Characterization of two homeodomain transcription factors with critical but distinct roles in virulence in the vascular pathogen Verticillium dahliae

Metabolic and physiological functions of Patatin-like phospholipase-A in plants

Patatin-like phospholipase-A (pPLA) is a class of lipid acyl hydrolase enzymes found in both, the animal and plant kingdoms. Plant pPLAs are related to the potato tuber storage protein patatin in solanaceous plants. Despite extensive investigation of pPLA functions in the animal system, the mechanistic functional details and regulatory roles of pPLA are poorly understood in plants. In recent years, research pertaining to pPLAs has gain some momentum as some of the key members of pPLA family have been characterized functionally. These findings have provided key insights into the structural features, biochemical activities, and functional roles of plant pPLAs. In this review, we are presenting a holistic overview of pPLAs in plants and providing the latest updates on pPLA research. We have highlighted the genomic diversity and structural features of pPLAs in plants. Importantly, we have discussed the role of pPLAs in lipid metabolism, including sphingolipid metabolism, lignin and cellulose accumulation, lipid breakdown and seed oil content enhancement. Moreover, regulatory roles of pPLAs in physiological processes, such as plant stress response, plant-pathogen interactions and plant development have been discussed. This information will be critical in the biotechnological programs for crop improvement.

Transcription factors containing both C2H2 and homeobox domains play different roles in Verticillium dahliae

Verticillium dahliae causes Verticillium wilt in more than 200 plant species worldwide. As a soilborne fungus, it forms melanized microsclerotia and colonizes the xylem of host plants. Our previous study revealed a subfamily of C2H2-homeobox transcription factors in V. dahliae, but their biological roles remain unknown. In this study, we systematically characterized the functions of seven C2H2-homeobox transcription factors in V. dahliae. Deletion of VdChtf3 and VdChtf6 significantly decreased the production of melanized microsclerotia, and knockout of VdChtf1 and VdChtf4 enhanced virulence. Loss of VdChtf2 and VdChtf6 increased conidium production, whereas loss of VdChtf5 and VdChtf7 did not affect growth, conidiation, microsclerotial formation, or virulence. Further research showed that VdChtf3 activated the expression of genes encoding pectic enzymes to participate in microsclerotial formation. In addition, VdChtf4 reduced the expression of VdSOD1 to disturb the scavenging of superoxide radicals but induced the expression of genes related to cell wall synthesis to maintain cell wall integrity. These findings highlight the diverse roles of different members of the C2H2-homeobox gene family in V. dahliae.

IMPORTANCE

Verticillium dahliae is a soilborne fungus that causes plant wilt and can infect a variety of economic crops and woody trees. The molecular basis of microsclerotial formation and infection by this fungus remains to be further studied. In this study, we analyzed the functions of seven C2H2-homobox transcription factors. Notably, VdChtf3 and VdChtf4 exhibited the most severe defects, affecting phenotypes associated with critical developmental stages in the V. dahliae disease cycle. Our results indicate that VdChtf3 is a potential specific regulator of microsclerotial formation, modulating the expression of pectinase-encoding genes. This finding could contribute to a better understanding of microsclerotial development in V. dahliae. Moreover, VdChtf4 was associated with cell wall integrity, reactive oxygen species (ROS) stress resistance, and increased virulence. These discoveries shed light on the biological significance of C2H2-homeobox transcription factors in V. dahliae's adaptation to the environment and infection of host plants.

Genome sequencing of Elaeocarpus spp. stem blight pathogen Pseudocryphonectria elaeocarpicola reveals potential adaptations to colonize woody bark

BACKGROUND

Elaeocarpus spp. stem blight, caused by Pseudocryphonectria elaeocarpicola, is a destructive disease, which will significantly reduce the productivity and longevity of Elaeocarpus spp. plants, especially in the Guangdong Province of China. However, few information is available for P. elaeocarpicola. To unravel the potential adaptation mechanism of stem adaptation, the whole genome of P. elaeocarpicola was sequenced by using the DNBSEQ and PacBio platforms.

