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Galvez-Llompart M, Zanni R, Vela-Corcía D, Polonio Á, Perez-Gimenez F, Martínez-Cruz J, Romero D, Fernández-Ortuño D, Pérez-García A, Galvez J. Rational Design of a Potential New Nematicide Targeting Chitin Deacetylase. J Agric Food Chem 2024; 72:2482-2491. [PMID: 38264997 PMCID: PMC10853968 DOI: 10.1021/acs.jafc.3c05258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/26/2023] [Accepted: 01/09/2024] [Indexed: 01/25/2024]
Abstract
In a previously published study, the authors devised a molecular topology QSAR (quantitative structure-activity relationship) approach to detect novel fungicides acting as inhibitors of chitin deacetylase (CDA). Several of the chosen compounds exhibited noteworthy activity. Due to the close relationship between chitin-related proteins present in fungi and other chitin-containing plant-parasitic species, the authors decided to test these molecules against nematodes, based on their negative impact on agriculture. From an overall of 20 fungal CDA inhibitors, six showed to be active against Caenorhabditis elegans. These experimental results made it possible to develop two new molecular topology-based QSAR algorithms for the rational design of potential nematicides with CDA inhibitor activity for crop protection. Linear discriminant analysis was employed to create the two algorithms, one for identifying the chemo-mathematical pattern of commercial nematicides and the other for identifying nematicides with activity on CDA. After creating and validating the QSAR models, the authors screened several natural and synthetic compound databases, searching for alternatives to current nematicides. Finally one compound, the N2-(dimethylsulfamoyl)-N-{2-[(2-methyl-2-propanyl)sulfanyl]ethyl}-N2-phenylglycinamide or nematode chitin deacetylase inhibitor, was selected as the best candidate and was further investigated both in silico, through molecular docking and molecular dynamic simulations, and in vitro, through specific experimental assays. The molecule shows favorable binding behavior on the catalytic pocket of C. elegans CDA and the experimental assays confirm potential nematicide activity.
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Affiliation(s)
- Maria Galvez-Llompart
- Department
of Preventive Medicine and Public Health, Food Science, Toxicology
and Forensic Medicine, Faculty of Pharmacy, University of Valencia, Burjassot, Valencia 46100, Spain
- Molecular
Topology and Drug Design Unit. Department of Physical Chemistry, University of Valencia, Burjassot, Valencia 46100, Spain
| | - Riccardo Zanni
- Molecular
Topology and Drug Design Unit. Department of Physical Chemistry, University of Valencia, Burjassot, Valencia 46100, Spain
| | - David Vela-Corcía
- Department
of Microbiology, Faculty of Science, Instituto de Hortofruticultura
Subtropical y Mediterránea La Mayora, IHSM-UMA-CSIC, University of Málaga, Málaga 29071, Spain
| | - Álvaro Polonio
- Department
of Microbiology, Faculty of Science, Instituto de Hortofruticultura
Subtropical y Mediterránea La Mayora, IHSM-UMA-CSIC, University of Málaga, Málaga 29071, Spain
| | - Facundo Perez-Gimenez
- Molecular
Topology and Drug Design Unit. Department of Physical Chemistry, University of Valencia, Burjassot, Valencia 46100, Spain
| | - Jesús Martínez-Cruz
- Department
of Microbiology, Faculty of Science, Instituto de Hortofruticultura
Subtropical y Mediterránea La Mayora, IHSM-UMA-CSIC, University of Málaga, Málaga 29071, Spain
| | - Diego Romero
- Department
of Microbiology, Faculty of Science, Instituto de Hortofruticultura
Subtropical y Mediterránea La Mayora, IHSM-UMA-CSIC, University of Málaga, Málaga 29071, Spain
| | - Dolores Fernández-Ortuño
- Department
of Microbiology, Faculty of Science, Instituto de Hortofruticultura
Subtropical y Mediterránea La Mayora, IHSM-UMA-CSIC, University of Málaga, Málaga 29071, Spain
| | - Alejandro Pérez-García
- Department
of Microbiology, Faculty of Science, Instituto de Hortofruticultura
Subtropical y Mediterránea La Mayora, IHSM-UMA-CSIC, University of Málaga, Málaga 29071, Spain
| | - Jorge Galvez
- Molecular
Topology and Drug Design Unit. Department of Physical Chemistry, University of Valencia, Burjassot, Valencia 46100, Spain
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Bakhat N, Vielba-Fernández A, Padilla-Roji I, Martínez-Cruz J, Polonio Á, Fernández-Ortuño D, Pérez-García A. Suppression of Chitin-Triggered Immunity by Plant Fungal Pathogens: A Case Study of the Cucurbit Powdery Mildew Fungus Podosphaera xanthii. J Fungi (Basel) 2023; 9:771. [PMID: 37504759 PMCID: PMC10381495 DOI: 10.3390/jof9070771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/17/2023] [Accepted: 07/17/2023] [Indexed: 07/29/2023] Open
Abstract
