scholarly journals RNA Modification and Its Implication in Plant Pathogenic Fungi

2021 ◽  
Vol 37 (6) ◽  
pp. 505-511
Author(s):  
Junhyun Jeon ◽  
Song Hee Lee
Keyword(s):  
Genetic Information ◽  
Fungal Pathogens ◽  
Pathogenic Fungi ◽  
Host Cells ◽  
Rna Modification ◽  
Environmental Cues ◽  
Plant Pathogenic Fungi ◽  
Rna Modifications ◽  
Evolutionarily Conserved ◽  
Rapid Shift

Interaction of a pathogen with its host plant requires both flexibility and rapid shift in gene expression programs in response to environmental cues associated with host cells. Recently, a growing volume of data on the diversity and ubiquity of internal RNA modifications has led to the realization that such modifications are highly dynamic and yet evolutionarily conserved system. This hints at these RNA modifications being an additional regulatory layer for genetic information, culminating in epitranscriptome concept. In plant pathogenic fungi, however, the presence and the biological roles of RNA modifications are largely unknown. Here we delineate types of RNA modifications, and provide examples demonstrating roles of such modifications in biology of filamentous fungi including fungal pathogens. We also discuss the possibility that RNA modification systems in fungal pathogens could be a prospective target for new agrochemicals.

scholarly journals Dissecting Disease-Suppressive Rhizosphere Microbiomes by Functional Amplicon Sequencing and 10× Metagenomics

mSystems ◽  
2021 ◽  
Author(s):  
Vittorio Tracanna ◽  
Adam Ossowicki ◽  
Marloes L. C. Petrus ◽  
Sam Overduin ◽  
Barbara R. Terlouw ◽  
...  
Keyword(s):  
Fungal Pathogens ◽  
Pathogenic Fungi ◽  
Amplicon Sequencing ◽  
Plant Pathogenic Fungi ◽  
Content Type ◽  
Major Threat ◽  
Wide Range

Soil-borne plant-pathogenic fungi continue to be a major threat to agriculture and horticulture. The genus Fusarium in particular is one of the most devastating groups of soilborne fungal pathogens for a wide range of crops.

scholarly journals “Lost and Found”: snoRNA Annotation in the Xenopus Genome and Implications for Evolutionary Studies

2019 ◽  
Vol 37 (1) ◽  
pp. 149-166
Author(s):  
Svetlana Deryusheva ◽  
Gaëlle J S Talhouarne ◽  
Joseph G Gall
Keyword(s):  
Ambystoma Mexicanum ◽  
Rna Modification ◽  
Oocyte Nucleus ◽  
Functional Domain ◽  
Sequencing Data ◽  
Rna Modifications ◽  
Guide Rnas ◽  
Lost And Found ◽  
Evolutionarily Conserved ◽  
Complete Set

Abstract Small nucleolar RNAs (snoRNAs) function primarily as guide RNAs for posttranscriptional modification of rRNAs and spliceosomal snRNAs, both of which are functionally important and evolutionarily conserved molecules. It is commonly believed that snoRNAs and the modifications they mediate are highly conserved across species. However, most relevant data on snoRNA annotation and RNA modification are limited to studies on human and yeast. Here, we used RNA-sequencing data from the giant oocyte nucleus of the frog Xenopus tropicalis to annotate a nearly complete set of snoRNAs. We compared the frog data with snoRNA sets from human and other vertebrate genomes, including mammals, birds, reptiles, and fish. We identified many Xenopus-specific (or nonhuman) snoRNAs and Xenopus-specific domains in snoRNAs from conserved RNA families. We predicted that some of these nonhuman snoRNAs and domains mediate modifications at unexpected positions in rRNAs and snRNAs. These modifications were mapped as predicted when RNA modification assays were applied to RNA from nine vertebrate species: frogs X. tropicalis and X. laevis, newt Notophthalmus viridescens, axolotl Ambystoma mexicanum, whiptail lizard Aspidoscelis neomexicana, zebrafish Danio rerio, chicken, mouse, and human. This analysis revealed that only a subset of RNA modifications is evolutionarily conserved and that modification patterns may vary even between closely related species. We speculate that each functional domain in snoRNAs (half of an snoRNA) may evolve independently and shuffle between different snoRNAs.