RESULTS

P. elaeocarpicola harbors 44.49 Mb genome with 10,894 predicted coding genes. Genome analysis revealed that the P. elaeocarpicola genome encodes a plethora of pathogenicity-related genes. Analysis of carbohydrate-active enzymes (CAZymes) revealed a rich variety of enzymes participated in plant cell wall degradation, which could effectively degrade cellulose, hemicellulose and xyloglucans in the plant cell wall and promote the invasion of the host plant. There are 213 CAZyme families found in P. elaeocarpicola, among which glycoside hydrolase (GH) family has the largest number, far exceeding other tested fungi by 53%. Besides, P. elaeocarpicola has twice as many genes encoding chitin and cellulose degradation as Cryphonectria parasitica, which belong to the same family. The predicted typical secreted proteins of P. elaeocarpicola are numerous and functional, including many known virulence effector factors, indicating that P. elaeocarpicola has great potential to secrete virulence effectors to promote pathogenicity on host plants. AntiSMASH revealed that the genome encoded 61 secondary metabolic gene clusters including 86 secondary metabolic core genes which was much higher than C. parasitica (49). Among them, two gene cluster of P. elaeocarpicola, cluster12 and cluster52 showed 100% similarity with the mycotoxins synthesis clusters from Aspergillus steynii and Alternaria alternata, respectively. In addition, we annotated cytochrome P450 related enzymes, transporters, and transcription factors in P. elaeocarpicola, which are important virulence determinants of pathogenic fungi.

CONCLUSIONS

Taken together, our study represents the first genome assembly for P. elaeocarpicola and reveals the key virulence factors in the pathogenic process of P. elaeocarpicola, which will promote our understanding of its pathogenic mechanism. The acquired knowledge lays a foundation for further exploration of molecular interactions with the host and provide target for management strategies in future research.

Kss1 of Verticillium dahliae regulates virulence, microsclerotia formation, and nitrogen metabolism

Verticillium dahliae causes destructive vascular wilt diseases on more than 200 plant species, including economically important crops and ornamental trees worldwide. The melanized microsclerotia (MS) enable V. dahliae to survive for years in soil, thus the fungus is especially difficult to control once it has become established. Previously, we found that the mitogen activated protein kinase VdSte11 (MAPKKK) plays key roles in MS formation, penetration, and virulence in V. dahliae. In this study, two MAPK homologs of the yeast Ste7p and Kss1p were identified and characterized in V. dahliae. Deletion of VdSte7 or VdKss1 reuslted in severe defects in melaninized MS formation and virulence. Furthermore, phosphorylation assays demonstrated that VdSte11 and VdSte7 can phosphorylate VdKss1 in V. dahliae. Proteomic analysis revealed a significant change in sterol biosynthesis with a fold change of ≥ 1.2 after the deletion of VdKss1. In addition, phosphoproteomic analysis showed that VdKss1 was involved in the regulation of nitrogen metabolism. Finally, we identified VdRlm1 as a potentially downstream target of VdKss1, which is involved in regulating ammonium nitrogen utilization. This study sheds light on the network of regulatory proteins in V. dahliae that affect MS formation and nitrogen metabolism.

An Oxidoreductase-like Protein is Required for Verticillium dahliae Infection and Participates in the Metabolism of Host Plant Defensive Compounds

Verticillium dahliae, a notorious phytopathogenic fungus, is responsible for vascular wilt diseases in numerous crops. Uncovering the molecular mechanisms underlying pathogenicity is crucial for controlling V. dahliae. Herein, we characterized a putative oxidoreductase-like protein (VdOrlp) from V. dahliae that contains a functional signal peptide. While the expression of VdOrlp was low in artificial media, it significantly increased during host infection. Deletion of VdOrlp had minimal effects on the growth and development of V. dahliae but severely impaired its pathogenicity. Metabolomic analysis revealed significant changes in organic heterocyclic compounds and phenylpropane compounds in cotton plants infected with ΔVdOrlp and V991. Furthermore, VdOrlp expression was induced by lignin, and its deletion affected the metabolism of host lignin and phenolic acids. In conclusion, our results demonstrated that VdOrlp plays an important role in the metabolism of plant phenylpropyl lignin and organic heterocyclic compounds and is required for fungal pathogenicity in V. dahliae.

