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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] [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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2
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Mart Nez-Cruz JS, Romero D, Hierrezuelo JS, Thon M, de Vicente A, P Rez-Garc A A. Effectors with chitinase activity (EWCAs), a family of conserved, secreted fungal chitinases that suppress chitin-triggered immunity. THE PLANT CELL 2021; 33:1319-1340. [PMID: 33793825 DOI: 10.1093/plcell/koab011] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 12/11/2020] [Indexed: 05/23/2023]
Abstract
In plants, chitin-triggered immunity is one of the first lines of defense against fungi, but phytopathogenic fungi have developed different strategies to prevent the recognition of chitin. Obligate biotrophs such as powdery mildew fungi suppress the activation of host responses; however, little is known about how these fungi subvert the immunity elicited by chitin. During epiphytic growth, the cucurbit powdery mildew fungus Podosphaera xanthii expresses a family of candidate effector genes comprising nine members with an unknown function. In this work, we examine the role of these candidates in the infection of melon (Cucumis melo L.) plants, using gene expression analysis, RNAi silencing assays, protein modeling and protein-ligand predictions, enzymatic assays, and protein localization studies. Our results show that these proteins are chitinases that are released at pathogen penetration sites to break down immunogenic chitin oligomers, thus preventing the activation of chitin-triggered immunity. In addition, these effectors, designated effectors with chitinase activity (EWCAs), are widely distributed in pathogenic fungi. Our findings reveal a mechanism by which fungi suppress plant immunity and reinforce the idea that preventing the perception of chitin by the host is mandatory for survival and development of fungi in plant environments.
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Affiliation(s)
- Jes S Mart Nez-Cruz
- Departamento de Microbiolog�a, Facultad de Ciencias, Universidad de M�laga, M�laga 29071, Spain
- Instituto de Hortofruticultura Subtropical y Mediterr�nea "La Mayora", Universidad de M�laga, Consejo Superior de Investigaciones Cient�ficas (IHSM‒UMA‒CSIC), M�laga 29071, Spain
| | - Diego Romero
- Departamento de Microbiolog�a, Facultad de Ciencias, Universidad de M�laga, M�laga 29071, Spain
- Instituto de Hortofruticultura Subtropical y Mediterr�nea "La Mayora", Universidad de M�laga, Consejo Superior de Investigaciones Cient�ficas (IHSM‒UMA‒CSIC), M�laga 29071, Spain
| | - Jes S Hierrezuelo
- Departamento de Microbiolog�a, Facultad de Ciencias, Universidad de M�laga, M�laga 29071, Spain
- Instituto de Hortofruticultura Subtropical y Mediterr�nea "La Mayora", Universidad de M�laga, Consejo Superior de Investigaciones Cient�ficas (IHSM‒UMA‒CSIC), M�laga 29071, Spain
| | - Michael Thon
- Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Salamanca 37185, Spain
| | - Antonio de Vicente
- Departamento de Microbiolog�a, Facultad de Ciencias, Universidad de M�laga, M�laga 29071, Spain
- Instituto de Hortofruticultura Subtropical y Mediterr�nea "La Mayora", Universidad de M�laga, Consejo Superior de Investigaciones Cient�ficas (IHSM‒UMA‒CSIC), M�laga 29071, Spain
| | - Alejandro P Rez-Garc A
- Departamento de Microbiolog�a, Facultad de Ciencias, Universidad de M�laga, M�laga 29071, Spain
- Instituto de Hortofruticultura Subtropical y Mediterr�nea "La Mayora", Universidad de M�laga, Consejo Superior de Investigaciones Cient�ficas (IHSM‒UMA‒CSIC), M�laga 29071, Spain
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3
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Kimura S, Shibata Y, Oi T, Kawakita K, Takemoto D. Effect of flutianil on the morphology and gene expression of powdery mildew. JOURNAL OF PESTICIDE SCIENCE 2021; 46:206-213. [PMID: 34135682 PMCID: PMC8175223 DOI: 10.1584/jpestics.d21-003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/26/2021] [Indexed: 06/12/2023]
Abstract
Flutianil, a fungicide effective only on powdery mildew, was previously reported to affect the host cell's haustorial formation and nutrient absorption. Studies were conducted to investigate flutianil's primary site of action on Blumeria graminis morphology using transmission electron microscope (TEM) observation and RNA sequencing (RAN-seq) techniques. TEM observation revealed that flutianil caused the extra-haustorial matrix and fungal cell wall to be obscured, without remarkable changes of other fungal organelles. RNA-seq analysis indicated that, unlike other powdery-mildew fungicides, flutianil did not significantly affect the constantly expressed genes for the survival of B. graminis. Genes whose expression is up- or downregulated by flutianil were found; these are the three sugar transporter genes and various effector genes, mainly expressed in haustoria. These findings indicate that the primary site of action of flutianil might be in the haustoria.
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Affiliation(s)
- Sachi Kimura
- Research and Development Division, OAT Agrio Co., Ltd., Tokushima, Japan
| | - Yusuke Shibata
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, 464–8601, Japan
| | - Takao Oi
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, 464–8601, Japan
| | - Kazuhito Kawakita
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, 464–8601, Japan
| | - Daigo Takemoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, 464–8601, Japan
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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. MOLECULAR PLANT PATHOLOGY 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] [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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5
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McGuffin LJ, Adiyaman R, Maghrabi AHA, Shuid AN, Brackenridge DA, Nealon JO, Philomina LS. IntFOLD: an integrated web resource for high performance protein structure and function prediction. Nucleic Acids Res 2020; 47:W408-W413. [PMID: 31045208 PMCID: PMC6602432 DOI: 10.1093/nar/gkz322] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/05/2019] [Accepted: 04/23/2019] [Indexed: 12/14/2022] Open
Abstract
The IntFOLD server provides a unified resource for the automated prediction of: protein tertiary structures with built-in estimates of model accuracy (EMA), protein structural domain boundaries, natively unstructured or disordered regions in proteins, and protein–ligand interactions. The component methods have been independently evaluated via the successive blind CASP experiments and the continual CAMEO benchmarking project. The IntFOLD server has established its ranking as one of the best performing publicly available servers, based on independent official evaluation metrics. Here, we describe significant updates to the server back end, where we have focused on performance improvements in tertiary structure predictions, in terms of global 3D model quality and accuracy self-estimates (ASE), which we achieve using our newly improved ModFOLD7_rank algorithm. We also report on various upgrades to the front end including: a streamlined submission process, enhanced visualization of models, new confidence scores for ranking, and links for accessing all annotated model data. Furthermore, we now include an option for users to submit selected models for further refinement via convenient push buttons. The IntFOLD server is freely available at: http://www.reading.ac.uk/bioinf/IntFOLD/.
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Affiliation(s)
- Liam J McGuffin
- School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, UK
| | - Recep Adiyaman
- School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, UK
| | - Ali H A Maghrabi
- School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, UK
| | - Ahmad N Shuid
- School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, UK.,Infectomics cluster, Advanced Medical and Dental Institute, University of Science, Malaysia, Bertam, 13200, Kepala Batas, Pulau Pinang, Malaysia
| | | | - John O Nealon
- School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, UK
| | - Limcy S Philomina
- School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, UK
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Sharma G, Aminedi R, Saxena D, Gupta A, Banerjee P, Jain D, Chandran D. Effector mining from the Erysiphe pisi haustorial transcriptome identifies novel candidates involved in pea powdery mildew pathogenesis. MOLECULAR PLANT PATHOLOGY 2019; 20:1506-1522. [PMID: 31603276 PMCID: PMC6804345 DOI: 10.1111/mpp.12862] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Pea powdery mildew (PM) is an important fungal disease caused by an obligate biotroph, Erysiphe pisi (Ep), which significantly impacts pea production worldwide. The phytopathogen secretes a plethora of effectors, primarily through specialized infection structures termed haustoria, to establish a dynamic relationship with its host. To identify Ep effector candidates, a cDNA library of enriched haustoria from Ep-infected pea leaves was sequenced. The Ep transcriptome encodes 622 Ep candidate secreted proteins (CSPs), of which 167 were predicted to be candidate secreted effector proteins (CSEPs). Phylogenetic analysis indicates that Ep CSEPs are highly diverse, but, unlike cereal PM CSEPs, exhibit extensive sequence similarity with effectors from other PMs. Quantitative real-time PCR of a subset of EpCSEP/CSPs revealed that the majority are preferentially expressed in haustoria and exhibit infection stage-specific expression patterns. The functional roles of EpCSEP001, EpCSEP009 and EpCSP083 were probed by host-induced gene silencing (HIGS) via a double-stranded (ds) RNA-mediated RNAi approach. Foliar application of individual EpCSEP/CSP dsRNAs resulted in a marked reduction in PM disease symptoms. These findings were consistent with microscopic and molecular studies, suggesting that these Ep CSEP/CSPs play important roles in pea PM pathogenesis. Homology modelling revealed that EpCSEP001 and EpCSEP009 are analogous to fungal ribonucleases and belong to the RALPH family of effectors. This is the first study to identify and functionally validate candidate effectors from the agriculturally relevant pea PM, and highlights the utility of transcriptomics and HIGS to elucidate the key proteins associated with Ep pathogenesis.
