause major global economic losses to agriculture and fisheries, with representative pathogens being Phytophthora infestans, the cause of late potato blight and Saprolegnia diclina, the instigator of “cotton molds” in fish. As in all eukaryotes, cytoplasmic Ca2+ is a key second messenger in oomycetes, regulating life-cycle transitions, controlling motility and chemotaxis and, in excess, leading to cell-death. Despite this, little is known about the molecular mechanisms regulating cytoplasmic Ca2+ concentrations in these organisms. Consequently, this review analyzed the presence of candidate calcium channels encoded within the nine oomycete genomes that are currently available. This revealed key differences between oomycetes and other eukaryotes, in particular the expansion and loss of different channel families, and the presence of a phylum-specific group of proteins, termed the polycystic kidney disease tandem ryanodine receptor domain (PKDRR) channels.
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Affiliation(s)
- Limian Zheng
- Department of Physiology, BioSciences Institute, University College Cork Cork, Ireland
| | - John J Mackrill
- Department of Physiology, BioSciences Institute, University College Cork Cork, Ireland
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21
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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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22
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Jahan SN, Åsman AKM, Corcoran P, Fogelqvist J, Vetukuri RR, Dixelius C. Plant-mediated gene silencing restricts growth of the potato late blight pathogen Phytophthora infestans. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:2785-94. [PMID: 25788734 PMCID: PMC4986879 DOI: 10.1093/jxb/erv094] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Phytophthora infestans is an oomycete that causes severe damage to potato, and is well known for its ability to evolve rapidly in order to overcome resistant potato varieties. An RNA silencing strategy was evaluated here to clarify if small interfering RNA homologous to selected genes in P. infestans could be targeted from the plant host to reduce the magnitude of the infection. As a proof-of-concept, a hairpin RNA (hp-RNA) construct using the GFP marker gene was designed and introduced in potato. At 72 hpi, a 55-fold reduction of the signal intensity of a corresponding GFP expressing P. infestans strain on leaf samples of transgenic plants, compared with wild-type potato, was detected. This suggests that an RNA interference construct in the potato host could be processed and target a transcript of the pathogen. Three genes important in the infection process of P. infestans, PiGPB1, PiCESA2, and PiPEC, together with PiGAPDH taking part in basic cell maintenance were subsequently tested using an analogous transgenic strategy. Out of these gene candidates, the hp-PiGPB1 targeting the G protein β-subunit (PiGPB1) important for pathogenicity resulted in most restricted disease progress. Further, Illumina sequencing of inoculated transgenic potato leaves revealed sRNAs of 24/25 nt size homologous to the PiGPB1 gene in the transgenic plants indicating post-transcriptional silencing of the target gene. The work demonstrates that a host-induced gene-silencing approach is functional against P. infestans but is highly dependent on target gene for a successful outcome. This finding broadens the arsenal of control strategies to this important plant disease.
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Affiliation(s)
- Sultana N Jahan
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, SE-75007 Uppsala, Sweden
| | - Anna K M Åsman
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, SE-75007 Uppsala, Sweden
| | - Pádraic Corcoran
- Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden
| | - Johan Fogelqvist
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, SE-75007 Uppsala, Sweden
| | - Ramesh R Vetukuri
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, SE-75007 Uppsala, Sweden
| | - Christina Dixelius
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, SE-75007 Uppsala, Sweden
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23
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Xiang Q, Judelson HS. Myb transcription factors and light regulate sporulation in the oomycete Phytophthora infestans. PLoS One 2014; 9:e92086. [PMID: 24704821 PMCID: PMC3976263 DOI: 10.1371/journal.pone.0092086] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 02/17/2014] [Indexed: 01/10/2023] Open
Abstract
Life cycle progression in eukaryotic microbes is often influenced by environment. In the oomycete Phytophthora infestans, which causes late blight on potato and tomato, sporangia have been reported to form mostly at night. By growing P. infestans under different light regimes at constant temperature and humidity, we show that light contributes to the natural pattern of sporulation by delaying sporulation until the following dark period. However, illumination does not permanently block sporulation or strongly affect the total number of sporangia that ultimately form. Based on measurements of sporulation-induced genes such as those encoding protein kinase Pks1 and Myb transcription factors Myb2R1 and Myb2R3, it appears that most spore-associated transcripts start to rise four to eight hours before sporangia appear. Their mRNA levels oscillate with the light/dark cycle and increase with the amount of sporangia. An exception to this pattern of expression is Myb2R4, which is induced several hours before the other genes and declines after cultures start to sporulate. Transformants over-expressing Myb2R4 produce twice the number of sporangia and ten-fold higher levels of Myb2R1 mRNA than wild-type, and chromatin immunoprecipitation showed that Myb2R4 binds the Myb2R1 promoter in vivo. Myb2R4 thus appears to be an early regulator of sporulation. We attempted to silence eight Myb genes by DNA-directed RNAi, but succeeded only with Myb2R3, which resulted in suppressed sporulation. Ectopic expression studies of seven Myb genes revealed that over-expression frequently impaired vegetative growth, and in the case of Myb3R6 interfered with sporangia dormancy. We observed that the degree of silencing induced by a hairpin construct was correlated with its copy number, and ectopic expression was often unstable due to epigenetic silencing and transgene excision.