Fungal pathogens are significant plant-destroying microorganisms that present an increasing threat to the world's crop production. Chitin is a crucial component of fungal cell walls and a conserved MAMP (microbe-associated molecular pattern) that can be recognized by specific plant receptors, activating chitin-triggered immunity. The molecular mechanisms underlying the perception of chitin by specific receptors are well known in plants such as rice and Arabidopsis thaliana and are believed to function similarly in many other plants. To become a plant pathogen, fungi have to suppress the activation of chitin-triggered immunity. Therefore, fungal pathogens have evolved various strategies, such as prevention of chitin digestion or interference with plant chitin receptors or chitin signaling, which involve the secretion of fungal proteins in most cases. Since chitin immunity is a very effective defensive response, these fungal mechanisms are believed to work in close coordination. In this review, we first provide an overview of the current understanding of chitin-triggered immune signaling and the fungal proteins developed for its suppression. Second, as an example, we discuss the mechanisms operating in fungal biotrophs such as powdery mildew fungi, particularly in the model species Podosphaera xanthii, the main causal agent of powdery mildew in cucurbits. The key role of fungal effector proteins involved in the modification, degradation, or sequestration of immunogenic chitin oligomers is discussed in the context of fungal pathogenesis and the promotion of powdery mildew disease. Finally, the use of this fundamental knowledge for the development of intervention strategies against powdery mildew fungi is also discussed.
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Affiliation(s)
- Nisrine Bakhat
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Malaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Malaga, Spain
| | - Alejandra Vielba-Fernández
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Malaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Malaga, Spain
| | - Isabel Padilla-Roji
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Malaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Malaga, Spain
| | - Jesús Martínez-Cruz
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Malaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Malaga, Spain
| | - Álvaro Polonio
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Malaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Malaga, Spain
| | - Dolores Fernández-Ortuño
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Malaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Malaga, Spain
| | - Alejandro Pérez-García
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Malaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Malaga, Spain
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Martínez-Cruz JM, Polonio Á, Zanni R, Romero D, Gálvez J, Fernández-Ortuño D, Pérez-García A. Chitin Deacetylase, a Novel Target for the Design of Agricultural Fungicides. J Fungi (Basel) 2021; 7:jof7121009. [PMID: 34946992 PMCID: PMC8706340 DOI: 10.3390/jof7121009] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 12/23/2022] Open
Abstract
Fungicide resistance is a serious problem for agriculture. This is particularly apparent in the case of powdery mildew fungi. Therefore, there is an urgent need to develop new agrochemicals. Chitin is a well-known elicitor of plant immunity, and fungal pathogens have evolved strategies to overcome its detection. Among these strategies, chitin deacetylase (CDA) is responsible for modifying immunogenic chitooligomers and hydrolysing the acetamido group in the N-acetylglucosamine units to avoid recognition. In this work, we tested the hypothesis that CDA can be an appropriate target for antifungals using the cucurbit powdery mildew pathogen Podosphaera xanthii. According to our hypothesis, RNAi silencing of PxCDA resulted in a dramatic reduction in fungal growth that was linked to a rapid elicitation of chitin-triggered immunity. Similar results were obtained with treatments with carboxylic acids such as EDTA, a well-known CDA inhibitor. The disease-suppression activity of EDTA was not associated with its chelating activity since other chelating agents did not suppress disease. The binding of EDTA to CDA was confirmed by molecular docking studies. Furthermore, EDTA also suppressed green and grey mould-causing pathogens applied to oranges and strawberries, respectively. Our results conclusively show that CDA is a promising target for control of phytopathogenic fungi and that EDTA could be a starting point for fungicide design.
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Affiliation(s)
- Jesús M. Martínez-Cruz
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain; (J.M.M.-C.); (Á.P.); (D.R.); (A.P.-G.)
