scholarly journals An automated and combinative method for the predictive ranking of candidate effector proteins of fungal plant pathogens

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Darcy A. B. Jones ◽  
Lina Rozano ◽  
Johannes W. Debler ◽  
Ricardo L. Mancera ◽  
Paula M. Moolhuijzen ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Broad Class ◽  
Learning To Rank ◽  
Effector Proteins ◽  
Disease Outcomes ◽  
Pairwise Learning ◽  
Fungal Plant Pathogens ◽  
Ranking Performance ◽  
Multiple Species ◽  
Reproducible Manner

AbstractFungal plant-pathogens promote infection of their hosts through the release of ‘effectors’—a broad class of cytotoxic or virulence-promoting molecules. Effectors may be recognised by resistance or sensitivity receptors in the host, which can determine disease outcomes. Accurate prediction of effectors remains a major challenge in plant pathology, but if achieved will facilitate rapid improvements to host disease resistance. This study presents a novel tool and pipeline for the ranking of predicted effector candidates—Predector—which interfaces with multiple software tools and methods, aggregates disparate features that are relevant to fungal effector proteins, and applies a pairwise learning to rank approach. Predector outperformed a typical combination of secretion and effector prediction methods in terms of ranking performance when applied to a curated set of confirmed effectors derived from multiple species. We present Predector (https://github.com/ccdmb/predector) as a useful tool for the ranking of predicted effector candidates, which also aggregates and reports additional supporting information relevant to effector and secretome prediction in a simple, efficient, and reproducible manner.

Predector: an automated and combinative method for the predictive ranking of candidate effector proteins of fungal plant-pathogens

2021 ◽  
Author(s):  
Darcy A. B. Jones ◽  
Lina Rozano ◽  
Johannes Debler ◽  
Ricardo L. Mancera ◽  
Paula Moolhuijzen ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Broad Class ◽  
Sequence Similarity ◽  
Learning To Rank ◽  
Research Area ◽  
Effector Proteins ◽  
Pairwise Learning ◽  
Fungal Plant Pathogens ◽  
Multiple Species ◽  
Distinguishing Features

Abstract ‘Effectors’ are a broad class of cytotoxic or virulence-promoting molecules that are released from plant-pathogen cells to cause disease in their host. Fungal effectors are a core research area for improving host disease resistance; however, because they generally lack common distinguishing features or obvious sequence similarity, discovery of effectors remains a major challenge. This study presents a novel tool and pipeline for effector prediction - Predector - which interfaces with multiple software tools and methods, aggregates disparate features that are relevant to fungal effector proteins, and ranks effector candidate proteins using a pairwise learning to rank approach. Predector outperformed alternative effector prediction methods that were applied to a curated set of confirmed effectors derived from multiple species. We present Predector as a useful tool for the prediction and ranking of effector candidates, which aggregates and reports additional supporting information relevant to effector and secretome prediction in a simple, efficient, and reproducible manner. Predector is available from https://github.com/ccdmb/predector and associated data from https://github.com/ccdmb/predector-data.

scholarly journals Publisher Correction: An automated and combinative method for the predictive ranking of candidate effector proteins of fungal plant pathogens

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Darcy A. B. Jones ◽  
Lina Rozano ◽  
Johannes W. Debler ◽  
Ricardo L. Mancera ◽  
Paula M. Moolhuijzen ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Effector Proteins ◽  
Fungal Plant Pathogens

scholarly journals Effector proteins of extracellular fungal plant pathogens that trigger host resistance

2010 ◽  
Vol 37 (10) ◽  
pp. 901 ◽  
Author(s):  
Ann-Maree Catanzariti ◽  
David A. Jones
Keyword(s):  
Biological Activity ◽  
Host Resistance ◽  
Fungal Pathogens ◽  
Plant Pathogens ◽  
Molecular Mechanisms ◽  
Host Tissue ◽  
Effector Proteins ◽  
Resistance Proteins ◽  
Recognitional Capacity ◽  
Fungal Plant Pathogens

An understanding of the molecular mechanisms that plant pathogens use to successfully colonise host tissue can be gained by studying the biological activity of pathogen proteins secreted during infection. Several secreted ‘effector’ proteins with possible roles in virulence have been isolated from extracellular fungal pathogens, including three that have been shown to negate host defences. In most cases, significant effector variation is observed between different pathogen isolates, driven by the recognitional capacity of disease resistance proteins arrayed against the pathogen by the host plant. This review summarises what is known about the expression, function and variation of effectors isolated from extracellular fungal pathogens.

Morphological, biochemical and molecular identification of rhizobacteria isolates with potential for biocontrol of fungal plant pathogens

2021 ◽  
pp. 1-14
Author(s):  
Stephen Larbi-Koranteng ◽  
Richard Tuyee Awuah ◽  
Fredrick Kankam ◽  
Muntala Abdulai ◽  
Marian Dorcas Quain ◽  
...  
Keyword(s):  
Molecular Identification ◽  
Plant Pathogens ◽  
Fungal Plant Pathogens

scholarly journals The carbon source-dependent pattern of antimicrobial activity and gene expression in Pseudomonas donghuensis P482

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Marta Matuszewska ◽  
Tomasz Maciąg ◽  
Magdalena Rajewska ◽  
Aldona Wierzbicka ◽  
Sylwia Jafra
Keyword(s):  
Gene Expression ◽  
Antimicrobial Activity ◽  
Carbon Source ◽  
Reference Genes ◽  
Plant Pathogens ◽  
Plant Protection ◽  
Carbon Sources ◽  
Unknown Compound ◽  
Fungal Plant Pathogens ◽  
The Impact