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Affiliation(s)
- Gunjan Sharma
- Laboratory of Plant–Microbe InteractionsRegional Centre for BiotechnologyNCR Biotech Science ClusterFaridabadHaryanaIndia
| | - Raghavendra Aminedi
- Laboratory of Plant–Microbe InteractionsRegional Centre for BiotechnologyNCR Biotech Science ClusterFaridabadHaryanaIndia
| | - Divya Saxena
- Laboratory of Plant–Microbe InteractionsRegional Centre for BiotechnologyNCR Biotech Science ClusterFaridabadHaryanaIndia
- School of Computational and Integrative SciencesJawaharlal Nehru UniversityNew DelhiIndia
| | - Arunima Gupta
- Laboratory of Plant–Microbe InteractionsRegional Centre for BiotechnologyNCR Biotech Science ClusterFaridabadHaryanaIndia
| | - Priyajit Banerjee
- Transcription Regulation Lab, Regional Centre for BiotechnologyNCR Biotech Science ClusterFaridabadHaryanaIndia
- Kalinga Institute of Industrial TechnologyBhubaneswarOrissaIndia
| | - Deepti Jain
- Transcription Regulation Lab, Regional Centre for BiotechnologyNCR Biotech Science ClusterFaridabadHaryanaIndia
| | - Divya Chandran
- Laboratory of Plant–Microbe InteractionsRegional Centre for BiotechnologyNCR Biotech Science ClusterFaridabadHaryanaIndia
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7
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Li L, Collier B, Spanu PD. Isolation of Powdery Mildew Haustoria from Infected Barley. Bio Protoc 2019; 9:e3299. [PMID: 33654812 DOI: 10.21769/bioprotoc.3299] [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: 04/24/2019] [Revised: 06/18/2019] [Accepted: 06/23/2019] [Indexed: 11/02/2022] Open
Abstract
Blumeria graminis is a fungus that causes powdery mildews on grasses, such as barley. Investigations of this pathogen present many challenges due to its obligate biotrophic nature. This means that the fungus can only grow in the presence of a living host plant. B. graminis forms epiphytic mycelia on the plant surface and feeding organs (haustoria) inside the epidermal cells of the host plant. Therefore, it is difficult to separate the fungus from plant tissues. This protocol shows how to obtain different fungal structures from powdery mildew infected barley leaves. The epiphytic mycelia including conidia and conidiophores can be separated after immersing the infected leaves into 5% cellulose acetate dissolved in acetone, and peeling off the cellulose acetate membrane. Then, the haustoria are isolated from dissected epidermis after cellulase degradation of plant cell walls. The isolated haustoria remain intact with few plant impurities. The haustoria may be visualized by epifluorescence microscopy after staining with the chitin-specific dye WGA-Alexa Fluor 488. Finally, dissected material can be either processed immediately or kept at -80 °C for long-term storage for studies on gene expression and protein identification, for example by mass spectrometry.
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Affiliation(s)
- Linhan Li
- Department of Life Sciences, Imperial College London, London, UK
| | - Benjamin Collier
- Department of Life Sciences, Imperial College London, London, UK
| | - Pietro D Spanu
- Department of Life Sciences, Imperial College London, London, UK
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8
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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] [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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9
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Bheri M, M Bhosle S, Makandar R. Shotgun proteomics provides an insight into pathogenesis-related proteins using anamorphic stage of the biotroph, Erysiphe pisi pathogen of garden pea. Microbiol Res 2019; 222:25-34. [PMID: 30928027 DOI: 10.1016/j.micres.2019.02.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/30/2018] [Accepted: 02/08/2019] [Indexed: 01/16/2023]
Abstract
E. pisi is an ascomycete member causing powdery mildew disease of garden pea. It is a biotrophic pathogen, requiring a living host for its survival. Our understanding of molecular mechanisms underlying its pathogenesis is limited. The identification of proteins expressed in the pathogen is required to gain an insight into the functional mechanisms of an obligate biotrophic fungal pathogen. In this study, the proteome of the anamorphic stage of E. pisi pathogen has been elucidated through the nano LC-MS/MS approach. A total of 328 distinct proteins were detected from Erysiphe isolates infecting the susceptible pea cultivar, Arkel. The proteome is available via ProteomeXchange with identifier PXD010238. The functional classification of protein accessions based on Gene Ontology revealed proteins related to signal transduction, secondary metabolite formation and stress which might be involved in virulence and pathogenesis. The functional validation carried through differential expression of genes encoding G-protein beta subunit, a Cyclophilin (Peptidyl prolyl cis-transisomerase) and ABC transporter in a time course study confirmed their putative role in pathogenesis between resistant and susceptible genotypes, JI2480 and Arkel. The garden pea-powdery mildew pathosystem is largely unexplored, therefore, the identified proteome provides a first-hand information and will form a basis to analyze mechanisms involving pathogen survival, pathogenesis and virulence.
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Affiliation(s)
- Malathi Bheri
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad- 500046, India
| | - Sheetal M Bhosle
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad- 500046, India
| | - Ragiba Makandar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad- 500046, India.
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Lambertucci S, Orman KM, Das Gupta S, Fisher JP, Gazal S, Williamson RJ, Cramer R, Bindschedler LV. Analysis of Barley Leaf Epidermis and Extrahaustorial Proteomes During Powdery Mildew Infection Reveals That the PR5 Thaumatin-Like Protein TLP5 Is Required for Susceptibility Towards Blumeria graminis f. sp. hordei. FRONTIERS IN PLANT SCIENCE 2019; 10:1138. [PMID: 31736984 PMCID: PMC6831746 DOI: 10.3389/fpls.2019.01138] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 08/20/2019] [Indexed: 05/18/2023]
Abstract
Powdery mildews are biotrophic pathogens causing fungal diseases in many economically important crops, including cereals, which are affected by Blumeria graminis. Powdery mildews only invade the epidermal cell layer of leaf tissues, in which they form haustorial structures. Haustoria are at the center of the biotrophic interaction by taking up nutrients from the host and by delivering effectors in the invaded cells to jeopardize plant immunity. Haustoria are composed of a fungal core delimited by a haustorial plasma membrane and cell wall. Surrounding these is the extrahaustorial complex, of which the extrahaustorial membrane is of plant origin. Although haustoria transcriptomes and proteomes have been investigated for Blumeria, the proteomes of barley epidermis upon infection and the barley components of the extrahaustorial complex remains unexplored. When comparing proteomes of infected and non-infected epidermis, several classical pathogenesis-related (PR) proteins were more abundant in infected epidermis. These included peroxidases, chitinases, cysteine-rich venom secreted proteins/PR1 and two thaumatin-like PR5 protein isoforms, of which TLP5 was previously shown to interact with the Blumeria effector BEC1054 (CSEP0064). Against expectations, transient TLP5 gene silencing suggested that TLP5 does not contribute to resistance but modulates susceptibility towards B. graminis. In a second proteomics comparison, haustorial structures were enriched from infected epidermal strips to identify plant proteins closely associated with the extrahaustorial complex. In these haustoria-enriched samples, relative abundances were higher for several V-type ATP synthase/ATPase subunits, suggesting the generation of proton gradients in the extrahaustorial space. Other haustoria-associated proteins included secreted or membrane proteins such as a PIP2 aquaporin, an early nodulin-like protein 9, an aspartate protease and other proteases, a lipase, and a lipid transfer protein, all of which are potential modulators of immunity, or the targets of pathogen effectors. Moreover, the ER BIP-like HSP70, may link ER stress responses and the idea of ER-like properties previously attributed to the extrahaustorial membrane. This initial investigation exploring the barley proteomes of Blumeria-infected tissues and haustoria, associated with a transient gene silencing approach, is invaluable to gain first insight of key players of resistance and susceptibility.
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Affiliation(s)
- Sebastien Lambertucci
- School of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
| | - Kate Mary Orman
- School of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
| | - Shaoli Das Gupta
- School of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
| | - James Paul Fisher
- School of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
| | - Snehi Gazal
- School of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
| | | | - Rainer Cramer
- Department of Chemistry, University of Reading, Reading, United Kingdom
| | - Laurence Véronique Bindschedler
- School of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
- *Correspondence: Laurence Véronique Bindschedler,
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Bourras S, Praz CR, Spanu PD, Keller B. Cereal powdery mildew effectors: a complex toolbox for an obligate pathogen. Curr Opin Microbiol 2018; 46:26-33. [DOI: 10.1016/j.mib.2018.01.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/22/2018] [Accepted: 01/31/2018] [Indexed: 01/25/2023]
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12
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Kallamadi PR, Dandu K, Kirti PB, Rao CM, Thakur SS, Mulpuri S. An Insight into Powdery Mildew-Infected, Susceptible, Resistant, and Immune Sunflower Genotypes. Proteomics 2018; 18:e1700418. [DOI: 10.1002/pmic.201700418] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 05/26/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Prathap Reddy Kallamadi
- ICAR- Indian Institute of Oilseeds Research; Rajendranagar 500 030 Hyderabad India
- University of Hyderabad; Prof. C.R. Rao Road 500 046 Hyderabad India
| | - Kamakshi Dandu
- CSIR- Centre for Cellular and Molecular Biology; Uppal Road, Habsiguda 500 007 Hyderabad India
| | | | - Chintalagiri Mohan Rao
- CSIR- Centre for Cellular and Molecular Biology; Uppal Road, Habsiguda 500 007 Hyderabad India
| | - Suman S Thakur
- CSIR- Centre for Cellular and Molecular Biology; Uppal Road, Habsiguda 500 007 Hyderabad India
| | - Sujatha Mulpuri
- ICAR- Indian Institute of Oilseeds Research; Rajendranagar 500 030 Hyderabad India
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Hu Y, Liang Y, Zhang M, Tan F, Zhong S, Li X, Gong G, Chang X, Shang J, Tang S, Li T, Luo P. Comparative transcriptome profiling of Blumeria graminis f. sp. tritici during compatible and incompatible interactions with sister wheat lines carrying and lacking Pm40. PLoS One 2018; 13:e0198891. [PMID: 29975700 PMCID: PMC6033381 DOI: 10.1371/journal.pone.0198891] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/25/2018] [Indexed: 11/18/2022] Open
Abstract
Blumeria graminis f. sp. tritici (Bgt) is an obligate biotrophic fungus that causes wheat powdery mildew, which is a devastating disease in wheat. However, little is known about the pathogenesis of this fungus, and differences in the pathogenesis of the same pathogen at various resistance levels in hosts have not been determined. In the present study, leaf tissues of both Pm40-expressing hexaploid wheat line L658 and its Pm40-deficient sister line L958 were harvested at 0 (without inoculation), 6, 12, 24, 48 and 72 hours post-inoculation (hpi) with Bgt race 15 and then subjected to RNA sequencing (RNA-seq). In addition, we also observed changes in fungal growth morphology at the aforementioned time points. There was a high correlation between percentage of reads mapped to the Bgt reference genome and biomass of the fungus within the leaf tissue during the growth process. The percentage of mapped reads of Bgt in compatible interactions was significantly higher (at the p<0.05 level) than that of reads in incompatible interactions from 24 to 72 hpi. Further functional annotations indicated that expression levels of genes encoding H+-transporting ATPase, putative secreted effector proteins (PSEPs) and heat shock proteins (HSPs) were significantly up-regulated in compatible interactions compared with these levels in incompatible interactions, particularly at 72 hpi. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis suggested that genes involved in the endocytosis pathway were also enriched in compatible interactions. Overall, genes encoding H+-transporting ATPase, PSEPs and HSPs possibly played crucial roles in successfully establishing the pathogenesis of compatible interactions during late stages of inoculation. The study results also indicated that endocytosis is likely to play a potential role in Bgt in establishing compatible interactions.