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010 Málaga, Spain
| | - Álvaro Polonio
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain; (J.M.M.-C.); (Á.P.); (D.R.); (A.P.-G.)
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010 Málaga, Spain
| | - Riccardo Zanni
- Molecular Topology and Drug Design Unit, Department of Physical Chemistry, University of Valencia, 46010 Valencia, Spain; (R.Z.); (J.G.)
| | - Diego Romero
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain; (J.M.M.-C.); (Á.P.); (D.R.); (A.P.-G.)
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010 Málaga, Spain
| | - Jorge Gálvez
- Molecular Topology and Drug Design Unit, Department of Physical Chemistry, University of Valencia, 46010 Valencia, Spain; (R.Z.); (J.G.)
| | - Dolores Fernández-Ortuño
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain; (J.M.M.-C.); (Á.P.); (D.R.); (A.P.-G.)
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010 Málaga, Spain
- Correspondence:
| | - Alejandro Pérez-García
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain; (J.M.M.-C.); (Á.P.); (D.R.); (A.P.-G.)
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010 Málaga, Spain
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Polonio Á, Fernández‐Ortuño D, de Vicente A, Pérez‐García A. A haustorial-expressed lytic polysaccharide monooxygenase from the cucurbit powdery mildew pathogen Podosphaera xanthii contributes to the suppression of chitin-triggered immunity. Mol Plant Pathol 2021; 22:580-601. [PMID: 33742545 PMCID: PMC8035642 DOI: 10.1111/mpp.13045] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 02/04/2021] [Accepted: 02/04/2021] [Indexed: 05/06/2023]
Abstract
Podosphaera xanthii is the main causal agent of cucurbit powdery mildew and a limiting factor of crop productivity. The lifestyle of this fungus is determined by the development of specialized parasitic structures inside epidermal cells, termed haustoria, that are responsible for the acquisition of nutrients and the release of effectors. A typical function of fungal effectors is the manipulation of host immunity, for example the suppression of pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI). Chitin is a major component of fungal cell walls, and chitin oligosaccharides are well-known PAMP elicitors. In this work, we examined the role of PHEC27213, the most highly expressed, haustorium-specific effector candidate of P. xanthii. According to different computational predictions, the protein folding of PHEC27213 was similar to that of lytic polysaccharide monooxygenases (LPMOs) and included a conserved histidine brace; however, PHEC27213 had low sequence similarity with LPMO proteins and displayed a putative chitin-binding domain that was different from the canonical carbohydrate-binding module. Binding and enzymatic assays demonstrated that PHEC27213 was able to bind and catalyse colloidal chitin, as well as chitooligosaccharides, acting as an LPMO. Furthermore, RNAi silencing experiments showed the potential of this protein to prevent the activation of chitin-triggered immunity. Moreover, proteins with similar features were found in other haustorium-forming fungal pathogens. Our results suggest that this protein is a new fungal LPMO that catalyses chitooligosaccharides, thus contributing to the suppression of plant immunity during haustorium development. To our knowledge, this is the first mechanism identified in the haustorium to suppress chitin signalling.