Rho2 involved in development, stress response and pathogenicity of Fusarium oxysporum

Rho GTPases regulate the activity of cell wall biosynthesis, actin assembly and polar cell secretion. However, the function of Rho GTPase in filamentous fungi is poorly understood. To understand the role of Rho2 GTPase in Fusarium oxysporum, which is one of root rot pathogens of Panax notoginseng, △rho2 mutant was constructed. Phenotypes of △rho2, including conidiation, germination of spores, stresses (osmotic-, cell membrane-, cell wall disturbing-, metal-, and high temperature-) tolerance and pathogenicity were analyzed. The results showed that the growth of △rho2 was destroyed under cell wall disturbing stress and high temperature stress, suggesting that Rho2 regulated the response of F. oxysporum to cell wall synthesis inhibitors and high temperature stress. Germination of spores and pathogenicity to P. notoginseng were reduced in △rho2 mutant. Western blot results showed that rho2 deletion increased the phosphorylation level of Mpk1. To identify genes regulated by Rho2, transcriptome sequencing was carried out. 2477 genes were identified as upregulated genes and 2177 genes were identified as downregulated genes after rho2 was deleted. These genes provide clues for further study of rho2 function.

The Frq-Frh Complex Light-Dependently Delays Sfl1-Induced Microsclerotia Formation in Verticillium dahliae

The vascular plant pathogenic fungus Verticillium dahliae has to adapt to environmental changes outside and inside its host. V. dahliae harbors homologs of Neurospora crassa clock genes. The molecular functions and interactions of Frequency (Frq) and Frq-interacting RNA helicase (Frh) in controlling conidia or microsclerotia development were investigated in V. dahliae JR2. Fungal mutant strains carrying clock gene deletions, an FRH point mutation, or GFP gene fusions were analyzed on transcript, protein, and phenotypic levels as well as in pathogenicity assays on tomato plants. Our results support that the Frq-Frh complex is formed and that it promotes conidiation, but also that it suppresses and therefore delays V. dahliae microsclerotia formation in response to light. We investigated a possible link between the negative element Frq and positive regulator Suppressor of flocculation 1 (Sfl1) in microsclerotia formation to elucidate the regulatory molecular mechanism. Both Frq and Sfl1 are mainly present during the onset of microsclerotia formation with decreasing protein levels during further development. Induction of microsclerotia formation requires Sfl1 and can be delayed at early time points in the light through the Frq-Frh complex. Gaining further molecular knowledge on V. dahliae development will improve control of fungal growth and Verticillium wilt disease.

α-Pheromone Precursor Protein Foc4-PP1 Is Essential for the Full Virulence of Fusarium oxysporum f. sp. cubense Tropical Race 4

Fusarium oxysporum f. sp. cubense (Foc), which causes Fusarium wilt of bananas, is considered one of the most destructive fungal pathogens of banana crops worldwide. During infection, Foc secretes many different proteins which promote its colonization of plant tissues. Although F. oxysporum has no sexual cycle, it has been reported to secrete an α-pheromone, which acts as a growth regulator, chemoattractant, and quorum-sensing signaling molecule; and to encode a putative protein with the hallmarks of fungal α-pheromone precursors. In this study, we identified an ortholog of the α-pheromone precursor gene, Foc4-PP1, in Foc tropical race 4 (TR4), and showed that it was necessary for the growth and virulence of Foc TR4. Foc4-PP1 deletion from the Foc TR4 genome resulted in decreased fungal growth, increased sensitivity to oxidative stress and cell-wall-damaging agents, and attenuation of pathogen virulence towards banana plantlets. Subcellular localization analysis revealed that Foc4-PP1 was concentrated in the nuclei and cytoplasm of Nicotiana benthamiana cells, where it could suppress BAX-induced programmed cell death. In conclusion, these findings suggest that Foc4-PP1 contributes to Foc TR4 virulence by promoting hyphal growth and abiotic stress resistance and inhibiting the immune defense responses of host plants.