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Affiliation(s)
- Yuting Hu
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yinping Liang
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Min Zhang
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Feiquan Tan
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shengfu Zhong
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xin Li
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Guoshu Gong
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaoli Chang
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jing Shang
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shengwen Tang
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Tao Li
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Peigao Luo
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
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Laur J, Ramakrishnan GB, Labbé C, Lefebvre F, Spanu PD, Bélanger RR. Effectors involved in fungal-fungal interaction lead to a rare phenomenon of hyperbiotrophy in the tritrophic system biocontrol agent-powdery mildew-plant. THE NEW PHYTOLOGIST 2018; 217:713-725. [PMID: 29044534 PMCID: PMC6079639 DOI: 10.1111/nph.14851] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 09/13/2017] [Indexed: 05/08/2023]
Abstract
Tritrophic interactions involving a biocontrol agent, a pathogen and a plant have been analyzed predominantly from the perspective of the biocontrol agent. We have conducted the first comprehensive transcriptomic analysis of all three organisms in an effort to understand the elusive properties of Pseudozyma flocculosa in the context of its biocontrol activity against Blumeria graminis f.sp. hordei as it parasitizes Hordeum vulgare. After inoculation of P. flocculosa, the tripartite interaction was monitored over time and samples collected for scanning electron microscopy and RNA sequencing. Based on our observations, P. flocculosa indirectly parasitizes barley, albeit transiently, by diverting nutrients extracted by B. graminis from barley leaves through a process involving unique effectors. This brings novel evidence that such molecules can also influence fungal-fungal interactions. Their release is synchronized with a higher expression of powdery mildew haustorial effectors, a sharp decline in the photosynthetic machinery of barley and a developmental peak in P. flocculosa. The interaction culminates with a collapse of B. graminis haustoria, thereby stopping P. flocculosa growth, as barley plants show higher metabolic activity. To conclude, our study has uncovered a complex and intricate phenomenon, described here as hyperbiotrophy, only achievable through the conjugated action of the three protagonists.
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Affiliation(s)
- Joan Laur
- Département de PhytologieUniversité LavalQuébecQCCanadaG1V 0A6
| | | | - Caroline Labbé
- Département de PhytologieUniversité LavalQuébecQCCanadaG1V 0A6
| | | | - Pietro D. Spanu
- Department of Life SciencesImperial College LondonSouth Kensington CampusLondonSW7 2AZUK
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15
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Franceschetti M, Maqbool A, Jiménez-Dalmaroni MJ, Pennington HG, Kamoun S, Banfield MJ. Effectors of Filamentous Plant Pathogens: Commonalities amid Diversity. Microbiol Mol Biol Rev 2017; 81:e00066-16. [PMID: 28356329 PMCID: PMC5485802 DOI: 10.1128/mmbr.00066-16] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fungi and oomycetes are filamentous microorganisms that include a diversity of highly developed pathogens of plants. These are sophisticated modulators of plant processes that secrete an arsenal of effector proteins to target multiple host cell compartments and enable parasitic infection. Genome sequencing revealed complex catalogues of effectors of filamentous pathogens, with some species harboring hundreds of effector genes. Although a large fraction of these effector genes encode secreted proteins with weak or no sequence similarity to known proteins, structural studies have revealed unexpected similarities amid the diversity. This article reviews progress in our understanding of effector structure and function in light of these new insights. We conclude that there is emerging evidence for multiple pathways of evolution of effectors of filamentous plant pathogens but that some families have probably expanded from a common ancestor by duplication and diversification. Conserved folds, such as the oomycete WY and the fungal MAX domains, are not predictive of the precise function of the effectors but serve as a chassis to support protein structural integrity while providing enough plasticity for the effectors to bind different host proteins and evolve unrelated activities inside host cells. Further effector evolution and diversification arise via short linear motifs, domain integration and duplications, and oligomerization.
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Affiliation(s)
- Marina Franceschetti
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Abbas Maqbool
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | | | - Helen G Pennington
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Mark J Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
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16
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Martínez-Cruz J, Romero D, de Vicente A, Pérez-García A. Transformation of the cucurbit powdery mildew pathogen Podosphaera xanthii by Agrobacterium tumefaciens. THE NEW PHYTOLOGIST 2017; 213:1961-1973. [PMID: 27864969 DOI: 10.1111/nph.14297] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 09/21/2016] [Indexed: 06/06/2023]
Abstract
The obligate biotrophic fungal pathogen Podosphaera xanthii is the main causal agent of powdery mildew in cucurbit crops all over the world. A major limitation of molecular studies of powdery mildew fungi (Erysiphales) is their genetic intractability. In this work, we describe a robust method based on the promiscuous transformation ability of Agrobacterium tumefaciens for reliable transformation of P. xanthii. The A. tumefaciens-mediated transformation (ATMT) system yielded transformants of P. xanthii with diverse transferred DNA (T-DNA) constructs. Analysis of the resultant transformants showed the random integration of T-DNA into the P. xanthii genome. The integrations were maintained in successive generations in the presence of selection pressure. Transformation was found to be transient, because in the absence of selection agent, the introduced genetic markers were lost due to excision of T-DNA from the genome. The ATMT system represents a potent tool for genetic manipulation of P. xanthii and will likely be useful for studying other biotrophic fungi. We hope that this method will contribute to the development of detailed molecular studies of the intimate interaction established between powdery mildew fungi and their host plants.
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Affiliation(s)
- Jesús Martínez-Cruz
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora' - Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, 29071, Spain
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga. Bulevar Louis Pasteur 31, Málaga, 29071, Spain
| | - Diego Romero
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora' - Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, 29071, Spain
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga. Bulevar Louis Pasteur 31, Málaga, 29071, Spain
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora' - Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, 29071, Spain
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga. Bulevar Louis Pasteur 31, Málaga, 29071, Spain
| | - Alejandro Pérez-García
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora' - Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, 29071, Spain
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga. Bulevar Louis Pasteur 31, Málaga, 29071, Spain
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17
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Affiliation(s)
- Noriko Inada
- The Graduate School of Biological Sciences, Nara Institute of Science and Technology
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18
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Douchkov D, Lueck S, Hensel G, Kumlehn J, Rajaraman J, Johrde A, Doblin MS, Beahan CT, Kopischke M, Fuchs R, Lipka V, Niks RE, Bulone V, Chowdhury J, Little A, Burton RA, Bacic A, Fincher GB, Schweizer P. The barley (Hordeum vulgare) cellulose synthase-like D2 gene (HvCslD2) mediates penetration resistance to host-adapted and nonhost isolates of the powdery mildew fungus. THE NEW PHYTOLOGIST 2016; 212:421-33. [PMID: 27352228 DOI: 10.1111/nph.14065] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 05/10/2016] [Indexed: 05/20/2023]
Abstract
Cell walls and cellular turgor pressure shape and suspend the bodies of all vascular plants. In response to attack by fungal and oomycete pathogens, which usually breach their host's cell walls by mechanical force or by secreting lytic enzymes, plants often form local cell wall appositions (papillae) as an important first line of defence. The involvement of cell wall biosynthetic enzymes in the formation of these papillae is still poorly understood, especially in cereal crops. To investigate the role in plant defence of a candidate gene from barley (Hordeum vulgare) encoding cellulose synthase-like D2 (HvCslD2), we generated transgenic barley plants in which HvCslD2 was silenced through RNA interference (RNAi). The transgenic plants showed no growth defects but their papillae were more successfully penetrated by host-adapted, virulent as well as avirulent nonhost isolates of the powdery mildew fungus Blumeria graminis. Papilla penetration was associated with lower contents of cellulose in epidermal cell walls and increased digestion by fungal cell wall degrading enzymes. The results suggest that HvCslD2-mediated cell wall changes in the epidermal layer represent an important defence reaction both for nonhost and for quantitative host resistance against nonadapted wheat and host-adapted barley powdery mildew pathogens, respectively.
