Adaptation to pH and role of PacC in the rice blast fungus Magnaporthe oryzae

Glutamate dehydrogenase MoGDH2 modulates the environmental and host pH to enhance adaptation and virulence of the rice blast fungus Pyricularia oryzae

pH adaptation and modulation are essential for the survival and infection of fungal pathogens. Pyricularia oryzae is a hemi-biotrophic fungal pathogen causes devastating blast disease on rice. How P. oryzae achieves host pH alkalization during the biotrophic-infection stage is unclear. Here, we characterized the NAD+-glutamate dehydrogenase encoding gene MoGDH2 in P. oryzae. The Δmogdh2 mutant failed to utilize glutamate to release NH3 and alkalize the environmental pH. MoGDH2 mediated pH homeostasis under acidic conditions but not alkaline environments. During glutamate utilization and fungal infection, MoGDH2 exhibited high expression levels, and modulated host pH at biotrophic stage. The apoplastic pH of host cells infected by wild-type strain P131 was sharply acidified at 24 h post inoculation (hpi), and the cytoplasmic pH gradually increased from 24 to 36 hpi. In comparison, the pH change patterns disappeared in cells infected by Δmogdh2. Furthermore, MoGDH2 is critical for reactive oxygen species tolerance and virulence, which is regulated via phosphorylation at the T47 site. Protein kinase MoDbf2 directly interacted with and phosphorylated MoGDH2. This study sheds new light on the function of MoGDH2 in pH modulation and infection.

Synthesis and characterization of allomelanin model from 1,8-dihydroxynaphthalene autooxidation

In this work a novel method for synthesis of 1,8-dihydroxynaphthalene melanin was presented, as well as the physicochemical properties, molecular structure, and characteristics of the pigment. The proposed synthesis protocol is simple and cost-effective with no enzymes or catalysts needed. The final product is not adsorbed on any surface, since the pigment is the result of autooxidation of 1,8-dihydroxynaphthalene. Performed analyses revealed that the solubility, optical and paramagnetic properties are typical for melanins, and in the EPR spectra an unusual hyperfine structure was observed. The molecular structure of the pigment consists of three different layers forming polar and non-polar surfaces. Additionally, the presence of ether bonds presence was revealed. The developed method creates new opportunities for melanin research and eliminates the need to extract melanins from biological samples, which often lead to structural changes in isolated melanins, which undermines the reliability of analyses of the properties and structure of these polymers. On the other hand, the ubiquity of melanins in living organisms and the diversity of their biological functions have let to the growing interest of researchers in this group of pigments. The analyses carried out show that the obtained synthetic DHN polymer can be considered as a model DHN-melanin in mycological studies and material research.

Trachemys scripta Eggs as Part of a Potential In Vivo Model for Studying Sea Turtle Egg Fusariosis

The fungal pathogens Fusarium keratoplasticum and Fusarium falciforme are responsible for the emerging infectious disease named sea turtle egg fusariosis (STEF). This disease affects all sea turtle species throughout the world, causing low hatching success and mass mortalities. In this study, we investigated the potential use of widely available and easy-to-handle eggs of the invasive alien red-eared slider turtle, Trachemys scripta, as part of an in vivo host model to improve our knowledge of the biological properties of the pathogens responsible of the STEF. Specifically, we performed in vivo experiments, in which T. scripta eggs were challenged with conidia of F. keratoplasticum isolated from diseased sea turtle eggs. We found that the pathogen could colonize and develop similar signs to those observed in nature and fulfill Koch's postulates. The pathogen showed high virulence properties (e.g., high disease incidence, severity, and low hatching success) and its ability to modify the pH in both the egg surface and culture media, confirming previously described fungal pathogen models. These results support the use of T. scripta as an experimental in vivo host model for studying the biological characteristics of STEF, thus providing valuable insights into the mechanisms underlying the emergence of this fungal disease.

Pyricularia oryzae enhances Streptomyces griseus growth via non-volatile alkaline metabolites

Chemical compounds that affect microbial interactions have attracted wide interest. In this study, Streptomyces griseus showed enhanced growth when cocultured with the rice blast fungus Pyricularia oryzae on potato dextrose agar (PDA) medium. An improvement in S. griseus growth was observed before contact with P. oryzae, and no growth-promoting effect was observed when the growth medium between the two microorganisms was separated. These results suggested that the chemicals produced by P. oryzae diffused through the medium and were not volatile. A PDA plate supplemented with phenol red showed that the pH of the area surrounding P. oryzae increased. The area with increased pH promoted S. griseus growth, suggesting that the alkaline compounds produced by P. oryzae were involved in this growth stimulation. In contrast, coculture with the soilborne plant pathogen Fusarium oxysporum and entomopathogenic fungus Cordyceps tenuipes did not promote S. griseus growth. Furthermore, DL-α-Difluoromethylornithine, a polyamine biosynthesis inhibitor, prevented the increase in pH and growth promotion of S. griseus by P. oryzae. These results indicated that P. oryzae increased pH by producing a polyamine.

pH/chitinase dual stimuli-responsive essential oil-delivery system based on mesoporous silica nanoparticles for control of rice blast

BACKGROUND

Owing to their surface modifiability, smart mesoporous silica nanoparticles (MSNs) can be designed to respond to plant disease-microenvironmental stimuli, thereby achieving on-demand release of active ingredients to control disease by effectively improving citral (CT) stability.

RESULTS

A pH/chitinase dual stimuli-responsive essential oil-delivery system (CT@HMS@CH/TA) was successfully fabricated by encapsulating CT in hollow mesoporous silica (HMS), and coating with tannic acid (TA) and chitosan (CH) within HMS by using the layer-by-layer assembly technique (LbL). CT@HMS@CH/TA with an average particle size of 125.12 ± 0.12 nm and a hollow mesoporous nanostructure showed high CT-loading efficiency (16.58% ± 0.17%). The photodegradation rate of CT@HMS@CH/TA under UV irradiation (48 h) was only 15.31%, indicating a 3.34-fold UV stability improvement. CT@HMS@CH/TA exhibited a higher CT release rate in response to acidic pH and the presence of chitinase, simulating the prevailing conditions as Magnaporthe oryzae infection. Furthermore, CT@HMS@CH/TA exhibited better adhesion without affecting normal rice growth, significantly upregulating chitinase gene expression and enhancing chitinase activity on M. oryzae, thus enhancing CT antifungal activity.

CONCLUSION

CT@HMS@CH/TA improved CT stability and showed intelligent, controlled release-performance and higher antifungal efficacy, thus providing a new strategy for efficient application of essential oils for green control of rice blast disease. © 2024 Society of Chemical Industry.

Strategies for the Enhancement of Secondary Metabolite Production via Biosynthesis Gene Cluster Regulation in Aspergillus oryzae

The filamentous fungus Aspergillus oryzae (A. oryzae) has been extensively used for the biosynthesis of numerous secondary metabolites with significant applications in agriculture and food and medical industries, among others. However, the identification and functional prediction of metabolites through genome mining in A. oryzae are hindered by the complex regulatory mechanisms of secondary metabolite biosynthesis and the inactivity of most of the biosynthetic gene clusters involved. The global regulatory factors, pathway-specific regulatory factors, epigenetics, and environmental signals significantly impact the production of secondary metabolites, indicating that appropriate gene-level modulations are expected to promote the biosynthesis of secondary metabolites in A. oryzae. This review mainly focuses on illuminating the molecular regulatory mechanisms for the activation of potentially unexpressed pathways, possibly revealing the effects of transcriptional, epigenetic, and environmental signal regulation. By gaining a comprehensive understanding of the regulatory mechanisms of secondary metabolite biosynthesis, strategies can be developed to enhance the production and utilization of these metabolites, and potential functions can be fully exploited.

