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González-Tobón J, Childers RR, Rodríguez A, Fry W, Myers KL, Thompson JR, Restrepo S, Danies G. Searching for the Mechanism that Mediates Mefenoxam-Acquired Resistance in Phytophthora infestans and How It Is Regulated. PHYTOPATHOLOGY 2022; 112:1118-1133. [PMID: 34763530 DOI: 10.1094/phyto-07-21-0280-r] [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: 06/13/2023]
Abstract
Phytophthora infestans, the causal agent of late blight disease of potatoes, is mainly controlled by the use of fungicides. Isolates that are resistant to commonly used fungicides have been reported. Also, several studies show that originally mefenoxam-sensitive isolates acquire resistance to this fungicide when exposed to sublethal concentrations. This phenomenon, termed "mefenoxam-acquired resistance," has been observed in different Phytophthora species and seems to be unique to mefenoxam. In this study, we aimed to elucidate the molecular mechanism mediating this type of resistance as well as a possible regulatory process behind it. A combination of computational analyses and experimental approaches was used to identify differentially expressed genes with a potential association to the phenomenon. These genes were classified into seven functional groups. Most of them seem to be associated with a pleiotropic drug resistance (PDR) phenotype, typically involved in the expulsion of diverse metabolites, drugs, or other substances out of the cell. Despite the importance of RNA Polymerase I for the constitutive resistance of P. infestans to mefenoxam, our results indicate no clear interaction between this protein and the acquisition of mefenoxam resistance. Several small non-coding RNAs were found to be differentially expressed and specifically related to genes mediating the PDR phenotype, thus suggesting a possible regulatory process. We propose a model of the molecular mechanisms acting within the cell when P. infestans acquires resistance to mefenoxam after exposed to sublethal concentrations of the fungicide. This study provides important insights into P. infestans' cellular and regulatory functionalities.
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Affiliation(s)
- Juliana González-Tobón
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia 111711
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY 14853, U.S.A
| | | | - Alejandra Rodríguez
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia 111711
| | - William Fry
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY 14853, U.S.A
| | - Kevin L Myers
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY 14853, U.S.A
| | - Jeremy R Thompson
- Plant Health and Environment Laboratory, Ministry for Primary Industries, Auckland 1072, New Zealand
| | - Silvia Restrepo
- Department of Food and Chemical Engineering, Universidad de los Andes, Bogotá, Colombia 111711
| | - Giovanna Danies
- Department of Design, Universidad de los Andes, Bogotá, Colombia 111711
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Chinchilla D, Bruisson S, Meyer S, Zühlke D, Hirschfeld C, Joller C, L'Haridon F, Mène-Saffrané L, Riedel K, Weisskopf L. A sulfur-containing volatile emitted by potato-associated bacteria confers protection against late blight through direct anti-oomycete activity. Sci Rep 2019; 9:18778. [PMID: 31889050 PMCID: PMC6937334 DOI: 10.1038/s41598-019-55218-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 11/12/2019] [Indexed: 12/14/2022] Open
Abstract
Plant diseases are a major cause for yield losses and new strategies to control them without harming the environment are urgently needed. Plant-associated bacteria contribute to their host’s health in diverse ways, among which the emission of disease-inhibiting volatile organic compounds (VOCs). We have previously reported that VOCs emitted by potato-associated bacteria caused strong in vitro growth inhibition of the late blight causing agent Phytophthora infestans. This work focuses on sulfur-containing VOCs (sVOCs) and demonstrates the high in planta protective potential of S-methyl methane thiosulfonate (MMTS), which fully prevented late blight disease in potato leaves and plantlets without phytotoxic effects, in contrast to other sVOCs. Short exposure times were sufficient to protect plants against infection. We further showed that MMTS’s protective activity was not mediated by the plant immune system but lied in its anti-oomycete activity. Using quantitative proteomics, we determined that different sVOCs caused specific proteome changes in P. infestans, indicating perturbations in sulfur metabolism, protein translation and redox balance. This work brings new perspectives for plant protection against the devastating Irish Famine pathogen, while opening new research avenues on the role of sVOCs in the interaction between plants and their microbiome.