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Affiliation(s)
- Álvaro Polonio
- Departamento de MicrobiologíaFacultad de CienciasUniversidad de MálagaMálagaSpain
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’Universidad de MálagaConsejo Superior de Investigaciones Científicas (IHSM−UMA−CSIC)MálagaSpain
| | - Dolores Fernández‐Ortuño
- Departamento de MicrobiologíaFacultad de CienciasUniversidad de MálagaMálagaSpain
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’Universidad de MálagaConsejo Superior de Investigaciones Científicas (IHSM−UMA−CSIC)MálagaSpain
| | - Antonio de Vicente
- Departamento de MicrobiologíaFacultad de CienciasUniversidad de MálagaMálagaSpain
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’Universidad de MálagaConsejo Superior de Investigaciones Científicas (IHSM−UMA−CSIC)MálagaSpain
| | - Alejandro Pérez‐García
- Departamento de MicrobiologíaFacultad de CienciasUniversidad de MálagaMálagaSpain
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’Universidad de MálagaConsejo Superior de Investigaciones Científicas (IHSM−UMA−CSIC)MálagaSpain
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Polonio Á, Díaz-Martínez L, Fernández-Ortuño D, de Vicente A, Romero D, López-Ruiz FJ, Pérez-García A. A Hybrid Genome Assembly Resource for Podosphaera xanthii, the Main Causal Agent of Powdery Mildew Disease in Cucurbits. Mol Plant Microbe Interact 2021; 34:319-324. [PMID: 33141618 DOI: 10.1094/mpmi-08-20-0237-a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Podosphaera xanthii is the main causal agent of powdery mildew in cucurbits and, arguably, the most important fungal pathogen of cucurbit crops. Here, we present the first reference genome assembly for P. xanthii. We performed a hybrid genome assembly, using reads from Illumina NextSeq550 and PacBio Sequel S3. The short and long reads were assembled into 1,727 scaffolds with an N50 size of 163,173 bp, resulting in a 142-Mb genome size. The combination of homology-based and ab initio predictions allowed the prediction of 14,911 complete genes. Repetitive sequences comprised 76.2% of the genome. Our P. xanthii genome assembly improves considerably the molecular resources for research on P. xanthii-cucurbit interactions and provides new opportunities for further genomics, transcriptomics, and evolutionary studies in powdery mildew fungi.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Álvaro Polonio
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain
| | - Luis Díaz-Martínez
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain
| | - Dolores Fernández-Ortuño
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain
| | - Antonio de Vicente
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain
| | - Diego Romero
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain
| | - Francisco J López-Ruiz
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
| | - Alejandro Pérez-García
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain
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Polonio Á, Seoane P, Claros MG, Pérez-García A. The haustorial transcriptome of the cucurbit pathogen Podosphaera xanthii reveals new insights into the biotrophy and pathogenesis of powdery mildew fungi. BMC Genomics 2019; 20:543. [PMID: 31272366 PMCID: PMC6611051 DOI: 10.1186/s12864-019-5938-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 06/26/2019] [Indexed: 12/11/2022] Open
Abstract
Background Podosphaera xanthii is the main causal agent of powdery mildew disease in cucurbits and is responsible for important yield losses in these crops worldwide. Powdery mildew fungi are obligate biotrophs. In these parasites, biotrophy is determined by the presence of haustoria, which are specialized structures of parasitism developed by these fungi for the acquisition of nutrients and the delivery of effectors. Detailed molecular studies of powdery mildew haustoria are scarce due mainly to difficulties in their isolation. Therefore, their analysis is considered an important challenge for powdery mildew research. The aim of this work was to gain insights into powdery mildew biology by analysing the haustorial transcriptome of P. xanthii. Results Prior to RNA isolation and massive-scale mRNA sequencing, a flow cytometric approach was developed to isolate P. xanthii haustoria free of visible contaminants. Next, several commercial kits were used to isolate total RNA and to construct the cDNA and Illumina libraries that were finally sequenced by the Illumina NextSeq system. Using this approach, the maximum amount of information from low-quality RNA that could be obtained was used to accomplish the de novo assembly of the P. xanthii haustorial transcriptome. The subsequent analysis of this transcriptome and comparison with the epiphytic transcriptome allowed us to identify the importance of several biological processes for haustorial cells such as protection against reactive oxygen species, the acquisition of different nutrients and genetic regulation mediated by non-coding RNAs. In addition, we could also identify several secreted proteins expressed exclusively in haustoria such as cell adhesion proteins that have not been related to powdery mildew biology to date. Conclusions This work provides a novel approach to study the molecular aspects of powdery mildew haustoria. In addition, the results of this study have also allowed us to identify certain previously unknown processes and proteins involved in the biology of powdery mildews that could be essential for their biotrophy and pathogenesis. Electronic supplementary material The online version of this article (10.1186/s12864-019-5938-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Álvaro Polonio
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur 31, 29071, Málaga, Spain.,Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur 31, 29071, Málaga, Spain
| | - Pedro Seoane
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur 31, 29071, Málaga, Spain
| | - M Gonzalo Claros
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur 31, 29071, Málaga, Spain
| | - Alejandro Pérez-García
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur 31, 29071, Málaga, Spain. .,Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur 31, 29071, Málaga, Spain.