Verticillium dahliae Asp1 regulates the transition from vegetative growth to asexual reproduction by modulating microtubule dynamic organization

Verticillium dahliae is a devastating pathogenic fungus that causes severe vascular wilts in more than 400 dicotyledonous plants. The conidiation of V. dahliae in plant vascular tissues is the key strategy for its adaptation to the nutrient-poor environment and is required for its pathogenicity. However, it remains unclear about the regulatory mechanism of conidium production of V. dahliae in vascular tissues. Here, we found that VdAsp1, encoding an inositol polyphosphate kinase, is indispensable for the pathogenicity of V. dahliae. Loss of VdAsp1 function does not affect the invasion of the host, but it impairs the colonization and proliferation in vascular tissues. The ΔVdAsp1 mutant shows defective initiation of conidiophore formation and reduced expression of genes associated with the central developmental pathway. By live-cell imaging, we observed that some of ΔVdAsp1 mutant hyphae are swollen, and microtubule arrangements at the apical region of these hyphae are disorganized. These results indicate that VdAsp1 regulates the transition from vegetative growth to asexual reproduction by modulating microtubule dynamic organization, which is essential for V. dahliae to colonize and proliferate in vascular tissues. These findings provided a potential new direction in the control of vascular wilt pathogen by targeting conidium production in vascular tissues.

Screening and Regulation Mechanism of Key Transcription Factors of Penicillium expansum Infecting Postharvest Pears by ATAC-Seq Analysis

Transcription factors play a key role in Penicillium expansum infection process. Although the crucial characteristics of some transcription factors of pathogenic fungi have been found, many transcription factors involved in P. expansum infections have not been explored and studied. This study aimed to screen the transcription factors of P. expansum involved in postharvest pear infections by ATAC-seq analysis and to analyze the differentially expressed peak-related genes by GO enrichment and KEGG pathway analysis. Our results found the up-regulation of differentially expressed peak-related genes involved in the MAPK signaling pathway, pentose phosphate pathway, starch and sucrose metabolism, and pentose and glucuronate interconversions. Our study especially confirmed the differential regulation of transcription factors MCM1, Ste12 and gene WSC in the MAPK signaling pathway and PG1, RPE1 in the pentose and glucuronate interconversions pathway. These transcription factors and related genes might play an essential role in pear fruit infection by P. expansum. RT-qPCR validation of twelve expressed peak-related genes in P. expansum showed that the expression levels of these twelve genes were compatible with the ATAC-Seq. Our findings might shed some light on the regulatory molecular networks consisting of transcription factors that engaged in P. expansum invasion and infection of pear fruits.

Tomato Xylem Sap Hydrophobins Vdh4 and Vdh5 Are Important for Late Stages of Verticillium dahliae Plant Infection

Verticillium dahliae causes economic losses to a wide range of crops as a vascular fungal pathogen. This filamentous ascomycete spends long periods of its life cycle in the plant xylem, a unique environment that requires adaptive processes. Specifically, fungal proteins produced in the xylem sap of the plant host may play important roles in colonizing the plant vasculature and in inducing disease symptoms. RNA sequencing revealed over 1500 fungal transcripts that are significantly more abundant in cells grown in tomato xylem sap compared with pectin-rich medium. Of the 85 genes that are strongly induced in the xylem sap, four genes encode the hydrophobins Vdh1, Vdh2, Vdh4 and Vdh5. Vdh4 and Vhd5 are structurally distinct from each other and from the three other hydrophobins (Vdh1-3) annotated in V. dahliae JR2. Their functions in the life cycle and virulence of V. dahliae were explored using genetics, cell biology and plant infection experiments. Our data revealed that Vdh4 and Vdh5 are dispensable for V. dahliae development and stress response, while both contribute to full disease development in tomato plants by acting at later colonization stages. We conclude that Vdh4 and Vdh5 are functionally specialized fungal hydrophobins that support pathogenicity against plants.

