Comparative genome analyses suggest a hemibiotrophic lifestyle and virulence differences for the beech bark disease fungal pathogens Neonectria faginata and Neonectria coccinea

Abstract Neonectria faginata and Neonectria coccinea are the causal agents of the insect-fungus disease complex known as beech bark disease (BBD), known to cause mortality in beech forest stands in North America and Europe. These fungal species have been the focus of extensive ecological and disease management studies, yet less progress has been made toward generating genomic resources for both micro- and macro-evolutionary studies. Here, we report a 42.1 and 42.7 mb highly contiguous genome assemblies of N. faginata and N. coccinea, respectively, obtained using Illumina technology. These species share similar gene number counts (12,941 and 12,991) and percentages of predicted genes with assigned functional categories (64 and 65%). Approximately 32% of the predicted proteomes of both species are homologous to proteins involved in pathogenicity, yet N. coccinea shows a higher number of predicted mitogen-activated protein kinase genes, virulence determinants possibly contributing to differences in disease severity between N. faginata and N. coccinea. A wide range of genes encoding for carbohydrate-active enzymes capable of degradation of complex plant polysaccharides and a small number of predicted secretory effector proteins, secondary metabolite biosynthesis clusters and cytochrome oxidase P450 genes were also found. This arsenal of enzymes and effectors correlates with, and reflects, the hemibiotrophic lifestyle of these two fungal pathogens. Phylogenomic analysis and timetree estimations indicated that the N. faginata and N. coccinea species divergence may have occurred at ∼4.1 million years ago. Differences were also observed in the annotated mitochondrial genomes as they were found to be 81.7 kb (N. faginata) and 43.2 kb (N. coccinea) in size. The mitochondrial DNA expansion observed in N. faginata is attributed to the invasion of introns into diverse intra- and intergenic locations. These first draft genomes of N. faginata and N. coccinea serve as valuable tools to increase our understanding of basic genetics, evolutionary mechanisms and molecular physiology of these two nectriaceous plant pathogenic species.

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Fungal LysM effectors that comprise two LysM domains bind chitin through intermolecular dimerization

10.1101/2020.06.11.146639 ◽

2020 ◽

Author(s):

Hui Tian ◽

Gabriel L. Fiorin ◽

Anja Kombrink ◽

Jeroen R. Mesters ◽

Bart P.H.J. Thomma

Keyword(s):

Fungal Pathogens ◽

Plant Immunity ◽

Effector Proteins ◽

Broad Host Range ◽

Fungal Cell ◽

Mould Fungus ◽

Colletotrichum Higginsianum ◽

Molecular Pattern ◽

Wide Range ◽

Binding Groove

SUMMARYChitin is a polymer of β-(1,4)-linked N-acetyl-D-glucosamine (GlcNAc) and a major structural component of fungal cell walls that acts as a microbe-associated molecular pattern (MAMP) that can be recognized by plant cell surface-localized pattern recognition receptors (PRRs) to activate a wide range of immune responses. In order to deregulate chitin-induced plant immunity and successfully establish their infection, many fungal pathogens secrete effector proteins with LysM domains. We previously determined that two of the three LysM domains of the LysM effector Ecp6 from the tomato leaf mould fungus Cladosporium fulvum cooperate to form a chitin-binding groove that binds chitin with ultra-high affinity, allowing to outcompete host PRRs for chitin binding. In this study, we describe functional and structural analyses aimed to investigate whether LysM effectors that contain two LysM domains bind chitin through intramolecular or intermolecular LysM dimerization. To this end, we focus on MoSlp1 from the rice blast fungus Magnaporthe oryzae, Vd2LysM from the broad host range vascular wilt fungus Verticillium dahliae, and ChElp1 and ChElp2 from the Brassicaceae anthracnose fungus Colletotrichum higginsianum. We show that these LysM effectors bind chitin through intermolecular LysM dimerization, allowing the formation of polymeric complexes that may precipitate in order to eliminate the presence of chitin oligomers at infection sites to suppress activation of chitin-induced plant immunity. In this manner, many fungal pathogens are able to subvert chitin-triggered immunity in their plant hosts.