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7
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Polonio Á, Pineda M, Bautista R, Martínez-Cruz J, Pérez-Bueno ML, Barón M, Pérez-García A. RNA-seq analysis and fluorescence imaging of melon powdery mildew disease reveal an orchestrated reprogramming of host physiology. Sci Rep 2019; 9:7978. [PMID: 31138852 PMCID: PMC6538759 DOI: 10.1038/s41598-019-44443-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 05/16/2019] [Indexed: 02/04/2023] Open
Abstract
The cucurbit powdery mildew elicited by Podosphaera xanthii is one of the most important limiting factors in cucurbit production. Our knowledge of the genetic and molecular bases underlying the physiological processes governing this disease is very limited. We used RNA-sequencing to identify differentially expressed genes in leaves of Cucumis melo upon inoculation with P. xanthii, using RNA samples obtained at different time points during the early stages of infection and their corresponding uninfected controls. In parallel, melon plants were phenotypically characterized using imaging techniques. We found a high number of differentially expressed genes (DEGs) in infected plants, which allowed for the identification of many plant processes that were dysregulated by the infection. Among those, genes involved in photosynthesis and related processes were found to be upregulated, whereas genes involved in secondary metabolism pathways, such as phenylpropanoid biosynthesis, were downregulated. These changes in gene expression could be functionally validated by chlorophyll fluorescence imaging and blue-green fluorescence imaging analyses, which corroborated the alterations in photosynthetic activity and the suppression of phenolic compound biosynthesis. The powdery mildew disease in melon is a consequence of a complex and multifaceted process that involves the dysregulation of many plant pathways such as primary and secondary metabolism.
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Affiliation(s)
- Álvaro Polonio
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur 31, 29071, Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur 31, 29071, Málaga, Spain
| | - Mónica Pineda
- Departamento de Bioquímica y Biología Celular y Molecular de Plantas, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Profesor Albareda 1, 18008, Granada, Spain
| | - Rocío Bautista
- Plataforma Andaluza de Bioinformática, Edificio de Bioinnovación, Severo Ochoa 34, Parque Tecnológico de Andalucía, 29590, Málaga, Spain
| | - Jesús Martínez-Cruz
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur 31, 29071, Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur 31, 29071, Málaga, Spain
| | - María Luisa Pérez-Bueno
- Departamento de Bioquímica y Biología Celular y Molecular de Plantas, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Profesor Albareda 1, 18008, Granada, Spain
| | - Matilde Barón
- Departamento de Bioquímica y Biología Celular y Molecular de Plantas, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Profesor Albareda 1, 18008, Granada, Spain
| | - Alejandro Pérez-García
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur 31, 29071, Málaga, Spain.
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur 31, 29071, Málaga, Spain.
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Polonio Á, Vida C, de Vicente A, Cazorla FM. Impact of motility and chemotaxis features of the rhizobacterium Pseudomonas chlororaphis PCL1606 on its biocontrol of avocado white root rot. Int Microbiol 2019; 20:95-104. [PMID: 28617527 DOI: 10.2436/20.1501.01.289] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 04/28/2017] [Indexed: 11/15/2022]
Abstract
The biocontrol rhizobacterium Pseudomonas chlororaphis PCL1606 has the ability to protect avocado plants against white root rot produced by the phytopathogenic fungus Rosellinia necatrix. Moreover, PCL1606 displayed direct interactions with avocado roots and the pathogenic fungus. Thus, nonmotile (flgK mutant) and non-chemotactic (cheA mutant) derivatives of PCL1606 were constructed to emphasize the importance of motility and chemotaxis in the biological behaviour of PCL1606 during the biocontrol interaction. Plate chemotaxis assay showed that PCL1606 was attracted to the single compounds tested, such as glucose, glutamate, succinate, aspartate and malate, but no chemotaxis was observed to avocado or R. necatrix exudates. Using the more sensitive capillary assay, it was reported that smaller concentrations (1 mM) of single compounds elicited high chemotactic responses, and strong attraction was confirmed to avocado and R. necatrix exudates. Finally, biocontrol experiments revealed that the cheA and fglK derivative mutants reduced root protection against R. necatrix, suggesting an important role for these biological traits in biocontrol by P. chlororaphis PCL1606. [Int Microbiol 20(2):94-104 (2017)].