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Affiliation(s)
- Dimitar Douchkov
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) Gatersleben, Corrensstrasse 3, Stadt Seeland, 06466, Germany
| | - Stefanie Lueck
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) Gatersleben, Corrensstrasse 3, Stadt Seeland, 06466, Germany
| | - Goetz Hensel
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) Gatersleben, Corrensstrasse 3, Stadt Seeland, 06466, Germany
| | - Jochen Kumlehn
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) Gatersleben, Corrensstrasse 3, Stadt Seeland, 06466, Germany
| | - Jeyaraman Rajaraman
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) Gatersleben, Corrensstrasse 3, Stadt Seeland, 06466, Germany
| | - Annika Johrde
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) Gatersleben, Corrensstrasse 3, Stadt Seeland, 06466, Germany
| | - Monika S Doblin
- ARC Centre of Excellence in Plant Cell Walls, School of Botany, University of Melbourne, Parkville, Vic., 3010, Australia
| | - Cherie T Beahan
- ARC Centre of Excellence in Plant Cell Walls, School of Botany, University of Melbourne, Parkville, Vic., 3010, Australia
| | - Michaela Kopischke
- Department of Plant Cell Biology, Albrecht-von-Haller-Institute, Georg-August-University Göttingen, Julia-Lermontowa-Weg 3, Göttingen, D-37077, Germany
| | - René Fuchs
- Department of Plant Cell Biology, Albrecht-von-Haller-Institute, Georg-August-University Göttingen, Julia-Lermontowa-Weg 3, Göttingen, D-37077, Germany
| | - Volker Lipka
- Department of Plant Cell Biology, Albrecht-von-Haller-Institute, Georg-August-University Göttingen, Julia-Lermontowa-Weg 3, Göttingen, D-37077, Germany
| | - Rients E Niks
- Plant Sciences, Wageningen University, PO Box 386, Wageningen, 6700AJ, the Netherlands
| | - Vincent Bulone
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
- Division of Glycocience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Center, Stockholm, SE-106 91, Sweden
| | - Jamil Chowdhury
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Alan Little
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Rachel A Burton
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Antony Bacic
- ARC Centre of Excellence in Plant Cell Walls, School of Botany, University of Melbourne, Parkville, Vic., 3010, Australia
| | - Geoffrey B Fincher
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Patrick Schweizer
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) Gatersleben, Corrensstrasse 3, Stadt Seeland, 06466, Germany.
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Lohnes K, Quebbemann NR, Liu K, Kobzeff F, Loo JA, Ogorzalek Loo RR. Combining high-throughput MALDI-TOF mass spectrometry and isoelectric focusing gel electrophoresis for virtual 2D gel-based proteomics. Methods 2016; 104:163-9. [PMID: 26826592 PMCID: PMC4930893 DOI: 10.1016/j.ymeth.2016.01.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 01/13/2016] [Accepted: 01/25/2016] [Indexed: 01/07/2023] Open
Abstract
The virtual two-dimensional gel electrophoresis/mass spectrometry (virtual 2D gel/MS) technology combines the premier, high-resolution capabilities of 2D gel electrophoresis with the sensitivity and high mass accuracy of mass spectrometry (MS). Intact proteins separated by isoelectric focusing (IEF) gel electrophoresis are imaged from immobilized pH gradient (IPG) polyacrylamide gels (the first dimension of classic 2D-PAGE) by matrix-assisted laser desorption/ionization (MALDI) MS. Obtaining accurate intact masses from sub-picomole-level proteins embedded in 2D-PAGE gels or in IPG strips is desirable to elucidate how the protein of one spot identified as protein 'A' on a 2D gel differs from the protein of another spot identified as the same protein, whenever tryptic peptide maps fail to resolve the issue. This task, however, has been extremely challenging. Virtual 2D gel/MS provides access to these intact masses. Modifications to our matrix deposition procedure improve the reliability with which IPG gels can be prepared; the new procedure is described. Development of this MALDI MS imaging (MSI) method for high-throughput MS with integrated 'top-down' MS to elucidate protein isoforms from complex biological samples is described and it is demonstrated that a 4-cm IPG gel segment can now be imaged in approximately 5min. Gel-wide chemical and enzymatic methods with further interrogation by MALDI MS/MS provide identifications, sequence-related information, and post-translational/transcriptional modification information. The MSI-based virtual 2D gel/MS platform may potentially link the benefits of 'top-down' and 'bottom-up' proteomics.
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Affiliation(s)
- Karen Lohnes
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Neil R Quebbemann
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kate Liu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Fred Kobzeff
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Joseph A Loo
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; DOE/UCLA Institute of Genomics and Proteomics and UCLA Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Rachel R Ogorzalek Loo
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; DOE/UCLA Institute of Genomics and Proteomics and UCLA Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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20
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Ahmed AA, Pedersen C, Thordal-Christensen H. The Barley Powdery Mildew Effector Candidates CSEP0081 and CSEP0254 Promote Fungal Infection Success. PLoS One 2016; 11:e0157586. [PMID: 27322386 PMCID: PMC4913928 DOI: 10.1371/journal.pone.0157586] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 06/01/2016] [Indexed: 11/19/2022] Open
Abstract
Effectors play significant roles in the success of pathogens. Recent advances in genome sequencing have revealed arrays of effectors and effector candidates from a wide range of plant pathogens. Yet, the vast majority of them remain uncharacterized. Among the ~500 Candidate Secreted Effector Proteins (CSEPs) predicted from the barley powdery mildew fungal genome, only a few have been studied and shown to have a function in virulence. Here, we provide evidence that CSEP0081 and CSEP0254 contribute to infection by the fungus. This was studied using Host-Induced Gene Silencing (HIGS), where independent silencing of the transcripts for these CSEPs significantly reduced the fungal penetration and haustoria formation rate. Both CSEPs are likely required during and after the formation of haustoria, in which their transcripts were found to be differentially expressed, rather than in epiphytic tissue. When expressed in barley leaf epidermal cells, both CSEPs appears to move freely between the cytosol and the nucleus, suggesting that their host targets locate in these cellular compartments. Collectively, our data suggest that, in addition to the previously reported effectors, the barley powdery mildew fungus utilizes these two CSEPs as virulence factors to enhance infection.
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Affiliation(s)
- Ali Abdurehim Ahmed
- Section for Plant and Soil Science, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Carsten Pedersen
- Section for Plant and Soil Science, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Hans Thordal-Christensen
- Section for Plant and Soil Science, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- * E-mail:
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Bryant L, Patole C, Cramer R. Proteomic analysis of the medicinal plant Artemisia annua: Data from leaf and trichome extracts. Data Brief 2016; 7:325-31. [PMID: 26977431 PMCID: PMC4781977 DOI: 10.1016/j.dib.2016.02.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 02/15/2016] [Accepted: 02/15/2016] [Indexed: 01/13/2023] Open
Abstract
This article contains raw and processed data related to research published by Bryant et al.[1]. Data was obtained by MS-based proteomics, analysing trichome-enriched, trichome-depleted and whole leaf samples taken from the medicinal plant Artemisia annua and searching the acquired MS/MS data against a recently published contig database [2] and other genomic and proteomic sequence databases for comparison. The processed data shows that an order-of-magnitude more proteins have been identified from trichome-enriched Artemisia annua samples in comparison to previously published data. Proteins known to have a role in the biosynthesis of artemisinin and other highly abundant proteins were found which imply additional enzymatically driven processes occurring within the trichomes that are significant for the biosynthesis of artemisinin.
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Affiliation(s)
- Laura Bryant
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - Chhaya Patole
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - Rainer Cramer
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK
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22
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Pennington HG, Gheorghe DM, Damerum A, Pliego C, Spanu PD, Cramer R, Bindschedler LV. Interactions between the Powdery Mildew Effector BEC1054 and Barley Proteins Identify Candidate Host Targets. J Proteome Res 2016; 15:826-39. [DOI: 10.1021/acs.jproteome.5b00732] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Helen G. Pennington
- Department
of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
| | - Dana M. Gheorghe
- Department
of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
| | - Annabelle Damerum
- Department
of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
| | - Clara Pliego
- Department
of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
| | - Pietro D. Spanu
- Department
of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
| | - Rainer Cramer
- Department
of Chemistry, University of Reading, Reading RG6 6AD, United Kingdom
| | - Laurence V. Bindschedler
- Department
of Chemistry, University of Reading, Reading RG6 6AD, United Kingdom
- School
of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, United Kingdom
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23
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Abstract
Protein-ligand binding site prediction methods aim to predict, from amino acid sequence, protein-ligand interactions, putative ligands, and ligand binding site residues using either sequence information, structural information, or a combination of both. In silico characterization of protein-ligand interactions has become extremely important to help determine a protein's functionality, as in vivo-based functional elucidation is unable to keep pace with the current growth of sequence databases. Additionally, in vitro biochemical functional elucidation is time-consuming, costly, and may not be feasible for large-scale analysis, such as drug discovery. Thus, in silico prediction of protein-ligand interactions must be utilized to aid in functional elucidation. Here, we briefly discuss protein function prediction, prediction of protein-ligand interactions, the Critical Assessment of Techniques for Protein Structure Prediction (CASP) and the Continuous Automated EvaluatiOn (CAMEO) competitions, along with their role in shaping the field. We also discuss, in detail, our cutting-edge web-server method, FunFOLD for the structurally informed prediction of protein-ligand interactions. Furthermore, we provide a step-by-step guide on using the FunFOLD web server and FunFOLD3 downloadable application, along with some real world examples, where the FunFOLD methods have been used to aid functional elucidation.
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24
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Abstract
Protein tertiary structure prediction algorithms aim to predict, from amino acid sequence, the tertiary structure of a protein. In silico protein structure prediction methods have become extremely important, as in vitro-based structural elucidation is unable to keep pace with the current growth of sequence databases due to high-throughput next-generation sequencing, which has exacerbated the gaps in our knowledge between sequences and structures.Here we briefly discuss protein tertiary structure prediction, the biennial competition for the Critical Assessment of Techniques for Protein Structure Prediction (CASP) and its role in shaping the field. We also discuss, in detail, our cutting-edge web-server method IntFOLD2-TS for tertiary structure prediction. Furthermore, we provide a step-by-step guide on using the IntFOLD2-TS web server, along with some real world examples, where the IntFOLD server can and has been used to improve protein tertiary structure prediction and aid in functional elucidation.
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Affiliation(s)
- Daniel Barry Roche
- Institut de Biologie Computationnelle, LIRMM, CNRS, Université de Montpellier, Montpellier, France.
- CEA, DSV, IG, Genoscope, Évry, France.
- CNRS-UMR8030, Évry, France.
- Université d'Évry Val d'Essonne, Évry, France.