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Comparative Study on Mitogen Activated Protein Kinase of Plasmodium Species by Using in silico Method

Scientific Research Journal ◽

10.24191/srj.v9i1.9411 ◽

2012 ◽

Vol 9 (1) ◽

pp. 1

Author(s):

Mohd Fakharul Zaman Raja Yahya ◽

Hasidah Mohd Sidek

Keyword(s):

Amino Acid ◽

In Silico ◽

Nuclear Export ◽

Nuclear Export Signal ◽

Plasmodium Species ◽

Mitogen Activated Protein Kinase ◽

Multiple Sequence ◽

Wide Range ◽

Mitogen Activated Protein ◽

Human Plasmodium

Malaria parasites, Plasmodium can infect a wide range of hosts including humans and rodents. There are two copies of mitogen activated protein kinases (MAPKs) in Plasmodium, namely MAPK1 and MAPK2. The MAPKs have been studied extensively in the human Plasmodium, P. falciparum. However, the MAPKs from other Plasmodium species have not been characterized and it is therefore the premise of presented study to characterize the MAPKs from other Plasmodium species-P. vivax, P. knowlesi, P. berghei, P. chabaudi and P.yoelli using a series of publicly available bioinformatic tools. In silico data indicates that all Plasmodium MAPKs are nuclear-localized and contain both a nuclear localization signal (NLS) and a Leucine-rich nuclear export signal (NES). The activation motifs of TDY and TSH were found to be fully conserved in Plasmodium MAPK1 and MAPK2, respectively. The detailed manual inspection of a multiple sequence alignment (MSA) construct revealed a total of 17 amino acid stack patterns comprising of different amino acids present in MAPKJ and MAPK2 respectively, with respect to rodent and human Plasmodia. It is proposed that these amino acid stack patterns may be useful in explaining the disparity between rodent and human Plasmodium MAPKs.

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Comparative Study on Mitogen Activated Protein Kinase of Plasmodium Species by Using In silico Method

Scientific Research Journal ◽

10.24191/srj.v9i1.5052 ◽

2012 ◽

Vol 9 (1) ◽

pp. 1

Author(s):

Mohd Fakharul Zaman Raja Yahya ◽

Hasidah Mohd Sidek

Keyword(s):

Amino Acid ◽

In Silico ◽

Nuclear Export ◽

Nuclear Export Signal ◽

Plasmodium Species ◽

Mitogen Activated Protein Kinase ◽

Multiple Sequence ◽

Bioinformatic Tools ◽

Wide Range ◽

Human Plasmodium

Malaria parasites, Plasmodium can infect a wide range ofhosts including humans and rodents. There are two copies ofmitogen activated protein kinases (MAPKs) in Plasmodium, namely MAPK1 and MAPK2. The MAPKs have been studied extensively in the human Plasmodium, P. falciparum. However, the MAPKs from other Plasmodium species have not been characterized and it is therefore the premise ofpresented study to characterize the MAPKs from other Plasmodium species-P. vivax, P. knowlesi, P. berghei, P. chabaudi and P.yoelli using a series ofpublicly available bioinformatic tools. In silico data indicates that all Plasmodium MAPKs are nuclear-localizedandcontain both a nuclear localization signal (NLS) anda Leucine-rich nuclear export signal (NES). The activation motifs ofTDYand TSH werefound to befully conserved in Plasmodium MAPK1 and MAPK2, respectively. The detailed manual inspection ofa multiple sequence alignment (MSA) construct revealed a total of 17 amino acid stack patterns comprising ofdifferent amino acids present in MAPK1 and MAPK2 respectively, with respect to rodent and human Plasmodia. 1t is proposed that these amino acid stack patterns may be useful in explaining the disparity between rodent and human Plasmodium MAPKs.

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Control of Winged Waterprimrose (Jussiaea decurrens) and Northern Jointvetch (Aeschynomene virginica) with Fungal Pathogens

Weed Science ◽

10.1017/s0043174500044477 ◽

1979 ◽

Vol 27 (5) ◽

pp. 497-501 ◽

Cited By ~ 46

Author(s):

C. D. Boyette ◽

G. E. Templeton ◽

R. J. Smith

Keyword(s):