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Affiliation(s)
- Qijun Xiang
- Department of Plant Pathology and Microbiology, University of California Riverside, Riverside, California, United States of America
| | - Howard S. Judelson
- Department of Plant Pathology and Microbiology, University of California Riverside, Riverside, California, United States of America
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24
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Ryanodine receptor calcium release channels: an evolutionary perspective. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 740:159-82. [PMID: 22453942 DOI: 10.1007/978-94-007-2888-2_7] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ryanodine receptors (RyRs), along with the related inositol 1,4,5-trisphosphate receptors (IP(3)Rs), mediate the release of Ca(2+) from intracellular organelles of eukaryotes. As discussed in other chapters, such increases in intracellular Ca(2+) levels act a fundamental second messenger, regulating a diverse array of cellular processes. For over two decades, it has been reported that vertebrates express multiple RYR genes, whereas non-vertebrate multicellular organisms possess a single homologue within their genomes. Recently, the existence of RyR-like channels in unicellular organisms has also been reported. This chapter exploits recent expansions in available genome data to generate an overview of the expression of RyR-like genes in organisms representing a broad range of viral, archaeal, bacterial and eukaryotic taxa. Analyses of the multidomain structures and phylogenetic relationships of these proteins has lead to a model in which, early during eukaryotic evolution, IP(3)R-like ancestral Ca(2+) release channels were converted to RyR proteins via the addition of promiscuous protein domains, possibly via horizontal gene transfer mechanisms.
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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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Maziero JMN, Maffia LA, Mizubuti ESG. Effects of Temperature on Events in the Infection Cycle of Two Clonal Lineages of Phytophthora infestans Causing Late Blight on Tomato and Potato in Brazil. PLANT DISEASE 2009; 93:459-466. [PMID: 30764133 DOI: 10.1094/pdis-93-5-0459] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In Brazil, US-1 and BR-1 clonal lineages of Phytophthora infestans are widely distributed throughout the major growing areas of tomato and potato, respectively. Quantitative information regarding the effects of temperature (10, 15, 22, and 27°C) on direct and indirect sporangia germination, incubation period (IP), latent period (LP), lesion area (LA), and sporulation (SP), as well as combined temperature and leaf wetness duration periods (6, 12, 18, and 24 h) on the number of lesions (NL) was obtained under controlled conditions on either detached leaflets or whole plants. The percentage of indirect germination was higher for BR-1 isolates than for US-1. The percentage of direct germination was higher for US-1 than for BR-1. The shortest IP and LP were recorded at 22°C for both lineages: 69.3 h and 93.3 h for US-1 isolates on detached tomato leaflets, and 44.0 h and 68 h for BR-1 isolates on detached potato leaflets, respectively. US-1 isolates did not sporulate at 10°C, and BR-1 isolates did not sporulate at 27°C. Isolates of both lineages induced the largest LA at 22°C. The NL was highest at 15°C for US-1 isolates on whole tomato plants, and at 10°C for BR-1 isolates on whole potato plants. The differential effects of temperature on US-1 and BR-1 suggest that current decision support systems initially developed for controlling US-1 in Brazil may now be inaccurate for controlling BR-1, and management strategies should be properly validated before being used.