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Affiliation(s)
- Delphine Chinchilla
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700, Fribourg, Switzerland
| | - Sébastien Bruisson
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700, Fribourg, Switzerland
| | - Silvan Meyer
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700, Fribourg, Switzerland
| | - Daniela Zühlke
- Department of Microbial Physiology and Molecular Biology, University of Greifswald, Felix-Hausdorff-Strasse 8, D-17489, Greifswald, Germany
| | - Claudia Hirschfeld
- Department of Microbial Proteomics, University of Greifswald, Felix-Hausdorff-Strasse 8, D-17489, Greifswald, Germany
| | - Charlotte Joller
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700, Fribourg, Switzerland
| | - Floriane L'Haridon
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700, Fribourg, Switzerland
| | - Laurent Mène-Saffrané
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700, Fribourg, Switzerland
| | - Katharina Riedel
- Department of Microbial Physiology and Molecular Biology, University of Greifswald, Felix-Hausdorff-Strasse 8, D-17489, Greifswald, Germany
| | - Laure Weisskopf
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700, Fribourg, Switzerland.
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Grünwald NJ, LeBoldus JM, Hamelin RC. Ecology and Evolution of the Sudden Oak Death Pathogen Phytophthora ramorum. ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:301-321. [PMID: 31226018 DOI: 10.1146/annurev-phyto-082718-100117] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The sudden oak and sudden larch death pathogen Phytophthora ramorum emerged simultaneously in the United States on oak and in Europe on Rhododendron in the 1990s. This pathogen has had a devastating impact on larch plantations in the United Kingdom as well as mixed conifer and oak forests in the Western United States. Since the discovery of this pathogen, a large body of research has provided novel insights into the emergence, epidemiology, and genetics of this pandemic. Genetic and genomic resources developed for P. ramorum have been instrumental in improving our understanding of the epidemiology, evolution, and ecology of this disease. The recent reemergence of EU1 in the United States and EU2 in Europe and the discovery of P. ramorum in Asia provide renewed impetus for research on the sudden oak death pathogen.
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Affiliation(s)
- Niklaus J Grünwald
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, Oregon 97330, USA;
| | - Jared M LeBoldus
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA
- Department of Forest Engineering, Resources, and Management, Oregon State University, Corvallis, OR 97331-5704, USA
| | - Richard C Hamelin
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Faculté de Foresterie et de Géomatique, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
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Pang Z, Chen L, Mu W, Liu L, Liu X. Insights into the adaptive response of the plant-pathogenic oomycete Phytophthora capsici to the fungicide flumorph. Sci Rep 2016; 6:24103. [PMID: 27050922 PMCID: PMC4822174 DOI: 10.1038/srep24103] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 03/21/2016] [Indexed: 01/11/2023] Open
Abstract
Phytophthora capsici is an important oomycete plant pathogen that causes significant losses worldwide. The carboxylic acid amide fungicide flumorph has shown excellent activity against oomycete plant pathogens. Despite its potential, there remains concern that the sexual reproduction of oomycete pathogens, which results in genetic recombination, could result in the rapid development of resistance to flumorph. The current study utilized an iTRAQ (isobaric tags for relative and absolute quantitation) based method to compare differences between the proteome of the parental P. capsici isolate PCAS1 and its sexual progeny S2-838, which exhibits significant resistance to flumorph. A total of 2396 individual proteins were identified, of these, 181 were considered to be associated with the adaptive response of P. capsici to flumorph. The subsequent bioinformatic analysis revealed that the adaptive response of P. capsici to flumorph was complex and regulated by multiple mechanisms, including utilising carbohydrate from the host environment to compensate for the cell wall stress induced by flumorph, a shift in energy generation, decreased amino acids biosynthesis, and elevated levels of proteins associated with the pathogen's response to stimulus and transmembrane transport. Moreover, the results of the study provided crucial data that could provide the basis for early monitoring of flumorph resistance in field populations of P. capsici.