scholarly journals Trends in Nanotechnology and Its Potentialities to Control Plant Pathogenic Fungi: A Review

Biology ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 881
Author(s):  
Abdulaziz Bashir Kutawa ◽  
Khairulmazmi Ahmad ◽  
Asgar Ali ◽  
Mohd Zobir Hussein ◽  
Mohd Aswad Abdul Wahab ◽  
...  
Keyword(s):  
Disease Control ◽  
Fungal Pathogens ◽  
Negative Impact ◽  
Control Plant ◽  
Pathogenic Fungi ◽  
Field Trials ◽  
Water Soluble ◽  
Plant Pathogenic Fungi ◽  
Negative Effects ◽  
Synthesis Of Nanoparticles

Approximately 15–18% of crops losses occur as a result of animal pests, while weeds and microbial diseases cause 34 and 16% losses, respectively. Fungal pathogens cause about 70–80% losses in yield. The present strategies for plant disease control depend transcendently on agrochemicals that cause negative effects on the environment and humans. Nanotechnology can help by reducing the negative impact of the fungicides, such as enhancing the solubility of low water-soluble fungicides, increasing the shelf-life, and reducing toxicity, in a sustainable and eco-friendly manner. Despite many advantages of the utilization of nanoparticles, very few nanoparticle-based products have so far been produced in commercial quantities for agricultural purposes. The shortage of commercial uses may be associated with many factors, for example, a lack of pest crop host systems usage and the insufficient number of field trials. In some areas, nanotechnology has been advanced, and the best way to be in touch with the advances in nanotechnology in agriculture is to understand the major aspect of the research and to address the scientific gaps in order to facilitate the development which can provide a rationale of different nanoproducts in commercial quantity. In this review, we, therefore, described the properties and synthesis of nanoparticles, their utilization for plant pathogenic fungal disease control (either in the form of (a) nanoparticles alone, that act as a protectant or (b) in the form of a nanocarrier for different fungicides), nano-formulations of agro-nanofungicides, Zataria multiflora, and ginger essential oils to control plant pathogenic fungi, as well as the biosafety and limitations of the nanoparticles applications.

scholarly journals Gene cluster conservation identifies melanin and perylenequinone biosynthesis pathways in multiple plant pathogenic fungi

2018 ◽  
Author(s):  
Malaika K. Ebert ◽  
Rebecca E. Spanner ◽  
Ronnie de Jonge ◽  
David J. Smith ◽  
Jason Holthusen ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Plant Pathogens ◽  
Phylogenetic Analyses ◽  
Pathogenic Fungi ◽  
Gene Clusters ◽  
Host Cells ◽  
Plant Pathogenic Fungi ◽  
Biosynthetic Pathways ◽  
Biosynthetic Gene ◽  
Melanin Production

SummaryPerylenequinones are a family of structurally related polyketide fungal toxins with nearly universal toxicity. These photosensitizing compounds absorb light energy which enables them to generate reactive oxygen species that damage host cells. This potent mechanism serves as an effective weapon for plant pathogens in disease establishment. The sugar beet pathogenCercospora beticolasecretes the perylenequinone cercosporin during infection. We have shown recently that the cercosporin toxin biosynthesis(CTB)gene cluster is present in several other phytopathogenic fungi, prompting the search for biosynthetic gene clusters (BGCs) of structurally similar perylenequinones in other fungi. Here, we report the identification of the elsinochrome and phleichrome BGCs ofElsinoё fawcettiiandCladosporium phlei,respectively, based on gene cluster conservation with theCTBand hypocrellin BGCs. Furthermore, we show that previously reported BGCs for elsinochrome and phleichrome are involved in melanin production. Phylogenetic analysis of the corresponding melanin polyketide synthases (PKSs) and alignment of melanin BGCs revealed high conservation between the established and newly identifiedC. beticola, E. fawcettii,andC. phleimelanin BGCs. Mutagenesis of the identified perylenequinone and melanin PKSs inC. beticolaandE. fawcettiicoupled with mass spectrometric metabolite analyses confirmed their roles in toxin and melanin production.Originality and significance statementGenes involved in secondary metabolite (SM) production are often clustered together to form biosynthetic pathways. These pathways frequently have highly conserved keystone enzymes which can complicate allocation of a biosynthetic gene cluster (BGC) to the cognate SM. In our study, we utilized a combination of comparative genomics, phylogenetic analyses and biochemical approaches to reliably identify BGCs for perylenequinone toxins and DHN-melanin in multiple plant pathogenic fungi. Furthermore, we show that earlier studies that aimed to identify these perylenequinone pathways were misdirected and actually reported DHN-melanin biosynthetic pathways. Our study outlines a reliable approach to successfully identify fungal SM pathways.