Oryza Sativa ◽

Glycine Max ◽

Fungal Pathogens ◽

Liquid Culture ◽

Field Experiments ◽

Colletotrichum Gloeosporioides ◽

Pathogenic Fungus ◽

Field Tests ◽

Wide Range ◽

Growing Region

An indigenous, host-specific, pathogenic fungus that parasitizes winged waterprimrose [Jussiaea decurrens(Walt.) DC.] is endemic in the rice growing region of Arkansas. The fungus was isolated and identified asColletotrichum gloeosporioides(Penz.) Sacc. f.sp. jussiaeae(CGJ). It is highly specific for parasitism of winged waterprimrose and not parasitic on creeping waterprimrose (J. repensL. var.glabrescensKtze.), rice (Oryza sativaL.), soybeans [Glycine max(L.) Merr.], cotton (Gossypium hirsutumL.), or 4 other crops and 13 other weeds. The fungus was physiologically distinct from C.gloeosporioides(Penz.) Sacc. f. sp.aeschynomene(CGA), an endemic anthracnose pathogen of northern jointvetch[Aeschynomene virginica(L.) B.S.P.], as indicated by cross inoculations of both weeds. Culture in the laboratory and inoculation of winged waterprimrose in greenhouse, growth chamber and field experiments indicated that the pathogen was stable, specific, and virulent in a wide range of environments. The pathogen yielded large quantities of spores in liquid culture. It is suitable for control of winged waterprimrose. Winged waterprimrose and northern jointvetch were controlled in greenhouse and field tests by application of spore mixtures of CGJ and CGA at concentrations of 1 to 2 million spores/ml of each fungus in 94 L/ha of water; the fungi did not damage rice or nontarget crops.

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Transfer of Plasmid DNA to Clinical Coagulase-Negative Staphylococcal Pathogens by Using a Unique Bacteriophage

Applied and Environmental Microbiology ◽

10.1128/aem.04190-14 ◽

2015 ◽

Vol 81 (7) ◽

pp. 2481-2488 ◽

Cited By ~ 19

Author(s):

Volker Winstel ◽

Petra Kühner ◽

Bernhard Krismer ◽

Andreas Peschel ◽

Holger Rohde

Keyword(s):

Plasmid Dna ◽

Genetic Manipulation ◽

Current Knowledge ◽

Virulence Determinants ◽

Coagulase Negative Staphylococci ◽

Reliable Technique ◽

Content Type ◽

Research Activities ◽

Wide Range ◽

Genetic Barriers

ABSTRACTGenetic manipulation of emerging bacterial pathogens, such as coagulase-negative staphylococci (CoNS), is a major hurdle in clinical and basic microbiological research. Strong genetic barriers, such as restriction modification systems or clustered regularly interspaced short palindromic repeats (CRISPR), usually interfere with available techniques for DNA transformation and therefore complicate manipulation of CoNS or render it impossible. Thus, current knowledge of pathogenicity and virulence determinants of CoNS is very limited. Here, a rapid, efficient, and highly reliable technique is presented to transfer plasmid DNA essential for genetic engineering to important CoNS pathogens from a uniqueStaphylococcus aureusstrain via a specificS. aureusbacteriophage, Φ187. Even strains refractory to electroporation can be transduced by this technique once donor and recipient strains share similar Φ187 receptor properties. As a proof of principle, this technique was used to delete the alternative transcription factor sigma B (SigB) via allelic replacement in nasal and clinicalStaphylococcus epidermidisisolates at high efficiencies. The described approach will allow the genetic manipulation of a wide range of CoNS pathogens and might inspire research activities to manipulate other important pathogens in a similar fashion.

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Melanogenesis Connection with Innate Immunity and Toll-Like Receptors

International Journal of Molecular Sciences ◽

10.3390/ijms21249769 ◽

2020 ◽

Vol 21 (24) ◽

pp. 9769

Author(s):

Saaya Koike ◽

Kenshi Yamasaki

Keyword(s):

Skin Pigmentation ◽

Innate Immune ◽

Mitogen Activated Protein Kinase ◽

Ultraviolet Rays ◽

Toll Like Receptors ◽

Pigment Formation ◽

Living Body ◽

Pigmentary Disorders ◽

Wide Range ◽

Griscelli Syndrome

The epidermis is located in the outermost layer of the living body and is the place where external stimuli such as ultraviolet rays and microorganisms first come into contact. Melanocytes and melanin play a wide range of roles such as adsorption of metals, thermoregulation, and protection from foreign enemies by camouflage. Pigmentary disorders are observed in diseases associated with immunodeficiency such as Griscelli syndrome, indicating molecular sharing between immune systems and the machineries of pigment formation. Melanocytes express functional toll-like receptors (TLRs), and innate immune stimulation via TLRs affects melanin synthesis and melanosome transport to modulate skin pigmentation. TLR2 enhances melanogenetic gene expression to augment melanogenesis. In contrast, TLR3 increases melanosome transport to transfer to keratinocytes through Rab27A, the responsible molecule of Griscelli syndrome. TLR4 and TLR9 enhance tyrosinase expression and melanogenesis through p38 MAPK (mitogen-activated protein kinase) and NFκB signaling pathway, respectively. TLR7 suppresses microphthalmia-associated transcription factor (MITF), and MITF reduction leads to melanocyte apoptosis. Accumulating knowledge of the TLRs function of melanocytes has enlightened the link between melanogenesis and innate immune system.