- PRES UniverSud Paris, Saint-Aubin, France.
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25
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Bindschedler LV, Panstruga R, Spanu PD. Mildew-Omics: How Global Analyses Aid the Understanding of Life and Evolution of Powdery Mildews. FRONTIERS IN PLANT SCIENCE 2016; 7:123. [PMID: 26913042 PMCID: PMC4753294 DOI: 10.3389/fpls.2016.00123] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 01/22/2016] [Indexed: 05/21/2023]
Abstract
The common powdery mildew plant diseases are caused by ascomycete fungi of the order Erysiphales. Their characteristic life style as obligate biotrophs renders functional analyses in these species challenging, mainly because of experimental constraints to genetic manipulation. Global large-scale ("-omics") approaches are thus particularly valuable and insightful for the characterisation of the life and evolution of powdery mildews. Here we review the knowledge obtained so far from genomic, transcriptomic and proteomic studies in these fungi. We consider current limitations and challenges regarding these surveys and provide an outlook on desired future investigations on the basis of the various -omics technologies.
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Affiliation(s)
| | - Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen UniversityAachen, Germany
- *Correspondence: Ralph Panstruga,
| | - Pietro D. Spanu
- Department of Life Sciences, Imperial College LondonLondon, UK
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26
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Roche DB, Brackenridge DA, McGuffin LJ. Proteins and Their Interacting Partners: An Introduction to Protein-Ligand Binding Site Prediction Methods. Int J Mol Sci 2015; 16:29829-42. [PMID: 26694353 PMCID: PMC4691145 DOI: 10.3390/ijms161226202] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Revised: 12/02/2015] [Accepted: 12/10/2015] [Indexed: 01/14/2023] Open
Abstract
Elucidating the biological and biochemical roles of proteins, and subsequently determining their interacting partners, can be difficult and time consuming using in vitro and/or in vivo methods, and consequently the majority of newly sequenced proteins will have unknown structures and functions. However, in silico methods for predicting protein-ligand binding sites and protein biochemical functions offer an alternative practical solution. The characterisation of protein-ligand binding sites is essential for investigating new functional roles, which can impact the major biological research spheres of health, food, and energy security. In this review we discuss the role in silico methods play in 3D modelling of protein-ligand binding sites, along with their role in predicting biochemical functionality. In addition, we describe in detail some of the key alternative in silico prediction approaches that are available, as well as discussing the Critical Assessment of Techniques for Protein Structure Prediction (CASP) and the Continuous Automated Model EvaluatiOn (CAMEO) projects, and their impact on developments in the field. Furthermore, we discuss the importance of protein function prediction methods for tackling 21st century problems.
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Affiliation(s)
- Daniel Barry Roche
- Institut de Biologie Computationnelle, LIRMM, CNRS, Université de Montpellier, Montpellier 34095, France.
- Centre de Recherche de Biochimie Macromoléculaire, CNRS-UMR 5237, Montpellier 34293, France.
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27
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Amselem J, Vigouroux M, Oberhaensli S, Brown JKM, Bindschedler LV, Skamnioti P, Wicker T, Spanu PD, Quesneville H, Sacristán S. Evolution of the EKA family of powdery mildew avirulence-effector genes from the ORF 1 of a LINE retrotransposon. BMC Genomics 2015; 16:917. [PMID: 26556056 PMCID: PMC4641428 DOI: 10.1186/s12864-015-2185-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 11/03/2015] [Indexed: 12/31/2022] Open
Abstract
Background The Avrk1 and Avra10 avirulence (AVR) genes encode effectors that increase the pathogenicity of the fungus Blumeria graminis f.sp. hordei (Bgh), the powdery mildew pathogen, in susceptible barley plants. In resistant barley, MLK1 and MLA10 resistance proteins recognize the presence of AVRK1 and AVRA10, eliciting the hypersensitive response typical of gene for gene interactions. Avrk1 and Avra10 have more than 1350 homologues in Bgh genome, forming the EKA (Effectors homologous to Avrk1 and Avra10) gene family. Results We tested the hypothesis that the EKA family originated from degenerate copies of Class I LINE retrotransposons by analysing the EKA family in the genome of Bgh isolate DH14 with bioinformatic tools specially developed for the analysis of Transposable Elements (TE) in genomes. The Class I LINE retrotransposon copies homologous to Avrk1 and Avra10 represent 6.5 % of the Bgh annotated genome and, among them, we identified 293 AVR/effector candidate genes. We also experimentally identified peptides that indicated the translation of several predicted proteins from EKA family members, which had higher relative abundance in haustoria than in hyphae. Conclusions Our analyses indicate that Avrk1 and Avra10 have evolved from part of the ORF1 gene of Class I LINE retrotransposons. The co-option of Avra10 and Avrk1 as effectors from truncated copies of retrotransposons explains the huge number of homologues in Bgh genome that could act as dynamic reservoirs from which new effector genes may evolve. These data provide further evidence for recruitment of retrotransposons in the evolution of new biological functions. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2185-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joelle Amselem
- INRA, UR1164 URGI Unité de Recherche Génomique-Info, Institut National de la Recherche Agronomique de Versailles-Grignon, Versailles, 78026, France. .,INRA, UR1290 BIOGER, Biologie et gestion des risques en agriculture, Campus AgroParisTech, 78850, Thiverval-Grignon, France.
| | | | - Simone Oberhaensli
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.
| | - James K M Brown
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
| | | | - Pari Skamnioti
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, TK 11855, Athens, Greece.
| | - Thomas Wicker
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.
| | - Pietro D Spanu
- Department of Life Sciences, Imperial College London, London, UK.
| | - Hadi Quesneville
- INRA, UR1164 URGI Unité de Recherche Génomique-Info, Institut National de la Recherche Agronomique de Versailles-Grignon, Versailles, 78026, France.
| | - Soledad Sacristán
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain.
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28
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Whigham E, Qi S, Mistry D, Surana P, Xu R, Fuerst G, Pliego C, Bindschedler LV, Spanu PD, Dickerson JA, Innes RW, Nettleton D, Bogdanove AJ, Wise RP. Broadly Conserved Fungal Effector BEC1019 Suppresses Host Cell Death and Enhances Pathogen Virulence in Powdery Mildew of Barley (Hordeum vulgare L.). MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:968-83. [PMID: 25938194 DOI: 10.1094/mpmi-02-15-0027-fi] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The interaction of barley, Hordeum vulgare L., with the powdery mildew fungus Blumeria graminis f. sp. hordei is a well-developed model to investigate resistance and susceptibility to obligate biotrophic pathogens. The 130-Mb Blumeria genome encodes approximately 540 predicted effectors that are hypothesized to suppress or induce host processes to promote colonization. Blumeria effector candidate (BEC)1019, a single-copy gene encoding a putative, secreted metalloprotease, is expressed in haustorial feeding structures, and host-induced gene silencing of BEC1019 restricts haustorial development in compatible interactions. Here, we show that Barley stripe mosaic virus-induced gene silencing of BEC1019 significantly reduces fungal colonization of barley epidermal cells, demonstrating that BEC1019 plays a central role in virulence. In addition, delivery of BEC1019 to the host cytoplasm via Xanthomonas type III secretion suppresses cultivar nonspecific hypersensitive reaction (HR) induced by Xanthomonas oryzae pv. oryzicola, as well as cultivar-specific HR induced by AvrPphB from Pseudomonas syringae pv. phaseolicola. BEC1019 homologs are present in 96 of 241 sequenced fungal genomes, including plant pathogens, human pathogens, and free-living nonpathogens. Comparative analysis revealed variation at several amino acid positions that correlate with fungal lifestyle and several highly conserved, noncorrelated motifs. Site-directed mutagenesis of one of these, ETVIC, compromises the HR-suppressing activity of BEC1019. We postulate that BEC1019 represents an ancient, broadly important fungal protein family, members of which have evolved to function as effectors in plant and animal hosts.
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Affiliation(s)
- Ehren Whigham
- 1 Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, 50011, U.S.A
| | - Shan Qi
- 2 Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, 14853, U.S.A
| | - Divya Mistry
- 3 Bioinformatics and Computational Biology, Iowa State University
| | - Priyanka Surana
- 1 Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, 50011, U.S.A
- 3 Bioinformatics and Computational Biology, Iowa State University
| | - Ruo Xu
- 4 Department of Statistics, Iowa State University
| | - Gregory Fuerst
- 1 Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, 50011, U.S.A
- 5 Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service, Iowa State University
| | - Clara Pliego
- 6 Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, U. K
| | - Laurence V Bindschedler
- 7 School of Biological Sciences, Royal Holloway University of London (RHUL), Egham, Surrey, TW20 0EX, U. K
| | - Pietro D Spanu
- 6 Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, U. K
| | - Julie A Dickerson
- 3 Bioinformatics and Computational Biology, Iowa State University
- 8 Department of Electrical and Computer Engineering, Iowa State University
| | - Roger W Innes
- 9 Department of Biology, Indiana University, Bloomington, IN, 47405, U.S.A
| | | | - Adam J Bogdanove
- 2 Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, 14853, U.S.A
| | - Roger P Wise
- 1 Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, 50011, U.S.A
- 3 Bioinformatics and Computational Biology, Iowa State University
- 5 Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service, Iowa State University
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29
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Bryant L, Flatley B, Patole C, Brown GD, Cramer R. Proteomic analysis of Artemisia annua--towards elucidating the biosynthetic pathways of the antimalarial pro-drug artemisinin. BMC PLANT BIOLOGY 2015; 15:175. [PMID: 26156581 PMCID: PMC4496932 DOI: 10.1186/s12870-015-0565-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 07/01/2015] [Indexed: 05/03/2023]
Abstract
BACKGROUND MS-based proteomics was applied to the analysis of the medicinal plant Artemisia annua, exploiting a recently published contig sequence database (Graham et al. (2010) Science 327, 328-331) and other genomic and proteomic sequence databases for comparison. A. annua is the predominant natural source of artemisinin, the precursor for artemisinin-based combination therapies (ACTs), which are the WHO-recommended treatment for P. falciparum malaria. RESULTS The comparison of various databases containing A. annua sequences (NCBInr/viridiplantae, UniProt/viridiplantae, UniProt/A. annua, an A. annua trichome Trinity contig database, the above contig database and another A. annua EST database) revealed significant differences in respect of their suitability for proteomic analysis, showing that an organism-specific database that has undergone extensive curation, leading to longer contig sequences, can greatly increase the number of true positive protein identifications, while reducing the number of false positives. Compared to previously published data an order-of-magnitude more proteins have been identified from trichome-enriched A. annua samples, including proteins which are known to be involved in the biosynthesis of artemisinin, as well as other highly abundant proteins, which suggest additional enzymatic processes occurring within the trichomes that are important for the biosynthesis of artemisinin. CONCLUSIONS The newly gained information allows for the possibility of an enzymatic pathway, utilizing peroxidases, for the less well understood final stages of artemisinin's biosynthesis, as an alternative to the known non-enzymatic in vitro conversion of dihydroartemisinic acid to artemisinin. Data are available via ProteomeXchange with identifier PXD000703.