Inhibition of Plant-Pathogenic Fungi by a Corn Trypsin Inhibitor Overexpressed in Escherichia coli

1999 ◽  
Vol 65 (3) ◽  
pp. 1320-1324 ◽  
Author(s):  
Zhi-Yuan Chen ◽  
Robert L. Brown ◽  
Alan R. Lax ◽  
Thomas E. Cleveland ◽  
John S. Russin
Keyword(s):  
Escherichia Coli ◽  
Trypsin Inhibitor ◽  
Fungal Pathogens ◽  
Active Form ◽  
Fungal Growth ◽  
Hyphal Growth ◽  
Pathogenic Fungi ◽  
Plant Pathogenic Fungi ◽  
Conidium Germination

ABSTRACT The cDNA of a 14-kDa trypsin inhibitor (TI) from corn was subcloned into an Escherichia coli overexpression vector. The overexpressed TI was purified based on its insolubility in urea and then refolded into the active form in vitro. This recombinant TI inhibited both conidium germination and hyphal growth of all nine plant pathogenic fungi studied, including Aspergillus flavus,Aspergillus parasiticus, and Fusarium moniliforme. The calculated 50% inhibitory concentration of TI for conidium germination ranged from 70 to more than 300 μg/ml, and that for fungal growth ranged from 33 to 124 μg/ml depending on the fungal species. It also inhibited A. flavus and F. moniliforme simultaneously when they were tested together. The results suggest that the corn 14-kDa TI may function in host resistance against a variety of fungal pathogens of crops.

scholarly journals Molecular Phylogeny of Endophytic Fungi from Rattan (Calamus castaneus Griff.) Spines and Their Antagonistic Activities against Plant Pathogenic Fungi

2021 ◽  
Vol 7 (4) ◽  
pp. 301
Author(s):  
Nurul Farizah Azuddin ◽  
Masratul Hawa Mohd ◽  
Nik Fadzly N. Rosely ◽  
Asyraf Mansor ◽  
Latiffah Zakaria
Keyword(s):  
Endophytic Fungi ◽  
Fungal Pathogens ◽  
Fungal Endophytes ◽  
Pathogenic Fungi ◽  
Inhibition Zone ◽  
Peninsular Malaysia ◽  
Plant Pathogenic Fungi ◽  
Trichoderma Spp ◽  
Palm Species ◽  
Rattan Palm

Calamus castaneus is a common rattan palm species in the tropical forests of Peninsular Malaysia and is noticeable by the yellow-based spines that cover the stems. This study aimed to determine the prevalence of fungal endophytes within C. castaneus spines and whether they inhibit the growth of fungal pathogens. Twenty-one genera with 40 species of fungal endophytes were isolated and identified from rattan palm spines. Based on molecular identification, the most common isolates recovered from the spines were Colletotrichum (n = 19) and Diaporthe spp. (n = 18), followed by Phyllosticta spp., Xylaria sp., Trichoderma spp., Helminthosporium spp., Penicillium spp., Fusarium spp., Neopestalotiopsis spp., Arthrinium sp., Cyphellophora sp., Cladosporium spp., Curvularia sp., Bionectria sp., and Acremonium spp. Non-sporulating fungi were also identified, namely Nemania primolutea, Pidoplitchkoviella terricola, Muyocopron laterale, Acrocalymma fici, Acrocalymma medicaginis, and Endomelanconiopsis endophytica. The isolation of these endophytes showed that the spines harbor endophytic fungi. Most of the fungal endophytes inhibited the growth of several plant pathogenic fungi, with 68% of the interactions resulting in mutual inhibition, producing a clear inhibition zone of <2 mm. Our findings demonstrate the potential of the fungal endophytes from C. castaneus spines as biocontrol agents.

scholarly journals Plant-Pathogenic Fungi in Seeds of Different Pea Cultivars in Poland