A pH-Responsive Essential Oil Delivery System Based on Metal-organic Framework (ZIF-8) for Preventing Fungal Disease

Smart metal-organic framework nanocarriers that respond to microenvironmental stimuli related to plant diseases can achieve the on-demand release of active ingredients to control diseases. The plant essential oil citral (CT) has significant biological activity against most pathogens but its poor stability limits its application in the field. To improve the applicability of plant essential oils, we aimed to construct a pH responsive essential oil delivery system (CT@ZIF-8) based on the zeolitic imidazolate framework-8 in this study. The high specific surface area of ZIF-8 enables CT@ZIF-8 remarkable loading capacity, and the metal-organic framework effectively delays the volatilization of CT. The results showed that CT@ZIF-8 was approximately 177 nm in size, had a stable nanostructure, and displayed a high pesticide loading efficiency (15.22%). The photodegradation rate of CT loaded in ZIF-8 under UV irradiation (48 h) was only 17.99%, much lower than that of CT alone (51.18%). The CT@ZIF-8 had a pH-responsive controlled release property, releasing CT from CT@ZIF-8 in a pH-dependent manner. The bioactivity results showed that CT@ZIF-8 had a lower EC50 than CT against three fungi (Magnaporthe oryzae, Botryosphaeria dothidea, and Fusarium oxysporum), enhancing the antifungal activity of CT. After 3 d of reagent treatment, only CT@ZIF-8 maintained good control against rice blast (75.76%) and soft rot (63.69%) infection. We have constructed a smart delivery system for essential oils, which provides a new pathway for the efficient application of plant-derived essential oils in the green control of plant diseases.

VmPacC-mediated pH regulation of Valsa mali confers to host acidification identified by comparative proteomics analysis

Apple valsa canker caused by the Ascomycete fungus Valsa mali is one of the most serious diseases of apple, resulting in huge economic losses in the apple-growing area of China. Previous study found that the pathogen could acidify the infected tissues to make lower ambient pH (from 6.0 to 3.5) for their successfully colonization. The pH signaling transcription factor VmPacC is required for acidification of its environment and for full virulence in V. mali. It is known that the functional cooperation of proteins secreted by V. mali plays pivotal role in its successful colonization of host plants. In this study, we used tandem mass tag (TMT) labeling coupled with LC-MS/MS-based quantitative proteomics to analyze the VmPacC-mediated pH regulation in V. mali, focusing on differentially expressed proteins (DEPs). We identified 222 DEPs specific to VmPacC deletion, and 921 DEPs specific to different pH conditions (pH 6.0 and 3.4). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that these DEPs were mainly involved in pathways associated with carbon metabolism, biosynthesis of antibiotics, citrate cycle (TCA cycle), glycolysis/gluconeogenesis, glutathione metabolism, ribosomes, and pentose phosphate pathways. Additionally, we identified 119 DEPs that were shared among the VmPacC deletion mutant and different pH conditions, which were mainly related to energy metabolism pathways, providing the energy required for the hyphal growth and responses to environmental stresses. A protein-protein interaction (PPI) network analysis indicated that most of the shared proteins were mapped to an interaction network with a medium confidence score of 0.4. Notably, one uncharacterized protein (KUI69106.1), and two known proteins (heat shock protein 60 (KUI73579.1), aspartate aminotransferase (KUI73864.1)) located in the core of the network were highly connected (with ≥ 38 directed edges) with the other shared DEPs. Our results suggest that VmPacC participates in the pathogen's regulation to ambient pH through the regulation of energy metabolism pathways such as the glycolysis/gluconeogenesis pathway and TCA cycle. Finally, we proposed a sophisticated molecular regulatory network to explain pH decrease in V. mali. Our study, by providing insights into V. mali regulating pH, helps to elucidate the mechanisms of host acidification during pathogen infection.

Complete genome analysis of pathogenic Metschnikowia bicuspidata strain MQ2101 isolated from diseased ridgetail white prawn, Exopalaemon carinicauda

BACKGROUND

Metschnikowia bicuspidata is a pathogenic yesst that can cause disease in many different economic aquatic animal species. In recent years, there was a new disease outbreak in ridgetail white prawn (Exopalaemon carinicauda) in coastal areas of Jiangsu Province China that was referred to as zombie disease by local farmers. The pathogen was first isolated and identified as M. bicuspidata. Although the pathogenicity and pathogenesis of this pathogen in other animals have been reported in some previous studies, research on its molecular mechanisms is still very limited. Therefore, a genome-wide study is necessary to better understand the physiological and pathogenic mechanisms of M. bicuspidata.

RESULT

In this study, we obtained a pathogenic strain, MQ2101, of M. bicuspidata from diseased E. carinicauda and sequenced its whole genome. The size of the whole genome was 15.98 Mb, and it was assembled into 5 scaffolds. The genome contained 3934 coding genes, among which 3899 genes with biological functions were annotated in multiple underlying databases. In KOG database, 2627 genes were annotated, which were categorized into 25 classes including general function prediction only, posttranslational modification, protein turnover, chaperones, and signal transduction mechanisms. In KEGG database, 2493 genes were annotated, which were categorized into five classes, including cellular processes, environmental information processing, genetic information processing, metabolism and organismal systems. In GO database, 2893 genes were annotated, which were mainly classified in cell, cell part, cellular processes and metabolic processes. There were 1055 genes annotated in the PHI database, accounting for 26.81% of the total genome, among which 5 genes were directly related to pathogenicity (identity ≥ 50%), including hsp90, PacC, and PHO84. There were also some genes related to the activity of the yeast itself that could be targeted by antiyeast drugs. Analysis based on the DFVF database showed that strain MQ2101 contained 235 potential virulence genes. BLAST searches in the CAZy database showed that strain MQ2101 may have a more complex carbohydrate metabolism system than other yeasts of the same family. In addition, two gene clusters and 168 putative secretory proteins were predicted in strain MQ2101, and functional analysis showed that some of the secretory proteins may be directly involved in the pathogenesis of the strain. Gene family analysis with five other yeasts revealed that strain MQ2101 has 245 unique gene families, including 274 genes involved in pathogenicity that could serve as potential targets.

CONCLUSION

Genome-wide analysis elucidated the pathogenicity-associated genes of M. bicuspidate while also revealing a complex metabolic mechanism and providing putative targets of action for the development of antiyeast drugs for this pathogen. The obtained whole-genome sequencing data provide an important theoretical basis for transcriptomic, proteomic and metabolic studies of M. bicuspidata and lay a foundation for defining its specific mechanism of host infestation.