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Affiliation(s)
- José Marcelo N Maziero
- Departamento de Fitopatologia - Universidade Federal de Viçosa, 36570-000 Viçosa-MG, Brazil
| | - Luiz A Maffia
- Departamento de Fitopatologia - Universidade Federal de Viçosa, 36570-000 Viçosa-MG, Brazil
| | - Eduardo S G Mizubuti
- Departamento de Fitopatologia - Universidade Federal de Viçosa, 36570-000 Viçosa-MG, Brazil
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López-Calcagno PE, Moreno J, Cedeño L, Labrador L, Concepción JL, Avilán L. Cloning, expression and biochemical characterization of mitochondrial and cytosolic malate dehydrogenase from Phytophthora infestans. ACTA ACUST UNITED AC 2009; 113:771-81. [PMID: 19249364 DOI: 10.1016/j.mycres.2009.02.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Revised: 01/26/2009] [Accepted: 02/18/2009] [Indexed: 11/26/2022]
Abstract
The genes of the mitochondrial and cytosolic malate dehydrogenase (mMDH and cMDH) of Phytophthora infestans were cloned and overexpressed in Escherichia coli as active enzymes. The catalytic properties of these proteins were determined: both enzymes have a similar specific activity. In addition, the natural mitochondrial isoenzyme was semi-purified from mycelia and its catalytic properties determined: the recombinant mitochondrial isoform behaved as the natural enzyme. A phylogenetic analysis indicated that mMDH, present in all stramenopiles studied, can be useful to study the relationships between these organisms. MDH with the conserved domain MDH_cytoplasmic_cytosolic is absent in some stramenopiles as well as in fungi. This enzyme seems to be less related within the stramenopile group. The Phytophthora cMDHs have an insertion of six amino acids that is also present in the stramenopile cMDHs studied, with the exception of Thalassiosira pseudonana cMDH, and is absent in other known eukaryotic cMDHs.
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Ah-Fong AM, Bormann-Chung CA, Judelson HS. Optimization of transgene-mediated silencing in Phytophthora infestans and its association with small-interfering RNAs. Fungal Genet Biol 2008; 45:1197-205. [DOI: 10.1016/j.fgb.2008.05.009] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2008] [Revised: 05/18/2008] [Accepted: 05/19/2008] [Indexed: 11/30/2022]
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Judelson HS, Ah-Fong AMV, Aux G, Avrova AO, Bruce C, Cakir C, da Cunha L, Grenville-Briggs L, Latijnhouwers M, Ligterink W, Meijer HJG, Roberts S, Thurber CS, Whisson SC, Birch PRJ, Govers F, Kamoun S, van West P, Windass J. Gene expression profiling during asexual development of the late blight pathogen Phytophthora infestans reveals a highly dynamic transcriptome. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2008; 21:433-47. [PMID: 18321189 DOI: 10.1094/mpmi-21-4-0433] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Much of the pathogenic success of Phytophthora infestans, the potato and tomato late blight agent, relies on its ability to generate from mycelia large amounts of sporangia, which release zoospores that encyst and form infection structures. To better understand these stages, Affymetrix GeneChips based on 15,650 unigenes were designed and used to profile the life cycle. Approximately half of P. infestans genes were found to exhibit significant differential expression between developmental transitions, with approximately (1)/(10) being stage-specific and most changes occurring during zoosporogenesis. Quantitative reverse-transcription polymerase chain reaction assays confirmed the robustness of the array results and showed that similar patterns of differential expression were obtained regardless of whether hyphae were from laboratory media or infected tomato. Differentially expressed genes encode potential cellular regulators, especially protein kinases; metabolic enzymes such as those involved in glycolysis, gluconeogenesis, or the biosynthesis of amino acids or lipids; regulators of DNA synthesis; structural proteins, including predicted flagellar proteins; and pathogenicity factors, including cell-wall-degrading enzymes, RXLR effector proteins, and enzymes protecting against plant defense responses. Curiously, some stage-specific transcripts do not appear to encode functional proteins. These findings reveal many new aspects of oomycete biology, as well as potential targets for crop protection chemicals.
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Affiliation(s)
- Howard S Judelson
- Department of Plant Pathology and Microbiology, University of California, Riverside 92521, USA.