Phosphoproteomic and Metabolomic Profiling Uncovers the Roles of CcPmk1 in the Pathogenicity of Cytospora chrysosperma

Pmk1, a highly conserved pathogenicity-related mitogen-activated protein kinase (MAPK) in pathogenic fungi, is phosphorylated and activated by MAP2K and acts as a global regulator of fungal infection and invasive growth by modulating downstream targets. However, the hierarchical CcPmk1 regulatory network in Cytospora chrysosperma, the main causal agent of canker disease in many woody plant species, is still unclear. In this study, we analyzed and compared the phosphoproteomes and metabolomes of ΔCcPmk1 and wild-type strains and identified pathogenicity-related downstream targets of CcPmk1. We found that CcPmk1 could interact with the downstream homeobox transcription factor CcSte12 and affect its phosphorylation. In addition, the ΔCcSte12 displayed defective phenotypes that were similar to yet not identical to that of the ΔCcPmk1 and included significantly reduced fungal growth, conidiation, and virulence. Remarkably, CcPmk1 could phosphorylate proteins translated from a putative secondary metabolism-related gene cluster, which is specific to C. chrysosperma, and the phosphorylation of several peptides was completely abolished in the ΔCcPmk1. Functional analysis of the core gene (CcPpns1) in this gene cluster revealed its essential roles in fungal growth and virulence. Metabolomic analysis showed that amino acid metabolism and biosynthesis of secondary metabolites, lipids, and lipid-like molecules significantly differed between wild type and ΔCcPmk1. Importantly, most of the annotated lipids and lipid-like molecules were significantly downregulated in the ΔCcPmk1 compared to the wild type. Collectively, these findings suggest that CcPmk1 may regulate a small number of downstream master regulators to control fungal growth, conidiation, and virulence in C. chrysosperma. IMPORTANCE Understanding the pathogenic mechanisms of plant pathogens is a prerequisite to developing effective disease-control methods. The Pmk1 MAPK is highly conserved among phytopathogenic fungi and acts as a global regulator of fungal pathogenicity by modulating downstream transcription factors or other components. However, the regulatory network of CcPmk1 from C. chrysosperma remains enigmatic. The present data provide evidence that the core pathogenicity regulator CcPmk1 modulates a few downstream master regulators to control fungal virulence in C. chrysosperma through transcription or phosphorylation and that CcPmk1 may be a potential target for disease control.

Transcription factor lineages in plant-pathogenic fungi, connecting diversity with fungal virulence

Plant-pathogenic fungi span diverse taxonomic lineages. Their host-infection strategies are often specialised and require the coordinated regulation of molecular virulence factors. Transcription factors (TFs) are fundamental regulators of gene expression, yet relatively few virulence-specific regulators are characterised in detail and their evolutionary trajectories are not well understood. Hence, this study compared the full range of TFs across taxonomically-diverse fungal proteomes and classified their lineages through an orthology analysis. The primary aims were to characterise differences in the range and profile of TF lineages broadly linked to plant-host association or pathogenic lifestyles, and to better characterise the evolutionary origin and trajectory of experimentally-validated virulence regulators. We observed significantly fewer TFs among obligate, host-associated pathogens, largely attributed to contractions in several Zn2Cys6 TF-orthogroup lineages. We also present novel insight into the key virulence-regulating TFs Ste12, Pf2 and EBR1, providing evidence for their ancestral origins, expansion and/or loss. Ultimately, the analysis presented here provides both primary evidence for TF evolution in fungal phytopathogenicity, as well as a practical phylogenetic resource to guide further detailed investigation on the regulation of virulence within key pathogen lineages.