Production of (10S,11S)-(—)-epi-Pyriculol and Its HPLC Quantification in Liquid Cultures of Pyricularia grisea, a Potential Mycoherbicide for the Control of Buffelgrass (Cenchrus ciliaris)

(10S,11S)-(—)-epi-pyriculol is a phytotoxic metabolite produced by Pyricularia grisea, a fungus identified as a foliar pathogen on the invasive weed species buffelgrass (Cenchrus ciliaris) in North America. The effective control of buffelgrass has not yet been achieved, and there is a need to develop effective and green solutions. Herbicides based on natural products and the use of phytopathogenic organisms could provide the most suitable tools for the control of weeds such as buffelgrass. Thus, one of the most relevant points to study about potential suitable phytotoxins such as (10S,11S)-(—)-epi-pyriculol is its production on a large scale, either by isolation from fungal fermentations or by synthesis. For these purposes, rapid and sensitive methods for the quantification of (10S,11S)-(—)-epi-pyriculol in complex mixtures are required. In this study, a high-pressure liquid chromatography (HPLC) method for its quantification was developed and applied to organic extracts from twelve P. grisea isolates obtained from diseased buffelgrass leaves and grown in potato dextrose broth (PDB) liquid cultures. The analysis proved that the production of (10S,11S)-(—)-epi-pyriculol is fungal-isolate dependent and strongly correlated with phytotoxic activity, shown by the P. grisea organic extracts in a buffelgrass radicle elongation test. The HPLC method reported herein allowed us to select the best strain for the production of (10S,11S)-(—)-epi-pyriculol and could be useful for selecting the best cultural conditions for its mass production, providing a tool for the use of this promising metabolite as a new bioherbicide for the control of buffelgrass.

URA3 as a Selectable Marker for Disruption and Functional Assessment of PacC Gene in the Entomopathogenic Fungus Isaria javanica

An effective selection marker is necessary for genetic engineering and functional genomics research in the post-genomic era. Isaria javanica is an important entomopathogenic fungus with a broad host range and prospective biocontrol potentials. Given that no antibiotic marker is available currently in this fungus, developing an effective selection marker is necessary. In this study, by applying overlap PCR and split-marker deletion strategy, combining PEG-mediated protoplasm transformation method, the uridine auxotrophy gene (ura3) in the I. javanica genome was knocked out. Then, using this transformation system, the pH response transcription factor gene (IjpacC) was disrupted successfully. Loss of IjpacC gene results in an obvious decrease in conidial production, but little impact on mycelial growth. The virulence of the ΔIjpacC mutant on caterpillars is similar to that of the wild-type strain. RT-qPCR detection shows that expression level of an acidic-expressed S53 gene (IF1G_06234) in ΔIjpacC mutant is more significantly upregulated than in the wild-type strain during the fungal infection on caterpillars. Our results indicate that a markerless transformation system based upon complementation of uridine auxotrophy is successfully developed in I. javanica, which is useful for exploring gene function and for genetic engineering to enhance biological control potential of the fungus.

FERONIA Receptor Kinase Integrates with Hormone Signaling to Regulate Plant Growth, Development, and Responses to Environmental Stimuli

Plant hormones are critical chemicals that participate in almost all aspects of plant life by triggering cellular response cascades. FERONIA is one of the most well studied members in the subfamily of Catharanthus roseus receptor-like kinase1-like (CrRLK1Ls) hormones. It has been proved to be involved in many different processes with the discovery of its ligands, interacting partners, and downstream signaling components. A growing body of evidence shows that FERONIA serves as a hub to integrate inter- and intracellular signals in response to internal and external cues. Here, we summarize the recent advances of FERONIA in regulating plant growth, development, and immunity through interactions with multiple plant hormone signaling pathways.

The pH signalling transcription factor PacC modulate growth, development, stress response and pathogenicity of Trichothecium roseum

pH is one of the important environmental factors that affect the growth, development and pathogenicity of postharvest pathogen. The transcription factor PacC dominates the pH signal pathway. PacC in Trichothecium roseum showed three typical conserved zinc finger domains and closest homology to Fusarium graminearum. T. roseum increased the environmental pH both in vitro and in vivo. Expression patterns of TrpacC under different pH showed that at increasing pH from 3 to 5, the wild-type (WT) strain induced the expression of TrPacC in parallel to increased fungal growth; however, TrPacC expression decline at higer pH than 5, while fungal growth continued to increase. Development of a ΔTrPacC mutant down-regulated the expression of TrbrlA, TrabaA and TrwetA, reduced sporulation and delayed spore germination, resulting in smaller spores and sparse hyphae. ΔTrPacC mutant was sensitive to ionic stress, oxidative stress and cell wall integrity stress compared to the WT strain, especially the ionic stress. In addition, ∆TrPacC mutant showed reduced pathogenicity to muskmelon and tomato fruits. Taken together, T. roseum is an alkalinizing fungus, and the acidic environment could induce TrPacC expression. TrPacC positively regulates fungal growth and development as well as pathogenicity showing effect on fungal response to different stresses.

Arrestin-Coding Genes Regulate Endocytosis, Sporulation, Pathogenicity, and Stress Resistance in Arthrobotrys oligospora

Arrestins are a family of scaffold proteins that play a crucial role in regulating numerous cellular processes, such as GPCR signaling. The Arthrobotrys oligospora arrestin family contains 12 members, which have highly conserved N-terminal and C-terminal domains. In the presence of ammonia, A. oligospora can change its lifestyle from saprotrophic to carnivorous. During this transition, the expression pattern of arrestin-coding (AoArc) genes was markedly upregulated. Therefore, we disrupted seven AoArc genes from A. oligospora to identify their functions. Although individual arrestin mutant strains display similar pathogenesis, phenotypes, and stress resistance, the fundamental data on the roles of AoArc genes in A. oligospora are obtained in this study. Membrane endocytosis in AoArc mutants was significantly reduced. Meanwhile, the capacity of trap device formation against nematodes and ammonia was impaired due to AoArc deletions. We also found that AoArc genes could regulate conidial phenotypes, cell nuclear distribution, pH response, and stress resistance. Results of qRT-PCR assays revealed that sporulation-regulated genes were affected after the deletion of AoArc genes. In particular, among the 12 arrestins, AoArc2 mediates pH signaling in the fungus A. oligospora. Notably, combined with the classical paradigm of arrestin–GPCR signal transduction, we suggest that arrestin-regulated trap formation in A. oligospora may be directly linked to the receptor endocytosis pathway.

ThpacC Acts as a Positive Regulator of Homodimericin A Biosynthesis and Antifungal Activities of Trichoderma harzianum 3.9236

The Pal/Rim pathway and its key transcription factor PacC play important roles in fungal adaptation to ambient pH regarding growth, secondary metabolism, and virulence. However, the effect of PacC on the secondary metabolism of the important biocontrol fungus Trichoderma harzianum remains elusive. To answer this question, ThpacC deletion (KO-ThpacC) and overexpression (OE-ThpacC) mutants of T. harzianum 3.9236 were constructed. Transcriptomic analysis of T. harzianum and KO-ThpacC suggested that ThpacC acted as both a positive and a negative regulator for secondary metabolite (SM) production. Further investigation revealed that deletion of ThpacC abolished homodimericin A and 8-epi-homodimericin A production. Moreover, ThpacC plays a role in the antagonism of T. harzianum against Sclerotinia sclerotiorum. 8-epi-Homodimericin A demonstrated moderate inhibitory activity against S. sclerotiorum. Our results contribute to a deeper understanding of the ThpacC function on SM production and the antifungal activity of T. harzianum.