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Walker CA, Köppe M, Grenville-Briggs LJ, Avrova AO, Horner NR, McKinnon AD, Whisson SC, Birch PRJ, van West P. A putative DEAD-box RNA-helicase is required for normal zoospore development in the late blight pathogen Phytophthora infestans. Fungal Genet Biol 2008; 45:954-62. [PMID: 18439859 DOI: 10.1016/j.fgb.2008.03.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2007] [Revised: 03/10/2008] [Accepted: 03/12/2008] [Indexed: 01/24/2023]
Abstract
The asexual multinucleated sporangia of Phytophthora infestans can germinate directly through a germ tube or indirectly by releasing zoospores. The molecular mechanisms controlling sporangial cytokinesis or sporangial cleavage, and zoospore release are largely unknown. Sporangial cleavage is initiated by a cold shock that eventually compartmentalizes single nuclei within each zoospore. Comparison of EST representation in different cDNA libraries revealed a putative ATP-dependent DEAD-box RNA-helicase gene in P. infestans, Pi-RNH1, which has a 140-fold increased expression level in young zoospores compared to uncleaved sporangia. RNA interference was employed to determine the role of Pi-RNH1 in zoospore development. Silencing efficiencies of up to 99% were achieved in some transiently-silenced lines. These Pi-RNH1-silenced lines produced large aberrant zoospores that had undergone partial cleavage and often had multiple flagella on their surface. Transmission electron microscopy revealed that cytoplasmic vesicles fused in the silenced lines, resulting in the formation of large vesicles. The Pi-RNH1-silenced zoospores were also sensitive to osmotic pressure and often ruptured upon release from the sporangia. These findings indicate that Pi-RNH1 has a major function in zoospore development and its potential role in cytokinesis is discussed.
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Affiliation(s)
- Claire A Walker
- Aberdeen Oomycete Group, College of Life Science and Medicine, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
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Morris J, Hawthorne KM, Hotze T, Abrams SA, Hirschi KD. Nutritional impact of elevated calcium transport activity in carrots. Proc Natl Acad Sci U S A 2008; 105:1431-5. [PMID: 18202180 PMCID: PMC2234161 DOI: 10.1073/pnas.0709005105] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2007] [Indexed: 11/18/2022] Open
Abstract
Nutrition recommendations worldwide emphasize ingestion of plant-based diets rather than diets that rely primarily on animal products. However, this plant-based diet could limit the intake of essential nutrients such as calcium. Osteoporosis is one of the world's most prevalent nutritional disorders, and inadequate dietary calcium is a known contributor to the pathophysiology of this condition. Previously, we have modified carrots to express increased levels of a plant calcium transporter (sCAX1), and these plants contain approximately 2-fold-higher calcium content in the edible portions of the carrots. However, it was unproven whether this change would increase the total amount of bioavailable calcium. In randomized trials, we labeled these modified carrots with isotopic calcium and fed them to mice and humans to assess calcium bioavailability. In mice feeding regimes (n = 120), we measured (45)Ca incorporation into bones and determined that mice required twice the serving size of control carrots to obtain the calcium found in sCAX1 carrots. We used a dual-stable isotope method with (42)Ca-labeled carrots and i.v. (46)Ca to determine the absorption of calcium from these carrots in humans. In a cross-over study of 15 male and 15 female adults, we found that when people were fed sCAX1 and control carrots, total calcium absorption per 100 g of carrots was 41% +/- 2% higher in sCAX1 carrots. Both the mice and human feeding studies demonstrate increased calcium absorption from sCAX1-expressing carrots compared with controls. These results demonstrate an alternative means of fortifying vegetables with bioavailable calcium.