AbstractPseudomonas donghuensis P482 is a tomato rhizosphere isolate with the ability to inhibit growth of bacterial and fungal plant pathogens. Herein, we analysed the impact of the carbon source on the antibacterial activity of P482 and expression of the selected genes of three genomic regions in the P482 genome. These regions are involved in the synthesis of pyoverdine, 7-hydroxytropolone (7-HT) and an unknown compound (“cluster 17”) and are responsible for the antimicrobial activity of P482. We showed that the P482 mutants, defective in these regions, show variations and contrasting patterns of growth inhibition of the target pathogen under given nutritional conditions (with glucose or glycerol as a carbon source). We also selected and validated the reference genes for gene expression studies in P. donghuensis P482. Amongst ten candidate genes, we found gyrB, rpoD and mrdA the most stably expressed. Using selected reference genes in RT-qPCR, we assessed the expression of the genes of interest under minimal medium conditions with glucose or glycerol as carbon sources. Glycerol was shown to negatively affect the expression of genes necessary for 7-HT synthesis. The significance of this finding in the light of the role of nutrient (carbon) availability in biological plant protection is discussed.

scholarly journals Stress-Activated Protein Kinase Signalling Regulates Mycoparasitic Hyphal-Hyphal Interactions in Trichoderma atroviride

2021 ◽  
Vol 7 (5) ◽  
pp. 365
Author(s):  
Dubraska Moreno-Ruiz ◽  
Linda Salzmann ◽  
Mark D. Fricker ◽  
Susanne Zeilinger ◽  
Alexander Lichius
Keyword(s):  
Protein Kinase ◽  
Map Kinases ◽  
Plant Pathogens ◽  
Tip Growth ◽  
Mitogen Activated Protein Kinase ◽  
Trichoderma Atroviride ◽  
Contact Phase ◽  
Fungal Plant Pathogens ◽  
Signalling Network ◽  
Mapk Signalling

Trichoderma atroviride is a mycoparasitic fungus used as biological control agent against fungal plant pathogens. The recognition and appropriate morphogenetic responses to prey-derived signals are essential for successful mycoparasitism. We established microcolony confrontation assays using T. atroviride strains expressing cell division cycle 42 (Cdc42) and Ras-related C3 botulinum toxin substrate 1 (Rac1) interactive binding (CRIB) reporters to analyse morphogenetic changes and the dynamic displacement of localized GTPase activity during polarized tip growth. Microscopic analyses showed that Trichoderma experiences significant polarity stress when approaching its fungal preys. The perception of prey-derived signals is integrated via the guanosine triphosphatase (GTPase) and mitogen-activated protein kinase (MAPK) signalling network, and deletion of the MAP kinases Trichoderma MAPK 1 (Tmk1) and Tmk3 affected T. atroviride tip polarization, chemotropic growth, and contact-induced morphogenesis so severely that the establishment of mycoparasitism was highly inefficient to impossible. The responses varied depending on the prey species and the interaction stage, reflecting the high selectivity of the signalling process. Our data suggest that Tmk3 affects the polarity-stress adaptation process especially during the pre-contact phase, whereas Tmk1 regulates contact-induced morphogenesis at the early-contact phase. Neither Tmk1 nor Tmk3 loss-of-function could be fully compensated within the GTPase/MAPK signalling network underscoring the crucial importance of a sensitive polarized tip growth apparatus for successful mycoparasitism.

scholarly journals The Ustilago hordei–Barley Interaction is a Versatile System for Characterization of Fungal Effectors

2021 ◽  
Vol 7 (2) ◽  
pp. 86
Author(s):  
Bilal Ökmen ◽  
Daniela Schwammbach ◽  
Guus Bakkeren ◽  
Ulla Neumann ◽  
Gunther Doehlemann
Keyword(s):  
Fungal Pathogens ◽  
Plant Pathogens ◽  
Expression System ◽  
Pathogenic Fungi ◽  
Effector Proteins ◽  
Mating Partner ◽  
Fungal Virulence ◽  
Functional Studies ◽  
Infection Structures ◽  
Ustilago Hordei

Obligate biotrophic fungal pathogens, such as Blumeria graminis and Puccinia graminis, are amongst the most devastating plant pathogens, causing dramatic yield losses in many economically important crops worldwide. However, a lack of reliable tools for the efficient genetic transformation has hampered studies into the molecular basis of their virulence or pathogenicity. In this study, we present the Ustilago hordei–barley pathosystem as a model to characterize effectors from different plant pathogenic fungi. We generate U. hordei solopathogenic strains, which form infectious filaments without the presence of a compatible mating partner. Solopathogenic strains are suitable for heterologous expression system for fungal virulence factors. A highly efficient Crispr/Cas9 gene editing system is made available for U. hordei. In addition, U. hordei infection structures during barley colonization are analyzed using transmission electron microscopy, showing that U. hordei forms intracellular infection structures sharing high similarity to haustoria formed by obligate rust and powdery mildew fungi. Thus, U. hordei has high potential as a fungal expression platform for functional studies of heterologous effector proteins in barley.

Metabolites of rhizobacteria antagonistic towards fungal plant pathogens

2007 ◽  
Vol 57 (1) ◽  
pp. 127-130 ◽  
Author(s):  
Garima Jha ◽  
Vanamala Anjaiah
Keyword(s):  
Plant Pathogens ◽  
Fungal Plant Pathogens
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