Transcription factor control of virulence in phytopathogenic fungi

Plant-pathogenic fungi are a significant threat to economic and food security worldwide. Novel protection strategies are required and therefore it is critical we understand the mechanisms by which these pathogens cause disease. Virulence factors and pathogenicity genes have been identified, but in many cases their roles remain elusive. It is becoming increasingly clear that gene regulation is vital to enable plant infection and transcription factors play an essential role. Efforts to determine their regulatory functions in plant-pathogenic fungi have expanded since the annotation of fungal genomes revealed the ubiquity of transcription factors from a broad range of families. This review establishes the significance of transcription factors as regulatory elements in plant-pathogenic fungi and provides a systematic overview of those that have been functionally characterized. Detailed analysis is provided on regulators from well-characterized families controlling various aspects of fungal metabolism, development, stress tolerance, and the production of virulence factors such as effectors and secondary metabolites. This covers conserved transcription factors with either specialized or nonspecialized roles, as well as recently identified regulators targeting key virulence pathways. Fundamental knowledge of transcription factor regulation in plant-pathogenic fungi provides avenues to identify novel virulence factors and improve our understanding of the regulatory networks linked to pathogen evolution, while transcription factors can themselves be specifically targeted for disease control. Areas requiring further insight regarding the molecular mechanisms and/or specific classes of transcription factors are identified, and direction for future investigation is presented.

Current progress on pathogenicity-related transcription factors in Fusarium oxysporum

Fusarium oxysporum is a well-known soilborne plant pathogen that causes severe vascular wilt in economically important crops worldwide. During the infection process, F. oxysporum not only secretes various virulence factors, such as cell wall-degrading enzymes (CWDEs), effectors, and mycotoxins, that potentially play important roles in fungal pathogenicity but it must also respond to extrinsic abiotic stresses from the environment and the host. Over 700 transcription factors (TFs) have been predicted in the genome of F. oxysporum, but only 26 TFs have been functionally characterized in various formae speciales of F. oxysporum. Among these TFs, a total of 23 belonging to 10 families are required for pathogenesis through various mechanisms and pathways, and the zinc finger TF family is the largest family among these 10 families, which consists of 15 TFs that have been functionally characterized in F. oxysporum. In this review, we report current research progress on the 26 functionally analysed TFs in F. oxysporum and sort them into four groups based on their roles in F. oxysporum pathogenicity. Furthermore, we summarize and compare the biofunctions, involved pathways, putative targets, and homologs of these TFs and analyse the relationships among them. This review provides a systematic analysis of the regulation of virulence-related genes and facilitates further mechanistic analysis of TFs important in F. oxysporum virulence.

Role of RIM101 for Sporulation at Alkaline pH in Ashbya gossypii

Microorganisms need to sense and adapt to fluctuations in the environmental pH. In fungal species, this response is mediated by the conserved pacC/RIM101 pathway. In Aspergillus nidulans, PacC activates alkaline-expressed genes and represses acid-controlled genes in response to alkaline pH and has important functions in regulating growth and conidia formation. In Saccharomyces cerevisiae, the PacC homolog Rim101 is required for adaptation to extracellular pH and to regulate transcription of IME1, the Initiator of MEiosis. S. cerevisiae rim101 mutants are defective in sporulation. In Ashbya gossypii, a filamentous fungus belonging to the family of Saccharomycetaceae, little is known about the role of pH in regulating growth and sporulation. Here, we deleted the AgRIM101 homolog (AFR190C). Our analyses show that Rim101 is important for growth and essential for sporulation at alkaline pH in A. gossypii. Acidic liquid sporulation media were alkalinized by sporulating strains, while the high pH of alkaline media (starting pH = 8.6) was reduced to a pH ~ 7.5 by these strains. However, Agrim101 mutants were unable to sporulate in alkaline media and failed to reduce the initial high pH, while they were capable of sporulation in acidic liquid media in which they increased the pH like the wild type.

Function of pH-dependent transcription factor PacC in regulating development, pathogenicity, and mycotoxin biosynthesis of phytopathogenic fungi

pH, as one of the most important environmental factors, affects various biological processes in pathogenic fungi. Sensing and responding to fluctuations in ambient pH are essential for these fungi to complete their life cycle. Fungi have evolved a complicated and conserved system, the so-called Pal-pH pathway, to regulate genes and adapt to alterations in ambient pH. PacC is the dominant transcription factor in the Pal-pH pathway and regulates various biological processes. The regulatory mode of PacC has been extensively studied in Aspergillus nidulans and is generally conserved in other fungal species, including numerous phytopathogenic fungi. However, species-specific alterations have been reported. This review summarizes recent advances in the regulatory mechanisms of PacC and its role in controlling development, pathogenicity, and mycotoxin biosynthesis in phytopathogenic fungi. Potential applications of these findings and some unresolved questions are also discussed.

The PAC-3 transcription factor critically regulates phenotype-associated genes in Neurospora crassa

Transcription factors play an important role in fungal environmental adaptive process by promoting adjustment to challenging stimuli via gene modulation and activation of signaling networks. The transcription factor encoded by the pac-3/rim101/pacC gene is involved in pH regulation and is associated with a wide variety of cellular functions. The deletion of pac-3 affects fungal development. In Neurospora crassa, the Δpac-3 strain presents diminished aerial growth and reduced conidiation. However, the PAC-3-regulated genes associated with this altered phenotype have not been elucidated. In this study, we used RNA-seq to analyze the phenotypic plasticity induced after pac-3 deletion in the filamentous fungus N. crassa cultivated in media supplemented with sufficient or limited inorganic phosphate. Genes related to morphology, hyphal development, and conidiation were of particular interest in this study. Our results suggest a pac-3 dependency in gene regulation in a Pi-dependent manner. Furthermore, our analysis suggested that the fungus attempts to overcome the deletion effects in a Δpac-3 mutant through a complex combined regulatory mechanism. Finally, the modulatory responses observed in the Δpac-3 strain, a double mutant generated based on the Δmus-52 mutant strain, is strain-specific, highlighting that the phenotypic impact may be attributed to pac-3 absence despite the combined mus-52 deletion.

Mutations of two FERONIA-like receptor genes enhance rice blast resistance without growth penalty

Genes that provide resistance to fungi and/or bacteria usually reduce plant growth and ultimately affect grain yield. Thus, crop breeding programs need to find genetic resources that balance disease resistance with growth. The receptor kinase FERONIA regulates cell growth and survival in Arabidopsis. Here, we investigate, in rice, the role of members of the FERONIA-like receptor (FLR) gene family in the balance between growth and the response to the fungal pathogen Magnaporthe oryzae (Pyricularia oryzae), which causes the most devastating disease in rice. We carried out genome-wide gene expression and functional screenings in rice via a gene knockout strategy, and we successfully knocked out 14 FLR genes in rice. Using these genetic resources, we found that mutations in the FLR2 and FLR11 genes provide resistance to rice blast without a profound growth penalty. Detailed analyses revealed that FLR2 mutation increased both defense-related gene expression and M. oryzae-triggered production of reactive oxygen species. Thus, our results highlight novel genetic tools for studying the underlying molecular mechanisms of enhancing disease resistance without growth penalty.