2014 ◽  
Vol 65 (3) ◽  
pp. 329-338 ◽  
Author(s):  
Karolina Wilman ◽  
Łukasz Stępień ◽  
Izabela Fabiańska ◽  
Piotr Kachlicki
Keyword(s):  
Botrytis Cinerea ◽  
Fungal Pathogens ◽  
Pathogenic Fungi ◽  
Field Resistance ◽  
Plant Pathogenic Fungi ◽  
Infection Level ◽  
Epicoccum Nigrum ◽  
Legume Crops ◽  
Lower Infection ◽  
Pea Seeds

AbstractLegume crops are exposed to infection by fungal pathogens, which often results in contamination with mycotoxins. The aim of this study was to evaluate the level of field resistance/susceptibility of edible and fodder pea cultivars to the colonization of seeds by fungal pathogens in two subsequent seasons, as well as to identify the pathogens present in the seeds of the tested cultivars. Alternaria spp. were the most common fungi isolated from pea seeds in both seasons, followed by Fusarium spp., Stemphylium spp., Ulocladium spp., Botrytis cinerea Pers., Epicoccum nigrum Link., and Phomapinodella L. K. Jones. The highest percentage of infected seeds (55 %) was recorded for cultivar Ezop. The presence of a large number of fungi was found in 2012 for cultivars Santana, Tarchalska, Medal, Cysterski, Mentor, Lasso, and Ezop. Fodder cultivars displayed a lower infection level than edible cultivars. We can conclude that Alternaria spp. were the most frequent fungi present in pea seeds in Poland and Fusarium spp. were likely the most dangerous, having in mind their established mycotoxigenic abilities.

scholarly journals The landscape of SARS-CoV-2 RNA modifications

2020 ◽  
Author(s):  
Milad Miladi ◽  
Jonas Fuchs ◽  
Wolfgang Maier ◽  
Sebastian Weigang ◽  
Núria Díaz i Pedrosa ◽  
...  
Keyword(s):  
Host Cell ◽  
Rna Virus ◽  
Open Reading Frames ◽  
Lung Epithelial Cells ◽  
Host Cells ◽  
Rna Modification ◽  
Rna Modifications ◽  
Positive Strand Rna Virus ◽  
Novel Therapeutic Strategies ◽  
Positive Strand Rna

AbstractIn 2019 the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the first documented cases of severe lung disease COVID-19. Since then, SARS-CoV-2 has been spreading around the globe resulting in a severe pandemic with over 500.000 fatalities and large economical and social disruptions in human societies. Gaining knowledge on how SARS-Cov-2 interacts with its host cells and causes COVID-19 is crucial for the intervention of novel therapeutic strategies. SARS-CoV-2, like other coronaviruses, is a positive-strand RNA virus. The viral RNA is modified by RNA-modifying enzymes provided by the host cell. Direct RNA sequencing (DRS) using nanopores enables unbiased sensing of canonical and modified RNA bases of the viral transcripts. In this work, we used DRS to precisely annotate the open reading frames and the landscape of SARS-CoV-2 RNA modifications. We provide the first DRS data of SARS-CoV-2 in infected human lung epithelial cells. From sequencing three isolates, we derive a robust identification of SARS-CoV-2 modification sites within a physiologically relevant host cell type. A comparison of our data with the DRS data from a previous SARS-CoV-2 isolate, both raised in monkey renal cells, reveals consistent RNA modifications across the viral genome. Conservation of the RNA modification pattern during progression of the current pandemic suggests that this pattern is likely essential for the life cycle of SARS-CoV-2 and represents a possible target for drug interventions.

scholarly journals The impact of Pseudomonas syringae bacteria on the plant pathogenic fungi and cherry plants

2020 ◽  
Vol 21 ◽  
pp. 00019
Author(s):  
Marina Maslova ◽  
Ekaterina Grosheva ◽  
Ivan Shamshin ◽  
Anna Kuznetsova ◽  
Alexander Fedorenko
Keyword(s):  
Pseudomonas Syringae ◽  
Bacterial Blight ◽  
Fungal Pathogens ◽  
Pathogenic Fungi ◽  
Plant Pathogenic Fungi ◽  
Horticultural Crops ◽  
Necrotrophic Fungi ◽  
Antagonist Action ◽  
The Impact ◽  
Association Effect