Live-cell imaging elaborating epidermal invasion and vascular proliferation/colonization strategy of Verticillium dahliae in host plants

The soilborne ascomycete fungus Verticillium dahliae causes destructive vascular wilt disease in hundreds of dicotyledonous plant species. However, our understanding of the early invasion from the epidermis to the vasculature and the prompt proliferation and colonization in the xylem tissues remains poor. To elaborate the detailed infection strategy of V. dahliae in host plants, we traced the whole infection process of V. dahliae by live-cell imaging combined with high-resolution scanning electron microscopy. The 4D image series demonstrated that the apex of invading hyphae becomes tapered and directly invades the intercellular space of root epidermal cells at the initial infection. Following successful epidermal invasion, the invading hyphae extend in the intercellular space of the root cortex toward the vascular tissues. Importantly, the high-resolution microscopic and live-cell images demonstrated (a) that conidia are formed via budding at the apex of the hyphae in the xylem vessels to promote systemic propagation vertically, and (b) that the hyphae freely cross adjacent xylem vessels through the intertracheary pits to achieve horizontal colonization. Our findings provide a solid cellular basis for future studies on both intracellular invasion and vascular colonization/proliferation during V. dahliae infection and pathogenesis in host plants.

The bZip Transcription Factor VdMRTF1 is a Negative Regulator of Melanin Biosynthesis and Virulence in Verticillium dahliae

The ascomycete fungus Verticillium dahliae infects over 400 plant species and causes serious losses of economically important crops, such as cotton and tomato, and also of woody plants, such as smoke tree, maple, and olive. Melanized long-term survival structures known as microsclerotia play crucial roles in the disease cycle of V. dahliae, enabling this soilborne fungus to survive for years in the soil in the absence of a host. Previously, we identified VdMRTF1 (microsclerotia-related transcription factor) encoding a bZip transcription factor which is downregulated during microsclerotial development in V. dahliae. In the present study, we showed that VdMRTF1 negatively controls melanin production and virulence by genetic, biological, and transcriptomic analyses. The mutant strain lacking VdMRTF1 (ΔVdMRTF1) exhibited increased melanin biosynthesis and the defect also promoted microsclerotial development and sensitivity to Ca²⁺. In comparison with the wild-type strain, the ΔVdMRTF1 strain showed a significant enhancement in virulence and displayed an increased capacity to eliminate reactive oxygen species in planta. Furthermore, analyses of transcriptomic profiles between the ΔVdMRTF1 and wild-type strains indicated that VdMRTF1 regulates the differential expression of genes associated with melanin biosynthesis, tyrosine metabolism, hydrogen peroxide catabolic processes, and oxidoreductase activity in V. dahliae. Taken together, these data show that VdMRTF1 is a negative transcriptional regulator of melanin biosynthesis, microsclerotia formation, and virulence in V. dahliae.

IMPORTANCE Verticillium wilt is difficult to manage because the pathogen colonizes the plant xylem tissue and produces melanized microsclerotia which survive for more than 10 years in soil without a host. The molecular mechanisms underlying microsclerotia formation are of great importance to control the disease. Here, we provide evidence that a bZip transcription factor, VdMRTF1, plays important roles in melanin biosynthesis, microsclerotial development, resistance to elevated Ca²⁺ levels, and fungal virulence of V. dahliae. The findings extend and deepen our understanding of the complexities of melanin biosynthesis, microsclerotia formation, and virulence that are regulated by bZip transcription factors in V. dahliae.

Melanin Promotes Spore Production in the Rice Blast Fungus Magnaporthe oryzae

The rice blast pathogen, Magnaporthe oryzae, spreads through spores and invades rice through appressoria. Melanin is necessary for an appressorium to penetrate plant cells, but there are many unknown aspects of its role in fungal conidiation. In this study, we confirmed that melanin promotes spore production in M. oryzae, and that this effect is related to the background melanin content of wild-type strains. In the wild-type 70-15 strain with low melanin content of aerial hyphae, increased melanin synthesis promoted sporulation. In contrast, increased melanin synthesis in the wild-type Guy11 strain, which has higher melanin content, did not promote sporulation. The transcription factor Cnf1 (conidial production negative regulatory factor 1), which negatively regulates melanin synthesis, has opposite effects in conidiophore differentiation of Guy11 and 70-15. Deletion of CNF1 did not abolish the defects of Δcos1 and Δhox2 (where COS1/conidiophore stalk-less 1 or HOX2/homeodomain protein 2 was deleted) in conidiation, while increased the conidiation of Δgcc1 and Δgcf3 (where GCC1/growth, conidiation and cell wall regulatory factor 1, or GCF3/growth and conidiation regulatory factor 3 was deleted). Pig1 (pigment of Magnaporthe 1) regulates the melanin synthesis of hyphae but not of conidiophores, spores, or appressoria. Deletion of the same gene in different wild-type strains can lead to different phenotypes, partly because of differences in melanin content between fungal strains. Overall, this study reveals the functional diversity and complexity of melanin in different M. oryzae strains.