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Affiliation(s)
- Jay Morris
- *Vegetable and Fruit Improvement Center, Texas A&M University, College Station, TX 77845; and
- U.S. Department of Agriculture/Agriculture Research Service, Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030
| | - Keli M. Hawthorne
- U.S. Department of Agriculture/Agriculture Research Service, Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030
| | - Tim Hotze
- U.S. Department of Agriculture/Agriculture Research Service, Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030
| | - Steven A. Abrams
- U.S. Department of Agriculture/Agriculture Research Service, Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030
| | - Kendal D. Hirschi
- *Vegetable and Fruit Improvement Center, Texas A&M University, College Station, TX 77845; and
- U.S. Department of Agriculture/Agriculture Research Service, Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030
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Architecture of the sporulation-specific Cdc14 promoter from the oomycete Phytophthora infestans. EUKARYOTIC CELL 2007; 6:2222-30. [PMID: 17951514 DOI: 10.1128/ec.00328-07] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The Cdc14 gene of Phytophthora infestans is transcribed specifically during sporulation, with no mRNA detectable in vegetative hyphae, and is required for sporangium development. To unravel the mechanisms regulating its transcription, mutated Cdc14 promoters plus chimeras of selected Cdc14 sequences and a minimal promoter were tested in stable transformants. This revealed that a tandem repeat of three copies of the motif CTYAAC, located between 67 and 90 nucleotides (nt) upstream of the major transcription start site, is sufficient to determine sporulation-specific expression. All three repeats need to be present for activity, suggesting that they bind a transcription factor through a cooperative mechanism. Electrophoretic mobility shift assays indicated that the CTYAAC repeats are specifically bound by a protein in nuclear extracts. Evidence was also obtained for a second region within the promoter that activates Cdc14 transcription during sporulation which does not involve those repeats. The CTYAAC motif also affects the specificity of transcription initiation. Wild-type Cdc14 is transcribed from a major start site and minor site(s) located about 100 nt upstream of the major site. However, stepwise mutations through the CTYAAC triad caused a graded shift to the upstream sites, as did mutating bases surrounding the major start site; transcripts initiated from the upstream site remained sporulation specific. Replacing the Cdc14 initiation region with the Inr-like region of the constitutive Piexo1 gene had no apparent effect on the pattern of transcription. Therefore, this study reports the first motif determining sporulation-induced transcription in oomycetes and helps define oomycete core promoters.
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Judelson HS, Tani S. Transgene-induced silencing of the zoosporogenesis-specific NIFC gene cluster of Phytophthora infestans involves chromatin alterations. EUKARYOTIC CELL 2007; 6:1200-9. [PMID: 17483289 PMCID: PMC1951104 DOI: 10.1128/ec.00311-06] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Clustered within the genome of the oomycete phytopathogen Phytophthora infestans are four genes encoding spore-specific nuclear LIM interactor-interacting factors (NIF proteins, a type of transcriptional regulator) that are moderately conserved in DNA sequence. NIFC1, NIFC2, and NIFC3 are zoosporogenesis-induced and grouped within 4 kb, and 20 kb away resides a sporulation-induced form, NIFS. To test the function of the NIFC family, plasmids expressing full-length hairpin constructs of NIFC1 or NIFC2 were stably transformed into P. infestans. This triggered silencing of the cognate gene in about one-third of transformants, and all three NIFC genes were usually cosilenced. However, NIFS escaped silencing despite its high sequence similarity to the NIFC genes. Silencing of the three NIFC genes impaired zoospore cyst germination by 60% but did not affect other aspects of the life cycle. Silencing was transcriptional based on nuclear run-on assays and associated with tighter chromatin packing based on nuclease accessibility experiments. The chromatin alterations extended a few hundred nucleotides beyond the boundaries of the transcribed region of the NIFC cluster and were not associated with increased DNA methylation. A plasmid expressing a short hairpin RNA having sequence similarity only to NIFC1 silenced both that gene and an adjacent member of the gene cluster, likely due to the expansion of a heterochromatic domain from the targeted locus. These data help illuminate the mechanism of silencing in Phytophthora and suggest that caution should be used when interpreting silencing experiments involving closely spaced genes.
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Affiliation(s)
- Howard S Judelson
- Department of Plant Pathology and Microbiology, University of California, Riverside, Riverside, CA 92521, USA.
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Judelson HS. Genomics of the plant pathogenic oomycete Phytophthora: insights into biology and evolution. ADVANCES IN GENETICS 2007; 57:97-141. [PMID: 17352903 DOI: 10.1016/s0065-2660(06)57003-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The genus Phytophthora includes many destructive pathogens of plants. Although having "fungus-like" appearances, Phytophthora species reside in a eukaryotic kingdom separate from that of true fungi. Distinct strategies are therefore required to study and defend against Phytophthora. Large sequence databases have recently been developed for several species, and tools for functional genomics have been enhanced. This chapter will review current progress in understanding the genome and transcriptome of Phytophthora, and provide examples of how genomics resources are advancing molecular studies of pathogenesis, development, transcription, and evolution. A better understanding of these remarkable pathogens should lead to new approaches for managing their diseases.