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Affiliation(s)
- Laura Bryant
- Department of Chemistry, Whiteknights, Reading, RG6 6AD, United Kingdom.
| | - Brian Flatley
- Department of Chemistry, Whiteknights, Reading, RG6 6AD, United Kingdom.
| | - Chhaya Patole
- Department of Chemistry, Whiteknights, Reading, RG6 6AD, United Kingdom.
| | - Geoffrey D Brown
- Department of Chemistry, Whiteknights, Reading, RG6 6AD, United Kingdom.
| | - Rainer Cramer
- Department of Chemistry, Whiteknights, Reading, RG6 6AD, United Kingdom.
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30
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Droce A, Holm KB, Olsson S, Frandsen RJN, Sondergaard TE, Sørensen JL, Giese H. Expression profiling and functional analyses of BghPTR2, a peptide transporter from Blumeria graminis f. sp. hordei. Fungal Biol 2015; 119:551-9. [PMID: 26058531 DOI: 10.1016/j.funbio.2015.02.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 02/20/2015] [Accepted: 02/23/2015] [Indexed: 02/04/2023]
Affiliation(s)
- Aida Droce
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg Ø, Denmark.
| | | | - Stefan Olsson
- Section for Genetics and Microbiology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Copenhagen, Denmark
| | - Rasmus J N Frandsen
- Section for Eukaryotic Biotechnology, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Build 223, 2800 Kgs. Lyngby, Denmark
| | - Teis Esben Sondergaard
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg Ø, Denmark
| | - Jens Laurids Sørensen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg Ø, Denmark
| | - Henriette Giese
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg Ø, Denmark
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31
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Ahmed AA, Pedersen C, Schultz-Larsen T, Kwaaitaal M, Jørgensen HJL, Thordal-Christensen H. The barley powdery mildew candidate secreted effector protein CSEP0105 inhibits the chaperone activity of a small heat shock protein. PLANT PHYSIOLOGY 2015; 168:321-33. [PMID: 25770154 PMCID: PMC4424032 DOI: 10.1104/pp.15.00278] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 03/10/2015] [Indexed: 05/24/2023]
Abstract
Pathogens secrete effector proteins to establish a successful interaction with their host. Here, we describe two barley (Hordeum vulgare) powdery mildew candidate secreted effector proteins, CSEP0105 and CSEP0162, which contribute to pathogen success and appear to be required during or after haustorial formation. Silencing of either CSEP using host-induced gene silencing significantly reduced the fungal haustorial formation rate. Interestingly, both CSEPs interact with the barley small heat shock proteins, Hsp16.9 and Hsp17.5, in a yeast two-hybrid assay. Small heat shock proteins are known to stabilize several intracellular proteins, including defense-related signaling components, through their chaperone activity. CSEP0105 and CSEP0162 localized to the cytosol and the nucleus of barley epidermal cells, whereas Hsp16.9 and Hsp17.5 are cytosolic. Intriguingly, only those specific CSEPs changed localization and became restricted to the cytosol when coexpressed with Hsp16.9 and Hsp17.5, confirming the CSEP-small heat shock protein interaction. As predicted, Hsp16.9 showed chaperone activity, as it could prevent the aggregation of Escherichia coli proteins during thermal stress. Remarkably, CSEP0105 compromised this activity. These data suggest that CSEP0105 promotes virulence by interfering with the chaperone activity of a barley small heat shock protein essential for defense and stress responses.
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Affiliation(s)
- Ali Abdurehim Ahmed
- Section for Plant and Soil Science, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Carsten Pedersen
- Section for Plant and Soil Science, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Torsten Schultz-Larsen
- Section for Plant and Soil Science, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Mark Kwaaitaal
- Section for Plant and Soil Science, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Hans Jørgen Lyngs Jørgensen
- Section for Plant and Soil Science, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Hans Thordal-Christensen
- Section for Plant and Soil Science, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
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32
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The Podosphaera xanthii haustorium, the fungal Trojan horse of cucurbit-powdery mildew interactions. Fungal Genet Biol 2014; 71:21-31. [PMID: 25151531 DOI: 10.1016/j.fgb.2014.08.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 08/08/2014] [Accepted: 08/11/2014] [Indexed: 01/04/2023]
Abstract
The powdery mildew fungi are obligate biotrophic plant pathogens that develop a specialized structure for parasitism termed haustorium, which is responsible for nutrient uptake and factor exchange with the plant. In this work, we present a detailed microscopy analysis of the haustoria of the cucurbit powdery mildew fungus Podosphaera xanthii, a major limiting factor for cucurbit production worldwide. Despite being located inside plant epidermal cells, transmission electron microscopy (TEM) analysis showed the characteristic highly irregular outline of the extrahaustorial membrane that separates the extrahaustorial matrix of haustoria from the cytoplasm of the plant cell. TEM analysis also revealed the presence of some vesicles and electron-dense plaques of material surrounding the haustoria. In confocal microscopy analysis and aniline blue staining we found a positive correlation between haustorial development and deposition of callose, which is distributed as plaques around haustorial complex. In this study, a method for the isolation of P. xanthii haustoria was also adapted, which permitted the analysis of the formation of haustorial lobes and the visualization of vacuoles and the pool of vesicles inside the haustorial complex. Our findings suggested that the haustorial lobes were responsible for vesicular trafficking and most likely act as the main mediators of the fungus-plant dialogue. All of these findings were integrated into a model of the P. xanthii-host cellular interactions.
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33
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Roche DB, Buenavista MT, McGuffin LJ. Assessing the quality of modelled 3D protein structures using the ModFOLD server. Methods Mol Biol 2014; 1137:83-103. [PMID: 24573476 DOI: 10.1007/978-1-4939-0366-5_7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Model quality assessment programs (MQAPs) aim to assess the quality of modelled 3D protein structures. The provision of quality scores, describing both global and local (per-residue) accuracy are extremely important, as without quality scores we are unable to determine the usefulness of a 3D model for further computational and experimental wet lab studies.Here, we briefly discuss protein tertiary structure prediction, along with the biennial Critical Assessment of Techniques for Protein Structure Prediction (CASP) competition and their key role in driving the field of protein model quality assessment methods (MQAPs). We also briefly discuss the top MQAPs from the previous CASP competitions. Additionally, we describe our downloadable and webserver-based model quality assessment methods: ModFOLD3, ModFOLDclust, ModFOLDclustQ, ModFOLDclust2, and IntFOLD-QA. We provide a practical step-by-step guide on using our downloadable and webserver-based tools and include examples of their application for improving tertiary structure prediction, ligand binding site residue prediction, and oligomer predictions.
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Affiliation(s)
- Daniel Barry Roche
- Genoscope, Institut de Génomique, Commissariat à l'Energie Atomique et aux Energies Alternatives, Evry, France
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34
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Agrawal GK, Sarkar A, Righetti PG, Pedreschi R, Carpentier S, Wang T, Barkla BJ, Kohli A, Ndimba BK, Bykova NV, Rampitsch C, Zolla L, Rafudeen MS, Cramer R, Bindschedler LV, Tsakirpaloglou N, Ndimba RJ, Farrant JM, Renaut J, Job D, Kikuchi S, Rakwal R. A decade of plant proteomics and mass spectrometry: translation of technical advancements to food security and safety issues. MASS SPECTROMETRY REVIEWS 2013; 32:335-65. [PMID: 23315723 DOI: 10.1002/mas.21365] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 09/10/2012] [Accepted: 09/10/2012] [Indexed: 05/21/2023]
Abstract
Tremendous progress in plant proteomics driven by mass spectrometry (MS) techniques has been made since 2000 when few proteomics reports were published and plant proteomics was in its infancy. These achievements include the refinement of existing techniques and the search for new techniques to address food security, safety, and health issues. It is projected that in 2050, the world's population will reach 9-12 billion people demanding a food production increase of 34-70% (FAO, 2009) from today's food production. Provision of food in a sustainable and environmentally committed manner for such a demand without threatening natural resources, requires that agricultural production increases significantly and that postharvest handling and food manufacturing systems become more efficient requiring lower energy expenditure, a decrease in postharvest losses, less waste generation and food with longer shelf life. There is also a need to look for alternative protein sources to animal based (i.e., plant based) to be able to fulfill the increase in protein demands by 2050. Thus, plant biology has a critical role to play as a science capable of addressing such challenges. In this review, we discuss proteomics especially MS, as a platform, being utilized in plant biology research for the past 10 years having the potential to expedite the process of understanding plant biology for human benefits. The increasing application of proteomics technologies in food security, analysis, and safety is emphasized in this review. But, we are aware that no unique approach/technology is capable to address the global food issues. Proteomics-generated information/resources must be integrated and correlated with other omics-based approaches, information, and conventional programs to ensure sufficient food and resources for human development now and in the future.