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.

Dynamics of Verticillium dahliae race 1 population under managed agricultural ecosystems

BACKGROUND

Plant pathogens and their hosts undergo adaptive changes in managed agricultural ecosystems, by overcoming host resistance, but the underlying genetic adaptations are difficult to determine in natural settings. Verticillium dahliae is a fungal pathogen that causes Verticillium wilt on many economically important crops including lettuce. We assessed the dynamics of changes in the V. dahliae genome under selection in a long-term field experiment.

RESULTS

In this study, a field was fumigated before the Verticillium dahliae race 1 strain (VdLs.16) was introduced. A derivative 145-strain population was collected over a 6-year period from this field in which a seggregating population of lettuce derived from Vr1/vr1 parents were evaluated. We de novo sequenced the parental genome of VdLs.16 strain and resequenced the derivative strains to analyze the genetic variations that accumulate over time in the field cropped with lettuce. Population genomics analyses identified 2769 single-nucleotide polymorphisms (SNPs) and 750 insertion/deletions (In-Dels) in the 145 isolates compared with the parental genome. Sequence divergence was identified in the coding sequence regions of 378 genes and in the putative promoter regions of 604 genes. Five-hundred and nine SNPs/In-Dels were identified as fixed. The SNPs and In-Dels were significantly enriched in the transposon-rich, gene-sparse regions, and in those genes with functional roles in signaling and transcriptional regulation.

CONCLUSIONS

Under the managed ecosystem continuously cropped to lettuce, the local adaptation of V. dahliae evolves at a whole genome scale to accumulate SNPs/In-Dels nonrandomly in hypervariable regions that encode components of signal transduction and transcriptional regulation.

The M35 Metalloprotease Effector FocM35_1 Is Required for Full Virulence of Fusarium oxysporum f. sp. cubense Tropical Race 4

Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) causes Fusarium wilt of banana, the most devastating disease on a banana plant. The genome of Foc TR4 encodes many candidate effector proteins. However, little is known about the functions of these effector proteins on their contributions to disease development and Foc TR4 virulence. Here, we discovered a secreted metalloprotease, FocM35_1, which is an essential virulence effector of Foc TR4. FocM35_1 was highly upregulated during the early stages of Foc TR4 infection progress in bananas. The FocM35_1 knockout mutant compromised the virulence of Foc TR4. FocM35_1 could interact with the banana chitinase MaChiA, and it decreased banana chitinase activity. FocM35_1 induced cell death in Nicotiana benthamiana while suppressing the INF1-induced hypersensitive response (HR), and its predicted enzymatic site was required for lesion formation and the suppression to INF1-induced HR on N. benthamiana leaves. Importantly, treatment of banana leaves with recombinant FocM35_1 accelerates Foc TR4 infection. Collectively, our study provides evidence that metalloprotease effector FocM35 seems to contribute to pathogen virulence by inhibiting the host immunity.