Influence of PacC on the environmental stress adaptability and cell wall components of Ganoderma lucidum

The transcription factor PacC/Rim101 participates in environmental pH adaptation, development and secondary metabolism in many fungi, but whether PacC/Rim101 contributes to fungal adaptation to environmental stress remains unclear. In our previous study, a homologous gene of PacC/Rim101 was identified, and PacC-silenced strains of the agaricomycete Ganoderma lucidum were constructed. In this study, we further investigated the functions of PacC in G. lucidum and found that PacC-silenced strains were hypersensitive to environmental stresses, such as osmotic stress, oxidative stress and cell wall stress, compared with wild-type (WT) and empty-vector control (CK) strains. In addition, transmission electron microscopy images of the cell wall structure showed that the cell walls of the PacC-silenced strains were thinner (by approximately 25-30%) than those of the WT and CK strains. Further analysis of cell wall composition showed that the β-1,3-glucan content in the PacC-silenced strains was only approximately 78-80% of that in the WT strain, and the changes in β-1,3-glucan content were consistent with downregulation of glucan synthase gene expression. The ability of PacC to bind to the promoters of glucan synthase-encoding genes confirms that PacC transcriptionally regulates these genes.

Genome sequence of Isaria javanica and comparative genome analysis insights into family S53 peptidase evolution in fungal entomopathogens

The fungus Isaria javanica is an important entomopathogen that parasitizes various insects and is effective for pest control. In this study, we sequenced and assembled the genomes (IJ1G and IJ2G) of two I. javanica strains isolated from different insects. The genomes were approximately 35 Mb in size with 11,441 and 11,143 protein-coding genes, respectively. Using a phylogenomic approach, we evaluated genome evolution across five entomopathogenic fungi in Cordycipitaceae. By comparative genome analysis, it was found that family S53 serine peptidases were expanded in Cordycipitaceae entomopathogens, particularly in I. javanica. Gene duplication events were identified based on phylogenetic relationships inferred from 82 S53 peptidases within six entomopathogenic fungal genomes. Moreover, we found that carbohydrate-active enzymes and proteinases were the largest secretory protein groups encoded in the I. javanica genome, especially chitinases (GH18), serine and aspartic peptidases (S53, S08, S10, A01). Pathogenesis-related genes and genes for bacterial-like toxins and secondary metabolites were also identified. By comparative transcriptome analysis, differentially expressed genes in response to insect nutrients (in vitro) were identified. Moreover, most S53 peptidases were detected to be significantly upregulated during the initial fungal infection process in insects (in vivo) by RT-qPCR. Our results provide new clues about understanding evolution of pathogenic proteases and may suggest that abundant S53 peptidases in the I. javanica genome may contribute to its effective parasitism on various insects.

Effects of exogenous salicylic acid and pH on pathogenicity of biotrophy-associated secreted protein 1 (BAS1)-overexpressing strain, Magnaporthe oryzae

Abiotic stress can influence the interactions between a pathogen and its host. In this paper, we analyzed the effects of salicylic acid (SA) and pH on the morphological development and pathogenicity of Magnaporthe oryzae, the pathogen that causes rice (Oryza sativa) blast. A strain of rice blast that overexpresses biotrophy-associated secreted protein 1 (BAS1) and a wild-type (WT) strain were pretreated with different levels of pH and different concentrations of SA to analyze M. oryzae colony growth, sporulation, spore germination, dry weight of hypha, and appressorium formation. Disease incidence and the expression of defense-related genes in infected rice were analyzed after pretreatment with pH 5.00 or pH 8.00 and 200 μM SA. The results showed that both SA and pH had some influence on morphological development, including sporulation and appressorium formation of the BAS1-overexpression strain. In the 200 μM SA pretreatment, there was a lower incidence of disease and higher expression levels of the rice defense-related genes PR1a, PAL, HSP90, and PR5 on leaves inoculated with the BAS1-overexpession strain compared with the WT strain, whereas, LOX2 appeared to be downregulated in the BAS1-overexpession strain compared with the WT. In both pH treatments, disease incidence and expression of HSP90 were higher and the expression of PR1a and PR10a and LOX2 and PAL was lower in leaves inoculated with the BAS1-overexpression strain compared with leaves inoculated with the WT strain. We conclude that SA and pH affect morphological development of the BAS1-overexpression blast strain, but that these factors have little influence on the pathogenicity of the strain, indicating that BAS1-overexpression may have enhanced the tolerance of this rice blast strain to abiotic stressors. This work suggests new molecular mechanisms that exogenous SA and pH affect the interactions between M. oryzae and rice.

Effects of exogenous salicylic acid and pH on pathogenicity of biotrophy-associated secreted protein 1 (BAS1)-overexpressing strain, Magnaporthe oryzae

Abiotic stress can influence the interactions between a pathogen and its host. In this paper, we analyzed the effects of salicylic acid (SA) and pH on the morphological development and pathogenicity of Magnaporthe oryzae, the pathogen that causes rice (Oryza sativa) blast. A strain of rice blast that overexpresses biotrophy-associated secreted protein 1 (BAS1) and a wild-type (WT) strain were pretreated with different levels of pH and different concentrations of SA to analyze M. oryzae colony growth, sporulation, spore germination, dry weight of hypha, and appressorium formation. Disease incidence and the expression of defense-related genes in infected rice were analyzed after pretreatment with pH 5.00 or pH 8.00 and 200 μM SA. The results showed that both SA and pH had some influence on morphological development, including sporulation and appressorium formation of the BAS1-overexpression strain. In the 200 μM SA pretreatment, there was a lower incidence of disease and higher expression levels of the rice defense-related genes PR1a, PAL, HSP90, and PR5 on leaves inoculated with the BAS1-overexpession strain compared with the WT strain, whereas, LOX2 appeared to be downregulated in the BAS1-overexpession strain compared with the WT. In both pH treatments, disease incidence and expression of HSP90 were higher and the expression of PR1a and PR10a and LOX2 and PAL was lower in leaves inoculated with the BAS1-overexpression strain compared with leaves inoculated with the WT strain. We conclude that SA and pH affect morphological development of the BAS1-overexpression blast strain, but that these factors have little influence on the pathogenicity of the strain, indicating that BAS1-overexpression may have enhanced the tolerance of this rice blast strain to abiotic stressors. This work suggests new molecular mechanisms that exogenous SA and pH affect the interactions between M. oryzae and rice.

A method to measure redox potential (Eh) and pH in agar media and plants shows that fungal growth is affected by and affects pH and Eh

The specificities of the plant environment and its effects on fungal growth are not yet fully explored. Both pH and Eh play a key role during this interaction, but are often studied independently or at different scales. We aimed at investigating whether the methods developed for the joint characterization of the pH and Eh in soil could be transposed to fungi. On artificial media, the growth of all 16 species tested significantly altered either Eh, pH or both. Measuring Eh reveals that even the species not modifying pH can have an impact on the surrounding environment. Reciprocally, fungi responded to pH and Eh parameters, both quantitatively with a decrease in colony diameter and qualitatively with colony aspect repeatedly and thoroughly modified. In infected oilseed rape plant stems, pH and Eh were significantly altered. The observed alcalinisation or acidification correlates with canker length. The joint characterization of both parameters will allow understanding the impact of fungi on their environment, and conversely of the environment on fungal growth. The availability of methods for measurement opens the prospect to study combinations of stresses, and get an understanding of the involvement of pH and Eh modifications in these interactions.