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Affiliation(s)
- Howard S Judelson
- Department of Plant Pathology, Center for Plant Cell Biology, University of California, Riverside, California 92521, USA
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Meijer HJG, Govers F. Genomewide analysis of phospholipid signaling genes in Phytophthora spp.: novelties and a missing link. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2006; 19:1337-47. [PMID: 17153918 DOI: 10.1094/mpmi-19-1337] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Phospholipids are cellular membrane components in eukaryotic cells that execute many important roles in signaling. Genes encoding enzymes required for phospholipid signaling and metabolism have been characterized in several organisms, but only a few have been described for oomycetes. In this study, the genome sequences of Phytophthora sojae and P. ramorum were explored to construct a comprehensive genomewide inventory of genes involved in the most universal phospholipid signaling pathways. Several genes and gene families were annotated, including those encoding phosphatidylinositol synthase (PIS), phosphatidylinositol (phosphate) kinase (PI[P]K), diacylglycerol kinase (DAG), and phospholipase D (PLD). The most obvious missing link is a gene encoding phospholipase C (PLC). In all eukaryotic genomes sequenced to date, PLC genes are annotated based on certain conserved features; however, these genes seem to be absent in Phytophthora spp. Analysis of the structural and regulatory domains and domain organization of the predicted isoforms of PIS, PIK, PIPK, DAG, and PLD revealed many novel features compared with characterized representatives in other eukaryotes. Examples are transmembrane proteins with a C-terminal catalytic PLD domain, secreted PLD-like proteins, and PIPKs that have an N-terminal G-protein-coupled receptor-transmembrane signature. Compared with other sequenced eukaryotes, the genus Phytophthora clearly has several exceptional features in its phospholipid-modifying enzymes.
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Affiliation(s)
- Harold J G Meijer
- Laboratory of Phytopathology, Plant Sciences Group, Wageningen University, Binnenhaven 5, NL-6709 PD Wageningen, The Netherlands.
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Abstract
The last 4 years have seen significant advances in our understanding of the cellular processes that underlie the infection of plants by a range of biotrophic and necrotrophic oomycete pathogens. Given that oomycete and fungal pathogens must overcome the same sets of physical and chemical barriers presented by plants, it is not surprising that many aspects of oomycete infection strategies are similar to those of fungal pathogens. A major difference, however, centres on the role of motile oomycete zoospores in actively moving the pathogen to favourable infection sites. Recent studies have shown that the plant defence response to invading oomycetes is similar to that mounted against fungi, but biochemical differences between oomycete and fungal surface molecules must have implications for plant recognition of and defence against oomycete pathogens. The aim of this short review is to provide a cell biological framework within which emerging data on the molecular basis of oomycete-plant interactions may be placed.
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Affiliation(s)
- Adrienne R Hardham
- Plant Cell Biology Group, Research School of Biological Sciences, The Australian National University, Canberra ACT 2601, Australia.
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Tani S, Judelson H. Activation of zoosporogenesis-specific genes in Phytophthora infestans involves a 7-nucleotide promoter motif and cold-induced membrane rigidity. EUKARYOTIC CELL 2006; 5:745-52. [PMID: 16607021 PMCID: PMC1459674 DOI: 10.1128/ec.5.4.745-752.2006] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Infections of plants by the oomycete Phytophthora infestans typically result from zoospores, which develop from sporangia at cold temperatures. To help understand the relevant cold-induced signaling pathway, factors regulating the transcription of the zoosporogenesis-specific NIF (nuclear LIM-interactor-interacting factor) gene family were examined. Sequences required for inducing PinifC3 were identified by analyzing truncated and mutated promoters using the beta-glucuronidase reporter in stable transformants. A 7-nucleotide (nt) sequence located 139 bases upstream of the major transcription start point (GGACGAG) proved essential for the induction of PinifC3 when sporangia were shifted from ambient to cold temperatures. The motif, named the cold box, also conferred cold inducibility to a promoter normally activated only during sexual development. An identical motif was detected in the two other zoosporogenesis-specific NIF genes from P. infestans and three Phytophthora sojae orthologues, and a closely related sequence was found in Phytophthora ramorum orthologues. The 7-nt motif was also found in the promoters of other zoosporogenesis-induced genes. The presence of a cold box-interacting protein in nuclear extracts of P. infestans sporangia was demonstrated using electrophoretic mobility shift assays. Furthermore, zoospore release and cold box-regulated transcription were stimulated by the membrane rigidizer dimethyl sulfoxide and inhibited by the membrane fluidizer benzyl alcohol. The data therefore delineate a pathway in which sporangia perceive cold temperatures through membrane rigidity, which activates signals that drive both zoosporogenesis and cold-box-mediated transcription.