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Affiliation(s)
- Zhili Pang
- Department of Plant Pathology, College of Agriculture and Biotechnology, China Agricultural University, Beijing, P. R. China
| | - Lei Chen
- Department of Plant Pathology, College of Agriculture and Biotechnology, China Agricultural University, Beijing, P. R. China
- College of Forestry, Beijing Forestry University, Beijing, P. R. China
| | - Wenjun Mu
- Department of Plant Pathology, College of Agriculture and Biotechnology, China Agricultural University, Beijing, P. R. China
- Zhengzhou Tobacco Research Institute of CNTC, P. R. China
| | - Li Liu
- Department of Plant Pathology, College of Agriculture and Biotechnology, China Agricultural University, Beijing, P. R. China
| | - Xili Liu
- Department of Plant Pathology, College of Agriculture and Biotechnology, China Agricultural University, Beijing, P. R. China
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Saha J, Sengupta A, Gupta K, Gupta B. Molecular phylogenetic study and expression analysis of ATP-binding cassette transporter gene family in Oryza sativa in response to salt stress. Comput Biol Chem 2014; 54:18-32. [PMID: 25531538 DOI: 10.1016/j.compbiolchem.2014.11.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 10/14/2014] [Accepted: 11/21/2014] [Indexed: 10/24/2022]
Abstract
ATP-binding cassette (ABC) transporter is a large gene superfamily that utilizes the energy released from ATP hydrolysis for transporting myriad of substrates across the biological membranes. Although many investigations have been done on the structural and functional analysis of the ABC transporters in Oryza sativa, much less is known about molecular phylogenetic and global expression pattern of the complete ABC family in rice. In this study, we have carried out a comprehensive phylogenetic analysis constructing neighbor-joining and maximum-likelihood trees based on various statistical methods of different ABC protein subfamily of five plant lineages including Chlamydomonas reinhardtii (green algae), Physcomitrella patens (moss), Selaginella moellendorffii (lycophyte), Arabidopsis thaliana (dicot) and O. sativa (monocot) to explore the origin and evolutionary patterns of these ABC genes. We have identified several conserved motifs in nucleotide binding domain (NBD) of ABC proteins among all plant lineages during evolution. Amongst the different ABC protein subfamilies, 'ABCE' has not yet been identified in lower plant genomes (algae, moss and lycophytes). The result indicated that gene duplication and diversification process acted upon these genes as a major operative force creating new groups and subgroups and functional divergence during evolution. We have demonstrated that rice ABCI subfamily consists of only half size transporters that represented highly dynamic members showing maximum sequence variations among the other rice ABC subfamilies. The evolutionary and the expression analysis contribute to a deep insight into the evolution and diversity of rice ABC proteins and their roles in response to salt stress that facilitate our further understanding on rice ABC transporters.
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Affiliation(s)
- Jayita Saha
- Department of Biological Sciences (Section Botany), Presidency University, 86/1 College Street, Kolkata 700073, India; Department of Biological Sciences (Section Biotechnology), Presidency University, 86/1 College Street, Kolkata 700073, India
| | - Atreyee Sengupta
- Department of Biological Sciences (Section Botany), Presidency University, 86/1 College Street, Kolkata 700073, India; Department of Biological Sciences (Section Biotechnology), Presidency University, 86/1 College Street, Kolkata 700073, India
| | - Kamala Gupta
- Department of Biological Sciences (Section Botany), Presidency University, 86/1 College Street, Kolkata 700073, India.
| | - Bhaskar Gupta
- Department of Biological Sciences (Section Biotechnology), Presidency University, 86/1 College Street, Kolkata 700073, India.
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Xu B, Luo CS, Liang JR, Chen DD, Zhuo WH, Gao YH, Chen CP, Song SS. Cellular metabolic responses of the marine diatom Pseudo-nitzschia multiseries associated with cell wall formation. Mar Genomics 2014; 16:29-38. [DOI: 10.1016/j.margen.2013.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Revised: 12/18/2013] [Accepted: 12/18/2013] [Indexed: 10/25/2022]
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Wang L, Kiuchi T, Fujii T, Daimon T, Li M, Banno Y, Kikuta S, Kikawada T, Katsuma S, Shimada T. Mutation of a novel ABC transporter gene is responsible for the failure to incorporate uric acid in the epidermis of ok mutants of the silkworm, Bombyx mori. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2013; 43:562-571. [PMID: 23567590 DOI: 10.1016/j.ibmb.2013.03.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 03/22/2013] [Accepted: 03/22/2013] [Indexed: 06/02/2023]
Abstract
ok mutants of the silkworm, Bombyx mori, exhibit highly translucent larval skin resulting from the inability to incorporate uric acid into the epidermal cells. Here we report the identification of a gene responsible for the ok mutation using positional cloning and RNAi experiments. In two independent ok mutant strains, we found a 49-bp deletion and a 233-bp duplication, respectively, in mRNAs of a novel gene, Bm-ok, which encodes a half-type ABC transporter, each of which results in translation of a truncated protein in each mutant. Although the Bm-ok sequence was homologous to well-known transporter genes, white, scarlet, and brown in Drosophila, the discovery of novel orthologs in the genomes of lepidopteran, hymenopteran, and hemipteran insects identifies it as a member of a new distinct subfamily of transporters. Embryonic RNAi of Bm-ok demonstrated that repression of Bm-ok causes a translucent phenotype in the first-instar silkworm larva. We discuss the possibility that Bm-ok forms a heterodimer with another half-type ABC transporter, Bmwh3, and acts as a uric acid transporter in the silkworm epidermis.