The pH regulator PacC: a host-dependent virulence factor in Botrytis cinerea

The phytopathogenic fungus Botrytis cinerea is able to infect a wide variety of plants and plant tissues with differing chemical compositions. During its interaction with the host, this pathogen modulates its ambient pH by secreting acids or ammonia. In this work, we examined the Pal/Pac pathway, the fungal ambient pH-responsive signalling circuit, and investigated the role of the PacC transcription factor. Characterization of the BcpacC deletion mutant revealed an alteration of both fungal growth and virulence depending on the pH of the culture medium or of the host tissue. The pathogenicity of the mutant was altered on plants exhibiting a neutral pH and not on plants with acidic tissues. The capacity of the mutant to acidify its environment and, more particularly, to produce oxalic acid was affected, as was production of reactive oxygen species. Finally, proteomic profiling of the mutant secretome revealed significant changes in plant cell wall polysaccharides proteins and lipid degradation and oxidoreduction, highlighting the importance of BcPacC in the necrotrophic lifestyle of B. cinerea.

Leaf Eh and pH: A Novel Indicator of Plant Stress. Spatial, Temporal and Genotypic Variability in Rice (Oryza sativa L.)

A wealth of knowledge has been published in the last decade on redox regulations in plants. However, these works remained largely at cellular and organelle levels. Simple indicators of oxidative stress at the plant level are still missing. We developed a method for direct measurement of leaf Eh and pH, which revealed spatial, temporal, and genotypic variations in rice. Eh (redox potential) and Eh@pH7 (redox potential corrected to pH 7) of the last fully expanded leaf decreased after sunrise. Leaf Eh was high in the youngest leaf and in the oldest leaves, and minimum for the last fully expanded leaf. Leaf pH decreased from youngest to oldest leaves. The same gradients in Eh-pH were measured for various varieties, hydric conditions, and cropping seasons. Rice varieties differed in Eh, pH, and/or Eh@pH7. Leaf Eh increases and leaf pH decreases with plant age. These patterns and dynamics in leaf Eh-pH are in accordance with the pattern and dynamics of disease infections. Leaf Eh-pH can bring new insight on redox processes at plant level and is proposed as a novel indicator of plant stress/health. It could be used by agronomists, breeders, and pathologists to accelerate the development of crop cultivation methods leading to agroecological crop protection.

VmPacC Is Required for Acidification and Virulence in Valsa mali

The role of the transcription factor PacC has been characterised in several pathogenic fungi, and it affects virulence via several mechanisms. In this study, we examined the role of the PacC homolog VmPacC in Valsa mali, the causal agent of apple canker disease. We found that the expression of VmPacC was up-regulated in neutral and alkaline pH and during infection. At pH 6–10, the radial growth of a VmPacC deletion mutant decreased compared to wild-type. In addition, the sensitivity to oxidative stress of the VmPacC deletion mutant was impaired, as its growth was more severely inhibited by H₂O₂ than that of the wild-type. The lesion size caused by the VmPacC deletion mutant was smaller than that of the wild-type on apple leaves and twigs. Interestingly, expression of pectinase genes increased in deletion mutant during infection. To further confirm the negative regulation, we generated dominant activated C-27 allele mutants that constitutively express VmPacC. The pectinase activity of activated mutants was reduced at pH 4. We further observed that V. mali can acidify the pH during infection, and that the capacity for acidification was impaired after VmPacC deletion. Furthermore, VmPacC is involved in the generation of citric acid, which affects virulence. These results indicate that VmPacC is part of the fungal responses to neutral and alkaline pH and oxidative stress. More importantly, VmPacC is required for acidification of its environment and for full virulence in V. mali.

Ammonia determines transcriptional profile of microorganisms in anaerobic digestion

Anaerobic digestion is important for the management of livestock manure with high ammonia level. Although ammonia effects on anaerobic digestion have been comprehensively studied, the molecular mechanism underlying ammonia inhibition still remains elusive. In this study, based on metatranscriptomic analysis, the transcriptional profile of microbial community in anaerobic digestion under low (1500 mg L⁻¹) and high NH₄⁺ (5000 mg L⁻¹) concentrations, respectively, were revealed. The results showed that high NH₄⁺ concentrations significantly inhibited methane production but facilitated the accumulations of volatile fatty acids. The expression of methanogenic pathway was significantly inhibited by high NH₄⁺ concentration but most of the other pathways were not significantly affected. Furthermore, the expressions of methanogenic genes which encode acetyl-CoA decarbonylase and methyl-coenzyme M reductase were significantly inhibited by high NH₄⁺ concentration. The inhibition of the co-expressions of the genes which encode acetyl-CoA decarbonylase was observed. Some genes involved in the pathways of aminoacyl-tRNA biosynthesis and ribosome were highly expressed under high NH₄⁺ concentration. Consequently, the ammonia inhibition on anaerobic digestion mainly focused on methanogenic process by suppressing the expressions of genes which encode acetyl-CoA decarbonylase and methyl-coenzyme M reductase. This study improved the accuracy and depth of understanding ammonia inhibition on anaerobic digestion.

A Deubiquitinating Enzyme Ubp14 Is Required for Development, Stress Response, Nutrient Utilization, and Pathogenesis of Magnaporthe oryzae

Ubiquitination is an essential protein modification in eukaryotic cells, which is reversible. Deubiquitinating enzymes (DUBs) catalyze deubiquitination process to reverse ubiquitination, maintain ubiquitin homeostasis or promote protein degradation by recycling ubiquitins. In order to investigate effects of deubiquitination process in plant pathogenic fungus Magnaporthe oryzae, we generated deletion mutants of MoUBP14. Ortholog of MoUbp14 was reported to play general roles in ubiquitin-mediated protein degradation in Saccharomyces cerevisiae. The ΔMoubp14 mutant lost its pathogenicity and was severely reduced in mycelial growth, sporulation, carbon source utilization, and increased in sensitivity to distinct stresses. The mutant was blocked in penetration, which could due to defect in turgor generation. It is also blocked in invasive growth, which could due to reduction in stress tolerance and nutrient utilization. Deletion of UBP14 also led to accumulation of free polyubiquitin chains. Pulldown assay identified some proteins related to carbohydrate metabolism and stress response may putatively interact with MoUbp14, including two key rate-limiting enzymes of gluconeogenesis, MoFbp1 and MoPck1. These two proteins were degraded when the glucose was supplied to M. oryzae grown in low glucose media for a short period of time (∼12 h), and this process required MoUbp14. In summary, pleiotropic phenotypes of the deletion mutants indicated that MoUbp14 is required for different developments and pathogenicity of M. oryzae.

Adaptation to the Host Environment by Plant-Pathogenic Fungi

Many fungi can live both saprophytically and as endophyte or pathogen inside a living plant. In both environments, complex organic polymers are used as sources of nutrients. Propagation inside a living host also requires the ability to respond to immune responses of the host. We review current knowledge of how plant-pathogenic fungi do this. First, we look at how fungi change their global gene expression upon recognition of the host environment, leading to secretion of effectors, enzymes, and secondary metabolites; changes in metabolism; and defense against toxic compounds. Second, we look at what is known about the various cues that enable fungi to sense the presence of living plant cells. Finally, we review literature on transcription factors that participate in gene expression in planta or are suspected to be involved in that process because they are required for the ability to cause disease.