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Investigation of Antifungal Mechanisms of Thymol in the Human Fungal Pathogen, Cryptococcus neoformans

Molecules ◽

10.3390/molecules26113476 ◽

2021 ◽

Vol 26 (11) ◽

pp. 3476

Author(s):

Kwang-Woo Jung ◽

Moon-Soo Chung ◽

Hyoung-Woo Bai ◽

Byung Yeoup Chung ◽

Sungbeom Lee

Keyword(s):

Cryptococcus Neoformans ◽

Fungal Pathogens ◽

Reverse Genetics ◽

Mapk Pathway ◽

Global Climate ◽

Mitogen Activated Protein Kinase ◽

Ergosterol Biosynthesis ◽

Thymus Vulgaris ◽

Dependent Manner ◽

Expression Levels

Due to lifespan extension and changes in global climate, the increase in mycoses caused by primary and opportunistic fungal pathogens is now a global concern. Despite increasing attention, limited options are available for the treatment of systematic and invasive mycoses, owing to the evolutionary similarity between humans and fungi. Although plants produce a diversity of chemicals to protect themselves from pathogens, the molecular targets and modes of action of these plant-derived chemicals have not been well characterized. Using a reverse genetics approach, the present study revealed that thymol, a monoterpene alcohol from Thymus vulgaris L., (Lamiaceae), exhibits antifungal activity against Cryptococcus neoformans by regulating multiple signaling pathways including calcineurin, unfolded protein response, and HOG (high-osmolarity glycerol) MAPK (mitogen-activated protein kinase) pathways. Thymol treatment reduced the intracellular concentration of Ca2+ by controlling the expression levels of calcium transporter genes in a calcineurin-dependent manner. We demonstrated that thymol decreased N-glycosylation by regulating the expression levels of genes involved in glycan-mediated post-translational modifications. Furthermore, thymol treatment reduced endogenous ergosterol content by decreasing the expression of ergosterol biosynthesis genes in a HOG MAPK pathway-dependent manner. Collectively, this study sheds light on the antifungal mechanisms of thymol against C. neoformans.

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

Journal of Fungi ◽

10.3390/jof7020086 ◽

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.

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Sordarins: In Vitro Activities of New Antifungal Derivatives against Pathogenic Yeasts, Pneumocystis carinii, and Filamentous Fungi

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.42.11.2863 ◽

1998 ◽

Vol 42 (11) ◽

pp. 2863-2869 ◽

Cited By ~ 65

Author(s):

E. Herreros ◽

C. M. Martinez ◽

M. J. Almela ◽

M. S. Marriott ◽

F. Gomez De Las Heras ◽

...

Keyword(s):