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Affiliation(s)
- Shuji Tani
- Department of Plant Pathology, University of California, Riverside, CA 92521, USA
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Abstract
SUMMARY Phytophthora cinnamomi Rands was first isolated from cinnamon trees in Sumatra in 1922. The pathogen is believed to have originated near Papua New Guinea but now has a worldwide distribution. P. cinnamomi is heterothallic with A1 and A2 mating types; however, even in areas in which both mating types are present, it appears that genetic diversity arises asexually rather than as a result of sexual recombination. P. cinnamomi can grow saprophytically in the soil for long periods, rapidly capitalizing on the advent of favourable conditions to sporulate and produce vast numbers of asexual, biflagellate zoospores. The motile zoospores are attracted to suitable infection sites, where they attach and invade the plant. Within a few days, hyphae ramify throughout the tissues of susceptible plants, forming sporangia on the plant surface and rapidly amplifying the disease inoculum. Over the last 10-15 years, molecular analyses have clarified details of the phylogeny of P. cinnamomi and other Oomycetes. Research on P. cinnamomi has given rise to a more comprehensive understanding of the structure and function of the motile zoospores. New methods have been developed for P. cinnamomi identification and diagnosis. Long-term studies of diseased sites, particular those in southern Australia, have produced a better understanding of the epidemiology of P. cinnamomi diseases. Research has also increased our knowledge of the mode of action and efficacy of inhibitors of P. cinnamomi diseases, especially the phosphonates. This review will present an overview of the advances these studies have made in our understanding of P. cinnamomi pathogenicity, epidemiology and control. TAXONOMY Phytophthora cinnamomi Rands; kingdom Chromista; phylum Oomycota; order Peronosporales; family Peronosporaceae; genus Phytophthora. HOST RANGE Likely to infect in excess of 3000 species of plants including over 2500 Australian native species, and crops such as avocado, pineapple, peach, chestnut and macadamia. Disease symptoms: A root pathogen which usually causes rotting of fine and fibrous roots but which can also cause stem cankers. Often causes dieback of young shoots and is thought to do so as a result of interference with transpiration from roots to shoots. USEFUL WEBSITES http://genome.jgi-psf.org/physo00.info.html; http://phytophthora.vbi.vt.edu.
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Affiliation(s)
- Adrienne R Hardham
- Plant Cell Biology Group, Research School of Biological Sciences, The Australian National University, Canberra, ACT 2601, Australia
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Blanco FA, Judelson HS. A bZIP transcription factor from Phytophthora interacts with a protein kinase and is required for zoospore motility and plant infection. Mol Microbiol 2005; 56:638-48. [PMID: 15819621 DOI: 10.1111/j.1365-2958.2005.04575.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Zoospores are critical in the disease cycle of Phytophthora infestans, a member of the oomycete group of fungus-like microbes and the cause of potato late blight. A protein kinase induced during zoosporogenesis, Pipkz1, was shown to interact in the yeast two-hybrid system with a putative bZIP transcription factor. This interaction was confirmed in vitro using a pull-down assay. The transcription factor gene, Pibzp1, was single copy and expressed in all tissues. Transformants of P. infestans stably silenced for Pibzp1 were generated using plasmids expressing its coding region in sense or antisense orientations. A protoplast transformation method induced silencing more efficiently than transformation by an electroporation scheme. Wild-type and silenced strains exhibited no differences in hyphal growth or morphology, mating, sporangia production or zoospore release. However, zoospores from the mutants spun in tight circles, instead of exhibiting the normal pattern of straight swimming punctuated by turns. Zoospore encystment was unaffected by silencing, but cysts germinated more efficiently than controls. Germinated cysts from the mutants failed to develop appressoria and were unable to infect plants; however, they could colonize wounded tissue. These phenotypes indicate that Pibzp1 is a key regulator of several stages of the zoospore-mediated infection pathway.