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Affiliation(s)
- Álvaro Polonio
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", IHSM-UMA-CSIC. Departamento de Microbiología, Facultad de Ciencias, Campus de Teatinos, 29071 Málaga, Spain
| | - Carmen Vida
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", IHSM-UMA-CSIC. Departamento de Microbiología, Facultad de Ciencias, Campus de Teatinos, 29071 Málaga, Spain
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", IHSM-UMA-CSIC. Departamento de Microbiología, Facultad de Ciencias, Campus de Teatinos, 29071 Málaga, Spain
| | - Francisco M Cazorla
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", IHSM-UMA-CSIC. Departamento de Microbiología, Facultad de Ciencias, Campus de Teatinos, 29071 Málaga, Spain
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Seoane P, Espigares M, Carmona R, Polonio Á, Quintana J, Cretazzo E, Bota J, Pérez-García A, Dios Alché JD, Gómez L, Claros MG. TransFlow: a modular framework for assembling and assessing accurate de novo transcriptomes in non-model organisms. BMC Bioinformatics 2018; 19:416. [PMID: 30453874 PMCID: PMC6245506 DOI: 10.1186/s12859-018-2384-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The advances in high-throughput sequencing technologies are allowing more and more de novo assembling of transcriptomes from many new organisms. Some degree of automation and evaluation is required to warrant reproducibility, repetitivity and the selection of the best possible transcriptome. Workflows and pipelines are becoming an absolute requirement for such a purpose, but the issue of assembling evaluation for de novo transcriptomes in organisms lacking a sequenced genome remains unsolved. An automated, reproducible and flexible framework called TransFlow to accomplish this task is described. RESULTS TransFlow with its five independent modules was designed to build different workflows depending on the nature of the original reads. This architecture enables different combinations of Illumina and Roche/454 sequencing data, and can be extended to other sequencing platforms. Its capabilities are illustrated with the selection of reliable plant reference transcriptomes and the assembling six transcriptomes (three case studies for grapevine leaves, olive tree pollen, and chestnut stem, and other three for haustorium, epiphytic structures and their combination for the phytopathogenic fungus Podosphaera xanthii). Arabidopsis and poplar transcriptomes revealed to be the best references. A common result regarding de novo assemblies is that Illumina paired-end reads of 100 nt in length assembled with OASES can provide reliable transcriptomes, while the contribution of longer reads is noticeable only when they complement a set of short, single-reads. CONCLUSIONS TransFlow can handle up to 181 different assembling strategies. Evaluation based on principal component analyses allows its self-adaptation to different sets of reads to provide a suitable transcriptome for each combination of reads and assemblers. As a result, each case study has its own behaviour, prioritises evaluation parameters, and gives an objective and automated way for detecting the best transcriptome within a pool of them. Sequencing data type and quantity (preferably several hundred millions of 2×100 nt or longer), assemblers (OASES for Illumina, MIRA4 and EULER-SR reconciled with CAP3 for Roche/454) and strategy (preferably scaffolding with OASES, and probably merging with Roche/454 when available) arise as the most impacting factors.
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Affiliation(s)
- Pedro Seoane
- Departmento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus de Teatinos s/n, Malaga, 29071 Spain
| | - Marina Espigares
- Departmento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus de Teatinos s/n, Malaga, 29071 Spain
| | - Rosario Carmona
- Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants. Estación Experimental del Zaidín. CSIC, Prof. Albareda, 1, Granada, 18160 Spain
| | - Álvaro Polonio
- Departamento de Microbiología, and Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus de Teatinos s/n, Malaga, 29071 Spain
| | - Julia Quintana
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA, 01609-2280 USA
| | - Enrico Cretazzo
- Instituto Andaluz de Investigación y Formación Agraria (IFAPA), Centro de Churriana, Cortijo de la Cruz s/n, Churriana, 29140 Spain
| | - Josefina Bota
- Grup de Recerca en Biologia de les Plantes en Condicions Mediterrànies, Departament de Biologia, Universitat de les Illes Balears, Carretera de Valldemossa, km 7.5, Palma de Mallorca, 07122 Spain
| | - Alejandro Pérez-García
- Departamento de Microbiología, and Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus de Teatinos s/n, Malaga, 29071 Spain
| | - Juan de Dios Alché
- Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants. Estación Experimental del Zaidín. CSIC, Prof. Albareda, 1, Granada, 18160 Spain
| | - Luis Gómez
- Departamento de Sistemas y Recursos Naturales, ETSI Forestal, de Montes y del Medio Natural, Universidad Politécnica de Madrid, Ciudad Universitaria, Madrid, 28040 Spain
- CBGP, INIA-Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Spain
| | - M. Gonzalo Claros
- Departmento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus de Teatinos s/n, Malaga, 29071 Spain
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