Stress Adaptation

Fungal species display an extraordinarily diverse range of lifestyles. Nevertheless, the survival of each species depends on its ability to sense and respond to changes in its natural environment. Environmental changes such as fluctuations in temperature, water balance or pH, or exposure to chemical insults such as reactive oxygen and nitrogen species exert stresses that perturb cellular homeostasis and cause molecular damage to the fungal cell. Consequently, fungi have evolved mechanisms to repair this damage, detoxify chemical insults, and restore cellular homeostasis. Most stresses are fundamental in nature, and consequently, there has been significant evolutionary conservation in the nature of the resultant responses across the fungal kingdom and beyond. For example, heat shock generally induces the synthesis of chaperones that promote protein refolding, antioxidants are generally synthesized in response to an oxidative stress, and osmolyte levels are generally increased following a hyperosmotic shock. In this article we summarize the current understanding of these and other stress responses as well as the signaling pathways that regulate them in the fungi. Model yeasts such as Saccharomyces cerevisiae are compared with filamentous fungi, as well as with pathogens of plants and humans. We also discuss current challenges associated with defining the dynamics of stress responses and with the elaboration of fungal stress adaptation under conditions that reflect natural environments in which fungal cells may be exposed to different types of stresses, either sequentially or simultaneously.

The Nep1-like protein family of Magnaporthe oryzae is dispensable for the infection of rice plants

The necrosis- and ethylene-inducing protein 1 (Nep1)-like proteins (NLPs) are a class of microbe-associated molecular patterns widely distributed across diverse groups of plant-associated microorganisms. In spite of the cytotoxic activity in dicot plants, the role of most NLPs in the virulence of plant pathogens is still largely unknown. We showed that the MoNLP family of rice blast fungus varied very little in amino acid sequence, transient expression of three MoNLPs induced cell death and the production of reactive oxygen species in Nicotiana benthamiana, and the expression of MoNLPs was induced during infection of susceptible rice plants. To further investigate the biological role of the MoNLP family, a marker-free gene replacement vector was developed and used to knock out the whole family in Magnaporthe oryzae. Results showed no significant difference in disease levels caused by wild type and the quadruple ΔMoNLP mutant strains. Likewise, the sporulation and radial growth of the two strains were similar under various unfavorable cultural conditions including malnutrition and abiotic stresses. These observations demonstrated that the MoNLP family is dispensable for the fungal tolerance to the tested adverse cultural conditions, and more importantly, for the virulence of blast fungus on susceptible rice plants.

Membrane lipids and soluble sugars dynamics of the alkaliphilic fungus Sodiomyces tronii in response to ambient pH

Alkaliphily, the ability of an organism to thrive optimally at high ambient pH, has been well-documented in several lineages: archaea, bacteria and fungi. The molecular mechanics of such adaptation has been extensively addressed in alkaliphilic bacteria and alkalitolerant fungi. In this study, we consider an additional property that may have enabled fungi to prosper at alkaline pH: altered contents of membrane lipids and cytoprotectant molecules. In the alkaliphilic Sodiomyces tronii, we showed that at its optimal growth pH 9.2, the fungus accumulates abundant cytosolic trehalose (4-10% dry weight) and phosphatidic acids in the membrane lipids, properties not normally observed in neutrophilic species. At a very high pH 10.2, the major carbohydrate, glucose, was rapidly substituted by mannitol and arabitol. Conversely, lowering the pH to 5.4-7.0 had major implications both on the content of carbohydrates and membrane lipids. It was shown that trehalose dominated at pH 5.4. Fractions of sphingolipids and sterols of plasma membranes rapidly elevated possibly indicating the formation of membrane structures called rafts. Overall, our results reveals complex dynamics of the contents of membrane lipids and cytoplasmic sugars in alkaliphilic S. tronii, suggesting their adaptive functionality against pH stress.

Regulators of plant biomass degradation in ascomycetous fungi

Fungi play a major role in the global carbon cycle because of their ability to utilize plant biomass (polysaccharides, proteins, and lignin) as carbon source. Due to the complexity and heterogenic composition of plant biomass, fungi need to produce a broad range of degrading enzymes, matching the composition of (part of) the prevalent substrate. This process is dependent on a network of regulators that not only control the extracellular enzymes that degrade the biomass, but also the metabolic pathways needed to metabolize the resulting monomers. This review will summarize the current knowledge on regulation of plant biomass utilization in fungi and compare the differences between fungal species, focusing in particular on the presence or absence of the regulators involved in this process.

Autophagy-associated alpha-arrestin signaling is required for conidiogenous cell development in Magnaporthe oryzae

Conidiation patterning is evolutionarily complex and mechanism concerning conidiogenous cell differentiation remains largely unknown. Magnaporthe oryzae conidiates in a sympodial way and uses its conidia to infect host and disseminate blast disease. Arrestins are multifunctional proteins that modulate receptor down-regulation and scaffold components of intracellular trafficking routes. We here report an alpha-arrestin that regulates patterns of conidiation and contributes to pathogenicity in M. oryzae. We show that disruption of ARRDC1 generates mutants which produce conidia in an acropetal array and ARRDC1 significantly affects expression profile of CCA1, a virulence-related transcription factor required for conidiogenous cell differentiation. Although germ tubes normally develop appressoria, penetration peg formation is dramatically impaired and Δarrdc1 mutants are mostly nonpathogenic. Fluorescent analysis indicates that EGFP-ARRDC1 puncta are well colocalized with DsRed2-Atg8, and this distribution profile could not be altered in Δatg9 mutants, suggesting ARRDC1 enters into autophagic flux before autophagosome maturation. We propose that M. oryzae employs ARRDC1 to regulate specific receptors in response to conidiation-related signals for conidiogenous cell differentiation and utilize autophagosomes for desensitization of conidiogenous receptor, which transmits extracellular signal to the downstream elements of transcription factors. Our investigation extends novel significance of autophagy-associated alpha-arrestin signaling to fungal parasites.

Characterization of 47 Cys2 -His2 zinc finger proteins required for the development and pathogenicity of the rice blast fungus Magnaporthe oryzae

The Cys2 -His2 (C2H2) zinc finger protein family is the second-largest family of transcription factors (TFs) in Magnaporthe oryzae, the causal fungus responsible for the destructive rice blast disease. However, little is known about the roles of most C2H2 TFs in the development and pathogenicity of M. oryzae. The roles of 47 C2H2 genes in development and pathogenicity were investigated by gene deletion in M. oryzae. The TF-dependent genes in mycelia or appressoria were analyzed with RNA sequencing and quantitative PCR (qPCR). Forty-four C2H2 genes are involved in growth (20 genes), conidiation (28 genes), appressorium formation (four genes) and pathogenicity (22 genes) in M. oryzae. Of these, MGG_14931, named as VRF1, is required for pathogenicity, specifically controlling appressorium maturation by affecting the expression of genes related to appressorial structure and function, including melanin biosynthesis, chitin catabolism, lipid metabolism, proteolysis, transmembrane transport, and response to oxidative stress; MGG_01776, named as VRF2, is required for plant penetration and invasive growth; conidiation-related gene CON7 is required for conidial differentiation; and MoCREA, encoding a carbon catabolite repression protein, is a novel repressor of lipid catabolism when glucose obtainable in M. oryzae. This study provides many insights into the regulation of growth, asexual development, appressorium formation, and pathogenicity by C2H2 TFs in M. oryzae.