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Affiliation(s)
- Flavio A Blanco
- Center for Plant Cell Biology and Department of Plant Pathology, University of California, Riverside, CA 92521, USA
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Kamoun S, Smart CD. Late Blight of Potato and Tomato in the Genomics Era. PLANT DISEASE 2005; 89:692-699. [PMID: 30791237 DOI: 10.1094/pd-89-0692] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
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Panabières F, Amselem J, Galiana E, Le Berre JY. Gene identification in the oomycete pathogen Phytophthora parasitica during in vitro vegetative growth through expressed sequence tags. Fungal Genet Biol 2005; 42:611-23. [PMID: 15950158 DOI: 10.1016/j.fgb.2005.03.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2005] [Revised: 03/07/2005] [Accepted: 03/08/2005] [Indexed: 10/25/2022]
Abstract
Phytophthora parasitica is a soilborne oomycete pathogen capable of infecting a wide range of plants, including many solanaceous plants. In a first step towards large-scale gene discovery, we generated expressed sequence tags (ESTs) from a cDNA library constructed using mycelium grown in synthetic medium. A total of 3568 ESTs were assembled into 2269 contiguous sequences. Functional categorization could be performed for 65.45% of ESTs. A significant portion of the transcripts encodes proteins of common metabolic pathways. The most prominent sequences correspond to members of the elicitin family, and enzymes involved in the lipid metabolism. A number of genes potentially involved in pathogenesis were also identified, which may constitute virulence determinants.
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Affiliation(s)
- Franck Panabières
- INRA UMR 1064, Unité Interactions Plantes-Microorganismes et Santé Végétale, 400 route des Chappes, F-06930 Sophia-Antipolis cedex, France.
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Abstract
Members of the genus Phytophthora are among the most serious threats to agriculture and food production, causing devastating diseases in hundreds of plant hosts. These fungus-like eukaryotes, which are taxonomically classified as oomycetes, generate asexual and sexual spores with characteristics that greatly contribute to their pathogenic success. The spores include survival and dispersal structures, and potent infectious propagules capable of actively locating hosts. Genetic tools and genomic resources developed over the past decade are now allowing detailed analysis of these important stages in the Phytophthora life cycle.
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Affiliation(s)
- Howard S Judelson
- Department of Plant Pathology and Center for Plant Cell Biology, University of California, Riverside, California 92521, USA.
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Shan W, Marshall JS, Hardham AR. Gene expression in germinated cysts of Phytophthora nicotianae. MOLECULAR PLANT PATHOLOGY 2004; 5:317-30. [PMID: 20565599 DOI: 10.1111/j.1364-3703.2004.00231.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
SUMMARY The life cycle of Phytophthora species contains several distinct asexual developmental stages that are important for plant infection and disease development. These include vegetative growth of filamentous hyphae, production of multinucleate sporangia, motile, uninucleate zoospores and germinated cysts, the stage at which plant colonization is initiated. To understand mechanisms regulating molecular and cellular processes in germinated cysts, differential hybridization analysis of a cDNA library was used to identify genes up-regulated after cyst germination in P. nicotianae. Arrays of 12 288 random cDNA clones derived from a germinated cyst cDNA library were screened with (32)P-labelled cDNA probes synthesized from mRNA isolated from four different developmental stages and tobacco tissues infected with P. nicotianae. The resultant expression profiles for each cDNA clone led to the identification of over 300 clones showing up-regulated expression in germinated cysts compared with the other three stages. Sequencing of the 5' end of 382 selected clones yielded 355 sequences representing 146 putative unigenes. Sequence analysis revealed similarities to genes encoding proteins involved in energy production, protein biosynthesis, signalling, cell-wall biogenesis and transcription regulation. Novel genes putatively involved in cell adhesion, cell-wall biogenesis and transcriptional regulation were identified. Thirty-one cDNA clones were analysed by Northern blotting and for 28 the pattern of expression in the Northern blots was the same as that indicated by the macroarray screening, verifying the fidelity of the colony hybridization data.
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Affiliation(s)
- Weixing Shan
- Plant Cell Biology Group, Research School of Biological Sciences, The Australian National University, Canberra, ACT 2601, Australia
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