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Affiliation(s)
- Lingyan Wang
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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Polo-López M, Oller I, Fernández-Ibáñez P. Benefits of photo-Fenton at low concentrations for solar disinfection of distilled water. A case study: Phytophthora capsici. Catal Today 2013. [DOI: 10.1016/j.cattod.2012.10.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Martens C, Van de Peer Y. The hidden duplication past of the plant pathogen Phytophthora and its consequences for infection. BMC Genomics 2010; 11:353. [PMID: 20525264 PMCID: PMC2996974 DOI: 10.1186/1471-2164-11-353] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Accepted: 06/03/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Oomycetes of the genus Phytophthora are pathogens that infect a wide range of plant species. For dicot hosts such as tomato, potato and soybean, Phytophthora is even the most important pathogen. Previous analyses of Phytophthora genomes uncovered many genes, large gene families and large genome sizes that can partially be explained by significant repeat expansion patterns. RESULTS Analysis of the complete genomes of three different Phytophthora species, using a newly developed approach, unveiled a large number of small duplicated blocks, mainly consisting of two or three consecutive genes. Further analysis of these duplicated genes and comparison with the known gene and genome duplication history of ten other eukaryotes including parasites, algae, plants, fungi, vertebrates and invertebrates, suggests that the ancestor of P. infestans, P. sojae and P. ramorum most likely underwent a whole genome duplication (WGD). Genes that have survived in duplicate are mainly genes that are known to be preferentially retained following WGDs, but also genes important for pathogenicity and infection of the different hosts seem to have been retained in excess. As a result, the WGD might have contributed to the evolutionary and pathogenic success of Phytophthora. CONCLUSIONS The fact that we find many small blocks of duplicated genes indicates that the genomes of Phytophthora species have been heavily rearranged following the WGD. Most likely, the high repeat content in these genomes have played an important role in this rearrangement process. As a consequence, the paucity of retained larger duplicated blocks has greatly complicated previous attempts to detect remnants of a large-scale duplication event in Phytophthora. However, as we show here, our newly developed strategy to identify very small duplicated blocks might be a useful approach to uncover ancient polyploidy events, in particular for heavily rearranged genomes.
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Affiliation(s)
- Cindy Martens
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Ghent, Belgium
- Bioinformatics and Evolutionary Genomics, Department of Molecular Genetics, Technologiepark 927, Ghent University, B-9052 Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Ghent, Belgium
- Bioinformatics and Evolutionary Genomics, Department of Molecular Genetics, Technologiepark 927, Ghent University, B-9052 Ghent, Belgium
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Kovalchuk A, Driessen AJM. Phylogenetic analysis of fungal ABC transporters. BMC Genomics 2010; 11:177. [PMID: 20233411 PMCID: PMC2848647 DOI: 10.1186/1471-2164-11-177] [Citation(s) in RCA: 160] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Accepted: 03/16/2010] [Indexed: 12/22/2022] Open
Abstract
Background The superfamily of ABC proteins is among the largest known in nature. Its members are mainly, but not exclusively, involved in the transport of a broad range of substrates across biological membranes. Many contribute to multidrug resistance in microbial pathogens and cancer cells. The diversity of ABC proteins in fungi is comparable with those in multicellular animals, but so far fungal ABC proteins have barely been studied. Results We performed a phylogenetic analysis of the ABC proteins extracted from the genomes of 27 fungal species from 18 orders representing 5 fungal phyla thereby covering the most important groups. Our analysis demonstrated that some of the subfamilies of ABC proteins remained highly conserved in fungi, while others have undergone a remarkable group-specific diversification. Members of the various fungal phyla also differed significantly in the number of ABC proteins found in their genomes, which is especially reduced in the yeast S. cerevisiae and S. pombe. Conclusions Data obtained during our analysis should contribute to a better understanding of the diversity of the fungal ABC proteins and provide important clues about their possible biological functions.
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Affiliation(s)
- Andriy Kovalchuk
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands.
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