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Affiliation(s)
- Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry, PO Box 13265, Kathmandu, Nepal.
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Roche DB, Buenavista MT, McGuffin LJ. The FunFOLD2 server for the prediction of protein-ligand interactions. Nucleic Acids Res 2013; 41:W303-7. [PMID: 23761453 PMCID: PMC3692132 DOI: 10.1093/nar/gkt498] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The FunFOLD2 server is a new independent server that integrates our novel protein-ligand binding site and quality assessment protocols for the prediction of protein function (FN) from sequence via structure. Our guiding principles were, first, to provide a simple unified resource to make our function prediction software easily accessible to all via a simple web interface and, second, to produce integrated output for predictions that can be easily interpreted. The server provides a clean web interface so that results can be viewed on a single page and interpreted by non-experts at a glance. The output for the prediction is an image of the top predicted tertiary structure annotated to indicate putative ligand-binding site residues. The results page also includes a list of the most likely binding site residues and the types of predicted ligands and their frequencies in similar structures. The protein-ligand interactions can also be interactively visualized in 3D using the Jmol plug-in. The raw machine readable data are provided for developers, which comply with the Critical Assessment of Techniques for Protein Structure Prediction data standards for FN predictions. The FunFOLD2 webserver is freely available to all at the following web site: http://www.reading.ac.uk/bioinf/FunFOLD/FunFOLD_form_2_0.html.
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Affiliation(s)
- Daniel B Roche
- Laboratoire de génomique et biochimie du métabolisme, Genoscope, Institut de Génomique, Commissariat à l'Energie Atomique et aux Energies Alternatives, Evry, Essonne 91057, France.
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Hacquard S, Kracher B, Maekawa T, Vernaldi S, Schulze-Lefert P, Ver Loren van Themaat E. Mosaic genome structure of the barley powdery mildew pathogen and conservation of transcriptional programs in divergent hosts. Proc Natl Acad Sci U S A 2013; 110:E2219-28. [PMID: 23696672 PMCID: PMC3683789 DOI: 10.1073/pnas.1306807110] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Barley powdery mildew, Blumeria graminis f. sp. hordei (Bgh), is an obligate biotrophic ascomycete fungal pathogen that can grow and reproduce only on living cells of wild or domesticated barley (Hordeum sp.). Domestication and deployment of resistant barley cultivars by humans selected for amplification of Bgh isolates with different virulence combinations. We sequenced the genomes of two European Bgh isolates, A6 and K1, for comparative analysis with the reference genome of isolate DH14. This revealed a mosaic genome structure consisting of large isolate-specific DNA blocks with either high or low SNP densities. Some of the highly polymorphic blocks likely accumulated SNPs for over 10,000 years, well before the domestication of barley. These isolate-specific blocks of alternating monomorphic and polymorphic regions imply an exceptionally large standing genetic variation in the Bgh population and might be generated and maintained by rare outbreeding and frequent clonal reproduction. RNA-sequencing experiments with isolates A6 and K1 during four early stages of compatible and incompatible interactions on leaves of partially immunocompromised Arabidopsis mutants revealed a conserved Bgh transcriptional program during pathogenesis compared with the natural host barley despite ~200 million years of reproductive isolation of these hosts. Transcripts encoding candidate-secreted effector proteins are massively induced in successive waves. A specific decrease in candidate-secreted effector protein transcript abundance in the incompatible interaction follows extensive transcriptional reprogramming of the host transcriptome and coincides with the onset of localized host cell death, suggesting a host-inducible defense mechanism that targets fungal effector secretion or production.
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Affiliation(s)
| | | | - Takaki Maekawa
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Saskia Vernaldi
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Paul Schulze-Lefert
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Emiel Ver Loren van Themaat
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
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Pliego C, Nowara D, Bonciani G, Gheorghe DM, Xu R, Surana P, Whigham E, Nettleton D, Bogdanove AJ, Wise RP, Schweizer P, Bindschedler LV, Spanu PD. Host-induced gene silencing in barley powdery mildew reveals a class of ribonuclease-like effectors. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2013; 26:633-42. [PMID: 23441578 DOI: 10.1094/mpmi-01-13-0005-r] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Obligate biotrophic pathogens of plants must circumvent or counteract defenses to guarantee accommodation inside the host. To do so, they secrete a variety of effectors that regulate host immunity and facilitate the establishment of pathogen feeding structures called haustoria. The barley powdery mildew fungus Blumeria graminis f. sp. hordei produces a large number of proteins predicted to be secreted from haustoria. Fifty of these Blumeria effector candidates (BEC) were screened by host-induced gene silencing (HIGS), and eight were identified that contribute to infection. One shows similarity to β-1,3 glucosyltransferases, one to metallo-proteases, and two to microbial secreted ribonucleases; the remainder have no similarity to proteins of known function. Transcript abundance of all eight BEC increases dramatically in the early stages of infection and establishment of haustoria, consistent with a role in that process. Complementation analysis using silencing-insensitive synthetic cDNAs demonstrated that the ribonuclease-like BEC 1011 and 1054 are bona fide effectors that function within the plant cell. BEC1011 specifically interferes with pathogen-induced host cell death. Both are part of a gene superfamily unique to the powdery mildew fungi. Structural modeling was consistent, with BEC1054 adopting a ribonuclease-like fold, a scaffold not previously associated with effector function.
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Affiliation(s)
- Clara Pliego
- Department of Life Science, Imperial College, London, UK
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38
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Müller SA, Findeiß S, Pernitzsch SR, Wissenbach DK, Stadler PF, Hofacker IL, von Bergen M, Kalkhof S. Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics. J Proteomics 2013; 86:27-42. [PMID: 23665149 DOI: 10.1016/j.jprot.2013.04.036] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 03/29/2013] [Accepted: 04/26/2013] [Indexed: 12/16/2022]
Abstract
UNLABELLED Correct annotation of protein coding genes is the basis of conventional data analysis in proteomic studies. Nevertheless, most protein sequence databases almost exclusively rely on gene finding software and inevitably also miss protein annotations or possess errors. Proteogenomics tries to overcome these issues by matching MS data directly against a genome sequence database. Here we report an in-depth proteogenomics study of Helicobacter pylori strain 26695. MS data was searched against a combined database of the NCBI annotations and a six-frame translation of the genome. Database searches with Mascot and X! Tandem revealed 1115 proteins identified by at least two peptides with a peptide false discovery rate below 1%. This represents 71% of the predicted proteome. So far this is the most extensive proteome study of Helicobacter pylori. Our proteogenomic approach unambiguously identified four previously missed annotations and furthermore allowed us to correct sequences of six annotated proteins. Since secreted proteins are often involved in pathogenic processes we further investigated signal peptidase cleavage sites. By applying a database search that accommodates the identification of semi-specific cleaved peptides, 63 previously unknown signal peptides were detected. The motif LXA showed to be the predominant recognition sequence for signal peptidases. BIOLOGICAL SIGNIFICANCE The results of MS-based proteomic studies highly rely on correct annotation of protein coding genes which is the basis of conventional data analysis. However, the annotation of protein coding sequences in genomic data is usually based on gene finding software. These tools are limited in their prediction accuracy such as the problematic determination of exact gene boundaries. Thus, protein databases own partly erroneous or incomplete sequences. Additionally, some protein sequences might also be missing in the databases. Proteogenomics, a combination of proteomic and genomic data analyses, is well suited to detect previously not annotated proteins and to correct erroneous sequences. For this purpose, the existing database of the investigated species is typically supplemented with a six-frame translation of the genome. Here, we studied the proteome of the major human pathogen Helicobacter pylori that is responsible for many gastric diseases such as duodenal ulcers and gastric cancer. Our in-depth proteomic study highly reliably identified 1115 proteins (FDR<0.01%) by at least two peptides (FDR<1%) which represent 71% of the predicted proteome deposited at NCBI. The proteogenomic data analysis of our data set resulted in the unambiguous identification of four previously missed annotations, the correction of six annotated proteins as well as the detection of 63 previously unknown signal peptides. We have annotated proteins of particular biological interest like the ferrous iron transport protein A, the coiled-coil-rich protein HP0058 and the lipopolysaccharide biosynthesis protein HP0619. For instance, the protein HP0619 could be a drug target for the inhibition of the LPS synthesis pathway. Furthermore it has been proven that the motif "LXA" is the predominant recognition sequence for the signal peptidase I of H. pylori. Signal peptidases are essential enzymes for the viability of bacterial cells and are involved in pathogenesis. Therefore signal peptidases could be novel targets for antibiotics. The inclusion of the corrected and new annotated proteins as well as the information of signal peptide cleavage sites will help in the study of biological pathways involved in pathogenesis or drug response of H. pylori.