The investigations are made of cherry biological peculiarities and disease excitants composition. The domination of necrotrophic fungi and Pseudomonas syringae van Hall bacteria in pathocenosis is shown. The fact of microbiota associative lesion of plants is established. The antagonist action of isolated bacterium in relation to Cytospora leucostoma (Pers.) Sacc., Alternaria alternata Keissl., Fusarium oxysporum Schlecht., Monillia cinerea Bonord is detected. The character of isolated bacterium metabolites, pathogenic fungi and their association effect on a host-plant is established. The ability of bacterium to lower the activity of phytotoxins secretion in fungi when cultivated together is identified. It has been found that it is the fungal pathogens causing the development of die-back in cherry in investigated gardens, whereas P. syringae bacterium, when in latent state, plays a part of protector and permits to suppress the development of fungal infection. Taking into account the fact that this bacterium is pathogenic, the works of advanced breeding for resistance of the horticultural crops to bacterial blight are recommended.

scholarly journals Identification of Diverse Mycoviruses through Metatranscriptomics Characterization of the Viromes of Five Major Fungal Plant Pathogens

2016 ◽  
Vol 90 (15) ◽  
pp. 6846-6863 ◽  
Author(s):  
Shin-Yi Lee Marzano ◽  
Berlin D. Nelson ◽  
Olutoyosi Ajayi-Oyetunde ◽  
Carl A. Bradley ◽  
Teresa J. Hughes ◽  
...  
Keyword(s):  
High Throughput ◽  
Fungal Pathogens ◽  
Plant Pathogens ◽  
High Throughput Sequencing ◽  
Pathogenic Fungi ◽  
Plant Diseases ◽  
Plant Pathogenic Fungi ◽  
Content Type ◽  
Fungal Plant Pathogens ◽  
Viral Sequences

ABSTRACTMycoviruses can have a marked effect on natural fungal communities and influence plant health and productivity. However, a comprehensive picture of mycoviral diversity is still lacking. To characterize the viromes of five widely dispersed plant-pathogenic fungi,Colletotrichum truncatum,Macrophomina phaseolina,Diaporthe longicolla,Rhizoctonia solani, andSclerotinia sclerotiorum, a high-throughput sequencing-based metatranscriptomic approach was used to detect viral sequences. Total RNA and double-stranded RNA (dsRNA) from mycelia and RNA from samples enriched for virus particles were sequenced. Sequence data were assembledde novo, and contigs with predicted amino acid sequence similarities to viruses in the nonredundant protein database were selected. The analysis identified 72 partial or complete genome segments representing 66 previously undescribed mycoviruses. Using primers specific for each viral contig, at least one fungal isolate was identified that contained each virus. The novel mycoviruses showed affinity with 15 distinct lineages:Barnaviridae,Benyviridae,Chrysoviridae,Endornaviridae,Fusariviridae,Hypoviridae,Mononegavirales,Narnaviridae,Ophioviridae,Ourmiavirus,Partitiviridae,Tombusviridae,Totiviridae,Tymoviridae, andVirgaviridae. More than half of the viral sequences were predicted to be members of theMitovirusgenus in the familyNarnaviridae, which replicate within mitochondria. Five viral sequences showed strong affinity with three families (Benyviridae,Ophioviridae, andVirgaviridae) that previously contained no mycovirus species. The genomic information provides insight into the diversity and taxonomy of mycoviruses and coevolution of mycoviruses and their fungal hosts.IMPORTANCEPlant-pathogenic fungi reduce crop yields, which affects food security worldwide. Plant host resistance is considered a sustainable disease management option but may often be incomplete or lacking for some crops to certain fungal pathogens or strains. In addition, the rising issues of fungicide resistance demand alternative strategies to reduce the negative impacts of fungal pathogens. Those fungus-infecting viruses (mycoviruses) that attenuate fungal virulence may be welcome additions for mitigation of plant diseases. By high-throughput sequencing of the RNAs from 275 isolates of five fungal plant pathogens, 66 previously undescribed mycoviruses were identified. In addition to identifying new potential biological control agents, these results expand the grand view of the diversity of mycoviruses and provide possible insights into the importance of intracellular and extracellular transmission in fungus-virus coevolution.

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