CmpacC regulates mycoparasitism, oxalate degradation and antifungal activity in the mycoparasitic fungus Coniothyrium minitans

The PacC/Rim101 pH-responsive transcription factor is an important pathogenicity element for many plant-pathogenic fungi. In this study, we investigated the roles of a PacC homologue, CmpacC, in the mycoparasitic fungus Coniothyrium minitans. CmpacC was confirmed to have the transcriptional activation activity by the transcriptional activation test in Saccharomyces cerevisiae. Disruption of CmpacC resulted in impaired fungal responses to ambient pH. Compared to the wild-type, the CmpacC-disruption mutant ΔCmpacC-29 was significantly suppressed for activities of chitinase and β-1,3-glucanase at pH 5 and 7, consistent with reduced expression levels of Cmch1 and Cmg1 coding for the two enzymes respectively. However, the mutant displayed acidity-mimicking phenotypes such as improved oxalate degradation and increased antifungal activity at pH 6 or higher. Improved efficacy in oxalate degradation by ΔCmpacC-29 was consistent with the enhanced expression level of Cmoxdc1 coding for oxalate decarboxylase. CmpacC transcriptional activation of Cmch1 and Cmg1 and repression of Cmoxdc1 were verified by the presence of the PacC/Rim101 consensus binding-motifs in gene promoter regions and by the promoter DNA-binding assays. This study suggests that CmpacC plays an activator role in regulation of C. minitans mycoparasitism, whereas plays a repressor role in regulation of oxalate degradation and possibly antifungal activity of C. minitans.

Refining the pH response in Aspergillus nidulans: a modulatory triad involving PacX, a novel zinc binuclear cluster protein

The Aspergillus nidulans PacC transcription factor mediates gene regulation in response to alkaline ambient pH which, signalled by the Pal pathway, results in the processing of PacC⁷² to PacC²⁷ via PacC⁵³. Here we investigate two levels at which the pH regulatory system is transcriptionally moderated by pH and identify and characterise a new component of the pH regulatory machinery, PacX. Transcript level analysis and overexpression studies demonstrate that repression of acid‐expressed palF, specifying the Pal pathway arrestin, probably by PacC²⁷ and/or PacC⁵³, prevents an escalating alkaline pH response. Transcript analyses using a reporter and constitutively expressed pacC  trans‐alleles show that pacC preferential alkaline‐expression results from derepression by depletion of the acid‐prevalent PacC⁷² form. We additionally show that pacC repression requires PacX. pacX mutations suppress PacC processing recalcitrant mutations, in part, through derepressed PacC levels resulting in traces of PacC²⁷ formed by pH‐independent proteolysis. pacX was cloned by impala transposon mutagenesis. PacX, with homologues within the Leotiomyceta, has an unusual structure with an amino‐terminal coiled‐coil and a carboxy‐terminal zinc binuclear cluster. pacX mutations indicate the importance of these regions. One mutation, an unprecedented finding in A. nidulans genetics, resulted from an insertion of an endogenous Fot1‐like transposon.

Coordinate responses to alkaline pH stress in budding yeast

Alkalinization of the medium represents a stress condition for the budding yeast Saccharomyces cerevisiae to which this organism responds with profound remodeling of gene expression. This is the result of the modulation of a substantial number of signaling pathways whose participation in the alkaline response has been elucidated within the last ten years. These regulatory inputs involve not only the conserved Rim101/PacC pathway, but also the calcium-activated phosphatase calcineurin, the Wsc1-Pkc1-Slt2 MAP kinase, the Snf1 and PKA kinases and oxidative stress-response pathways. The uptake of many nutrients is perturbed by alkalinization of the environment and, consequently, an impact on phosphate, iron/copper and glucose homeostatic mechanisms can also be observed. The analysis of available data highlights cases in which diverse signaling pathways are integrated in the gene promoter to shape the appropriate response pattern. Thus, the expression of different genes sharing the same signaling network can be coordinated, allowing functional coupling of their gene products.

The effects of extracellular pH and of the transcriptional regulator PACI on the transcriptome of Trichoderma reesei

Background

Extracellular pH is one of the several environmental factors affecting protein production by filamentous fungi. Regulatory mechanisms ensure that extracellular enzymes are produced under pH-conditions in which the enzymes are active. In filamentous fungi, the transcriptional regulation in different ambient pH has been studied especially in Aspergilli, whereas the effects of pH in the industrial producer of hydrolytic enzymes, Trichoderma reesei, have mainly been studied at the protein level. In this study, the pH-dependent expression of T. reesei genes was investigated by genome-wide transcriptional profiling and by analysing the effects of deletion of the gene encoding the transcriptional regulator pac1, the orthologue of Aspergillus nidulans pacC gene.

Results

Transcriptional analysis revealed the pH-responsive genes of T. reesei, and functional classification of the genes identified the activities most affected by changing pH. A large number of genes encoding especially transporters, signalling-related proteins, extracellular enzymes and proteins involved in different metabolism-related functions were found to be pH-responsive. Several cellulase- and hemicellulase-encoding genes were found among the pH-responsive genes. Especially, genes encoding hemicellulases with the similar type of activity were shown to include both genes up-regulated at low pH and genes up-regulated at high pH. However, relatively few of the cellulase- and hemicellulase-encoding genes showed direct PACI-mediated regulation, indicating the importance of other regulatory mechanisms affecting expression in different pH conditions. New information was gained on the effects of pH on the genes involved in ambient pH-signalling and on the known and candidate regulatory genes involved in regulation of cellulase and hemicellulase encoding genes. In addition, co-regulated genomic clusters responding to change of ambient pH were identified.

Conclusions

Ambient pH was shown to be an important determinant of T. reesei gene expression. The pH-responsive genes, including those affected by the regulator of ambient pH sensing, were identified, and novel information on the activity of genes encoding carbohydrate active enzymes at different pH was gained.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-015-0247-z) contains supplementary material, which is available to authorized users.

The Cryptococcus neoformans alkaline response pathway: identification of a novel rim pathway activator

The Rim101/PacC transcription factor acts in a fungal-specific signaling pathway responsible for sensing extracellular pH signals. First characterized in ascomycete fungi such as Aspergillus nidulans and Saccharomyces cerevisiae, the Rim/Pal pathway maintains conserved features among very distantly related fungi, where it coordinates cellular adaptation to alkaline pH signals and micronutrient deprivation. However, it also directs species-specific functions in fungal pathogens such as Cryptococcus neoformans, where it controls surface capsule expression. Moreover, disruption of the Rim pathway central transcription factor, Rim101, results in a strain that causes a hyper-inflammatory response in animal infection models. Using targeted gene deletions, we demonstrate that several genes encoding components of the classical Rim/Pal pathway are present in the C. neoformans genome. Many of these genes are in fact required for Rim101 activation, including members of the ESCRT complex (Vps23 and Snf7), ESCRT-interacting proteins (Rim20 and Rim23), and the predicted Rim13 protease. We demonstrate that in neutral/alkaline pH, Rim23 is recruited to punctate regions on the plasma membrane. This change in Rim23 localization requires upstream ESCRT complex components but does not require other Rim101 proteolysis components, such as Rim20 or Rim13. Using a forward genetics screen, we identified the RRA1 gene encoding a novel membrane protein that is also required for Rim101 protein activation and, like the ESCRT complex, is functionally upstream of Rim23-membrane localization. Homologs of RRA1 are present in other Cryptococcus species as well as other basidiomycetes, but closely related genes are not present in ascomycetes. These findings suggest that major branches of the fungal Kingdom developed different mechanisms to sense and respond to very elemental extracellular signals such as changing pH levels.