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Affiliation(s)
- Stephan A Müller
- Department of Proteomics, UFZ, Helmholtz-Centre for Environmental Research Leipzig, 04318 Leipzig, Germany
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Pedersen C, Ver Loren van Themaat E, McGuffin LJ, Abbott JC, Burgis TA, Barton G, Bindschedler LV, Lu X, Maekawa T, Wessling R, Cramer R, Thordal-Christensen H, Panstruga R, Spanu PD. Structure and evolution of barley powdery mildew effector candidates. BMC Genomics 2012; 13:694. [PMID: 23231440 PMCID: PMC3582587 DOI: 10.1186/1471-2164-13-694] [Citation(s) in RCA: 150] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 11/28/2012] [Indexed: 11/11/2022] Open
Abstract
Background Protein effectors of pathogenicity are instrumental in modulating host immunity and disease resistance. The powdery mildew pathogen of grasses Blumeria graminis causes one of the most important diseases of cereal crops. B. graminis is an obligate biotrophic pathogen and as such has an absolute requirement to suppress or avoid host immunity if it is to survive and cause disease. Results Here we characterise a superfamily predicted to be the full complement of Candidates for Secreted Effector Proteins (CSEPs) in the fungal barley powdery mildew parasite B. graminis f.sp. hordei. The 491 genes encoding these proteins constitute over 7% of this pathogen’s annotated genes and most were grouped into 72 families of up to 59 members. They were predominantly expressed in the intracellular feeding structures called haustoria, and proteins specifically associated with the haustoria were identified by large-scale mass spectrometry-based proteomics. There are two major types of effector families: one comprises shorter proteins (100–150 amino acids), with a high relative expression level in the haustoria and evidence of extensive diversifying selection between paralogs; the second type consists of longer proteins (300–400 amino acids), with lower levels of differential expression and evidence of purifying selection between paralogs. An analysis of the predicted protein structures underscores their overall similarity to known fungal effectors, but also highlights unexpected structural affinities to ribonucleases throughout the entire effector super-family. Candidate effector genes belonging to the same family are loosely clustered in the genome and are associated with repetitive DNA derived from retro-transposons. Conclusions We employed the full complement of genomic, transcriptomic and proteomic analyses as well as structural prediction methods to identify and characterize the members of the CSEPs superfamily in B. graminis f.sp. hordei. Based on relative intron position and the distribution of CSEPs with a ribonuclease-like domain in the phylogenetic tree we hypothesize that the associated genes originated from an ancestral gene, encoding a secreted ribonuclease, duplicated successively by repetitive DNA-driven processes and diversified during the evolution of the grass and cereal powdery mildew lineage.
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Affiliation(s)
- Carsten Pedersen
- Department of Agriculture & Ecology, Plant and Soil Science, University ofCopenhagen, Copenhagen, Denmark
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Weßling R, Schmidt SM, Micali CO, Knaust F, Reinhardt R, Neumann U, Ver Loren van Themaat E, Panstruga R. Transcriptome analysis of enriched Golovinomyces orontii haustoria by deep 454 pyrosequencing. Fungal Genet Biol 2012; 49:470-82. [PMID: 22521876 DOI: 10.1016/j.fgb.2012.04.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 03/30/2012] [Accepted: 04/03/2012] [Indexed: 12/24/2022]
Abstract
Powdery mildews are phytopathogenic ascomycetes that have an obligate biotrophic lifestyle and establish intimate relationships with their plant hosts. A crucial aspect of this plant-fungus interaction is the formation of specialized fungal infection structures termed haustoria. Although located within the cell boundaries of plant epidermal cells, haustoria remain separated from the plant cytoplasm by a host plasma membrane derivative, the extrahaustorial membrane. Haustoria are thought to represent pivotal sites of nutrient uptake and effector protein delivery. We enriched haustorial complexes from Arabidopsis thaliana plants infected with the powdery mildew fungus Golovinomyces orontii and performed in-depth transcriptome analysis by 454-based pyrosequencing of haustorial cDNAs. We assembled 7077 expressed sequence tag (EST) contigs with greater than 5-fold average coverage and analyzed these with regard to the respective predicted protein functions. We found that transcripts coding for gene products with roles in protein turnover, detoxification of reactive oxygen species and fungal pathogenesis are abundant in the haustorial EST contigs, while surprisingly transcripts encoding presumptive nutrient transporters were not highly represented in the haustorial cDNA library. A substantial proportion (∼38%) of transcripts coding for predicted secreted proteins comprises effector candidates. Our data provide valuable insights into the transcriptome of the key infection structure of a model obligate biotrophic phytopathogen.
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Affiliation(s)
- Ralf Weßling
- Max-Planck-Institute for Plant Breeding Research, Department of Plant-Microbe Interactions, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
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41
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Translational plant proteomics: a perspective. J Proteomics 2012; 75:4588-601. [PMID: 22516432 DOI: 10.1016/j.jprot.2012.03.055] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2011] [Revised: 02/25/2012] [Accepted: 03/25/2012] [Indexed: 11/21/2022]
Abstract
Translational proteomics is an emerging sub-discipline of the proteomics field in the biological sciences. Translational plant proteomics aims to integrate knowledge from basic sciences to translate it into field applications to solve issues related but not limited to the recreational and economic values of plants, food security and safety, and energy sustainability. In this review, we highlight the substantial progress reached in plant proteomics during the past decade which has paved the way for translational plant proteomics. Increasing proteomics knowledge in plants is not limited to model and non-model plants, proteogenomics, crop improvement, and food analysis, safety, and nutrition but to many more potential applications. Given the wealth of information generated and to some extent applied, there is the need for more efficient and broader channels to freely disseminate the information to the scientific community. This article is part of a Special Issue entitled: Translational Proteomics.
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42
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Cramer R. Editorial for "advances in biological mass spectrometry and proteomics". Methods 2012; 54:349-50. [PMID: 21839395 DOI: 10.1016/j.ymeth.2011.07.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2011] [Indexed: 12/21/2022] Open
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Abstract
Biotrophy is a pervasive trait that evolved independently in plant pathogenic fungi and oomycetes. Comparative genomics of the first sequenced biotrophic pathogens highlight remarkable convergences, including gene losses in the metabolism of inorganic nitrogen, inorganic sulfur, and thiamine, and genes encoding carbohydrate active enzymes and secondary metabolism enzymes. Some biotrophs, but not all, display marked increases in overall genome size because of a proliferation of retrotransposons. I argue here that the release of constraints on transposon activity is driven by the advantages conferred by the genetic variability that results from transposition, in particular by the creation and diversification of broad palettes of effector genes. Increases in genome size and gene losses are the consequences of this trade-off. Genes that are not necessary for growth on a plant disappeared, but we still do not know what lost functions make some of these pathogens obligate.
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Affiliation(s)
- Pietro D Spanu
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom.
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Helmy M, Sugiyama N, Tomita M, Ishihama Y. The Rice Proteogenomics Database OryzaPG-DB: Development, Expansion, and New Features. FRONTIERS IN PLANT SCIENCE 2012; 3:65. [PMID: 22639657 PMCID: PMC3355581 DOI: 10.3389/fpls.2012.00065] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2012] [Accepted: 03/18/2012] [Indexed: 05/21/2023]
Abstract
Our recently developed rice proteogenomics database (OryzaPG-DB) is the first sustainable resource for rice shotgun-based proteogenomics, providing information on peptides identified in rice protein digested peptides measured by means of liquid chromatography-tandem mass spectrometry (LC-MS/MS), and mapping of the peptides to their genomic origins and the genomic novelty of each peptide. The sequences of the peptides, proteins, cDNAs and genes, and the gene annotations are available for download in FASTA and GFF3 formats, respectively. Further, an annotated visualization of the gene models, corresponding peptides, and genomic novelty is available for each gene, and MS/MS spectra are available for each peptide. In this article, we discuss the utilization of OryzaPG-DB and report on its development, recent content expansions, and newly added features in the current version (OryzaPG-DB v1.1).
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Affiliation(s)
- Mohamed Helmy
- Institute for Advanced Biosciences, Keio UniversityTokyo, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio UniversityTokyo, Japan
| | | | - Masaru Tomita
- Institute for Advanced Biosciences, Keio UniversityTokyo, Japan
| | - Yasushi Ishihama
- Institute for Advanced Biosciences, Keio UniversityTokyo, Japan
- Department of Molecular and Cellular Bioanalysis, Graduate School of Pharmaceutical Sciences, Kyoto UniversityKyoto, Japan
- *Correspondence: Yasushi Ishihama, Department of Molecular and Cellular Bioanalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan. e-mail:
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Hückelhoven R, Panstruga R. Cell biology of the plant-powdery mildew interaction. CURRENT OPINION IN PLANT BIOLOGY 2011; 14:738-46. [PMID: 21924669 DOI: 10.1016/j.pbi.2011.08.002] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 08/09/2011] [Accepted: 08/17/2011] [Indexed: 05/08/2023]
Abstract
Powdery mildew fungi represent a paradigm for obligate biotrophic parasites, which only propagate in long-lasting intimate interactions with living host cells. These highly specialized phytopathogens induce re-organization of host cell architecture and physiology for their own demands. This probably includes the corruption of basal host cellular functions for successful fungal pathogenesis. Recent studies revealed secretory processes by both interaction partners as key incidents of the combat at the plant-fungus interface. The analysis of cellular events during plant-powdery mildew interactions may not only lead to a better understanding of plant pathological features, but may also foster novel discoveries in the area of plant cell biology.
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Affiliation(s)
- Ralph Hückelhoven
- Lehrstuhl für Phytopathologie, Technische Universität München, Emil-Ramann-Straße 2, 85350 Freising-Weihenstephan, Germany
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Roche DB, Buenavista MT, Tetchner SJ, McGuffin LJ. The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction. Nucleic Acids Res 2011; 39:W171-6. [PMID: 21459847 PMCID: PMC3125722 DOI: 10.1093/nar/gkr184] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The IntFOLD server is a novel independent server that integrates several cutting edge methods for the prediction of structure and function from sequence. Our guiding principles behind the server development were as follows: (i) to provide a simple unified resource that makes our prediction software accessible to all and (ii) to produce integrated output for predictions that can be easily interpreted. The output for predictions is presented as a simple table that summarizes all results graphically via plots and annotated 3D models. The raw machine readable data files for each set of predictions are also provided for developers, which comply with the Critical Assessment of Methods for Protein Structure Prediction (CASP) data standards. The server comprises an integrated suite of five novel methods: nFOLD4, for tertiary structure prediction; ModFOLD 3.0, for model quality assessment; DISOclust 2.0, for disorder prediction; DomFOLD 2.0 for domain prediction; and FunFOLD 1.0, for ligand binding site prediction. Predictions from the IntFOLD server were found to be competitive in several categories in the recent CASP9 experiment. The IntFOLD server is available at the following web site: http://www.reading.ac.uk/bioinf/IntFOLD/.
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Affiliation(s)
- Daniel B Roche
- School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, UK
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