Cryptococcus Neoformans ◽

Filamentous Fungi ◽

Fungal Pathogens ◽

Pneumocystis Carinii ◽

Pathogenic Fungi ◽

Pseudallescheria Boydii ◽

Absidia Corymbifera ◽

Wide Range ◽

Blastoschizomyces Capitatus

ABSTRACT GM 193663, GM 211676, GM 222712, and GM 237354 are new semisynthetic derivatives of the sordarin class. The in vitro antifungal activities of GM 193663, GM 211676, GM 222712, and GM 237354 against 111 clinical yeast isolates of Candida albicans,Candida kefyr, Candida glabrata, Candida parapsilosis, Candida krusei, and Cryptococcus neoformans were compared. The in vitro activities of some of these compounds against Pneumocystis carinii, 20 isolates each of Aspergillus fumigatus and Aspergillus flavus, and 30 isolates of emerging less-common mold pathogens and dermatophytes were also compared. The MICs of GM 193663, GM 211676, GM 222712, and GM 237354 at which 90% of the isolates were inhibited (MIC90s) were 0.03, 0.03, 0.004, and 0.015 μg/ml, respectively, for C. albicans, including strains with decreased susceptibility to fluconazole; 0.5, 0.5, 0.06, and 0.12 μg/ml, respectively, for C. tropicalis; and 0.004, 0.015, 0.008, and 0.03 μg/ml, respectively, forC. kefyr. GM 222712 and GM 237354 were the most active compounds against C. glabrata, C. parapsilosis, and Cryptococcus neoformans. AgainstC. glabrata and C. parapsilosis, the MIC90s of GM 222712 and GM 237354 were 0.5 and 4 μg/ml and 1 and 16 μg/ml, respectively. The MIC90s of GM 222712 and GM 237354 againstCryptococcus neoformans were 0.5 and 0.25 μg/ml, respectively. GM 193663, GM 211676, GM 222712, and GM 237354 were extremely active against P. carinii. The efficacies of sordarin derivatives against this organism were determined by measuring the inhibition of the uptake and incorporation of radiolabelled methionine into newly synthesized proteins. All compounds tested showed 50% inhibitory concentrations of <0.008 μg/ml. Against A. flavus and A. fumigatus, the MIC90s of GM 222712 and GM 237354 were 1 and 32 μg/ml and 32 and >64 μg/ml, respectively. In addition, GM 237354 was tested against the most important emerging fungal pathogens which affect immunocompromised patients. Cladosporium carrioni, Pseudallescheria boydii, and the yeast-like fungi Blastoschizomyces capitatus and Geotrichum clavatum were the most susceptible of the fungi to GM 237354, with MICs ranging from ≤0.25 to 2 μg/ml. The MICs of GM 237354 against Trichosporon beigelii and the zygomycetesAbsidia corymbifera, Cunninghamella bertholletiae, and Rhizopus arrhizus ranged from ≤0.25 to 8 μg/ml. Against dermatophytes, GM 237354 MICs were ≥2 μg/ml. In summary, we concluded that some sordarin derivatives, such as GM 222712 and GM 237354, showed excellent in vitro activities against a wide range of pathogenic fungi, includingCandida spp., Cryptococcus neoformans, P. carinii, and some filamentous fungi and emerging invasive fungal pathogens.

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Adaptation of Newcastle Disease Virus (NDV) in Feral Birds and their Potential Role in Interspecies Transmission

The Open Virology Journal ◽

10.2174/1874357901812010052 ◽

2018 ◽

Vol 12 (1) ◽

pp. 52-68 ◽

Cited By ~ 5

Author(s):

Aziz-ul- Rahman ◽

Momena Habib ◽

Muhammad Zubair Shabbir

Keyword(s):

Newcastle Disease ◽

Potential Role ◽

Vital Role ◽

Wild Birds ◽

Avian Species ◽

Phylogenomic Analysis ◽

Susceptible Host ◽

Domestic Poultry ◽

Wide Range

Introduction:Newcastle Disease (ND), caused by Avian avulavirus 1 (AAvV 1, avulaviruses), is a notifiable disease throughout the world due to the economic impact on trading restrictions and its embargoes placed in endemic regions. The feral birds including aquatic/migratory birds and other wild birds may act as natural reservoir hosts of ND Viruses (NDVs) and may play a remarkable role in the spread of the virus in environment. In addition, other 19 avulaviruses namely: AAvV 2 to 20, have been potentially recognized from feral avian species.Expalantion:Many previous studies have investigated the field prevailing NDVs to adapt a wide range of susceptible host. Still the available data is not enough to declare the potential role of feral birds in transmission of the virus to poultry and/or other avian birds. In view of the latest evidence related to incidences of AAvVs in susceptible avian species, it is increasingly important to understand the potential of viruses to transmit within the domestic poultry and other avian hosts. Genomic and phylogenomic analysis of several investigations has shown the same (RK/RQRR↓F) motif cleavage site among NDV isolates with same genotypes from domestic poultry and other wild hosts. So, the insight of this, various semi-captive/free-ranging wild avian species could play a vital role in the dissemination of the virus, which is an important consideration to control the disease outbreaks. Insufficient data on AAvV 1 transmission from wild birds to poultry and vice versa is the main constraint to understand about its molecular biology and genomic potential to cause infection in all susceptible hosts.Conclusion:The current review details the pertinent features of several historical and contemporary aspects of NDVs and the vital role of feral birds in its molecular epidemiology and ecology.

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