Unfolded Protein Response and Scaffold Independent Pheromone MAP Kinase Signaling Control Verticillium dahliae Growth, Development, and Plant Pathogenesis

Differentiation, growth, and virulence of the vascular plant pathogen Verticillium dahliae depend on a network of interconnected cellular signaling cascades. The transcription factor Hac1 of the endoplasmic reticulum-associated unfolded protein response (UPR) is required for initial root colonization, fungal growth, and vascular propagation by conidiation. Hac1 is essential for the formation of microsclerotia as long-time survival resting structures in the field. Single endoplasmic reticulum-associated enzymes for linoleic acid production as precursors for oxylipin signal molecules support fungal growth but not pathogenicity. Microsclerotia development, growth, and virulence further require the pheromone response mitogen-activated protein kinase (MAPK) pathway, but without the Ham5 scaffold function. The MAPK phosphatase Rok1 limits resting structure development of V.dahliae, but promotes growth, conidiation, and virulence. The interplay between UPR and MAPK signaling cascades includes several potential targets for fungal growth control for supporting disease management of the vascular pathogen V.dahliae.

Molecular Mechanisms Controlling the Disease Cycle in the Vascular Pathogen Verticillium dahliae Characterized Through Forward Genetics and Transcriptomics

The soil-borne pathogen Verticillium dahliae has a worldwide distribution and a plethora of hosts of agronomic value. Molecular analysis of virulence processes can identify targets for disease control. In this work, we compared the global gene transcription profile of random T-DNA insertion mutant strain D-10-8F, which exhibits reduced virulence and alterations in microsclerotium formation and polar growth, with that of the wild-type strain. Three genes identified as differentially expressed were selected for functional characterization. To produce deletion mutants, we developed an updated version of one-step construction of Agrobacterium-recombination-ready plasmids (OSCAR) that included the negative selection marker HSVtk (herpes simplex virus thymidine kinase gene) to prevent ectopic integration of the deletion constructs. Deletion of VdRGS1 (VDAG_00683), encoding a regulator of G protein signaling (RGS) protein and highly upregulated in the wild type versus D-10-8F, resulted in phenotypic alterations in development and virulence that were indistinguishable from those of the random T-DNA insertion mutant. In contrast, deletion of the other two genes selected, vrg1 (VDAG_07039) and vvs1 (VDAG_01858), showed that they do not play major roles in morphogenesis or virulence in V. dahliae. Taken together the results presented here on the transcriptomic analysis and phenotypic characterization of D-10-8F and ∆VdRGS1 strains provide evidence that variations in G protein signaling control the progression of the disease cycle in V. dahliae. We propose that G protein-mediated signals induce the expression of multiple virulence factors during biotrophic growth, whereas massive production of microsclerotia at late stages of infection requires repression of G protein signaling via upregulation of VdRGS1 activity.

The Verticillium dahliae Sho1-MAPK pathway regulates melanin biosynthesis and is required for cotton infection

Verticillium dahliae is a soil‐borne fungus that causes vascular wilt on numerous plants worldwide. The fungus survives in the soil for up to 14 years by producing melanized microsclerotia. The protective function of melanin in abiotic stresses is well documented. Here, we found that the V. dahliae tetraspan transmembrane protein VdSho1, a homolog of the Saccharomyces cerevisiae Sho1, acts as an osmosensor, and is required for plant penetration and melanin biosynthesis. The deletion mutant ΔSho1 was incubated on a cellophane membrane substrate that mimics the plant epidermis, revealing that the penetration of ΔSho1 strain was reduced compared to the wild‐type strain. Furthermore, VdSho1 regulates melanin biosynthesis by a signalling mechanism requiring a kinase‐kinase signalling module of Vst50‐Vst11‐Vst7. Strains, ΔVst50, ΔVst7 and ΔVst11 also displayed defective penetration and melanin production like the ΔSho1 strain. Defects in penetration and melanin production in ΔSho1 were restored by overexpression of Vst50, suggesting that Vst50 lies downstream of VdSho1 in the regulatory pathway governing penetration and melanin biosynthesis. Data analyses revealed that the transmembrane portion of VdSho1 was essential for both membrane penetration and melanin production. This study demonstrates that Vst50‐Vst11‐Vst7 module regulates VdSho1‐mediated plant penetration and melanin production in V. dahliae, contributing to virulence.

Two Verticillium dahliae MAPKKKs, VdSsk2 and VdSte11, Have Distinct Roles in Pathogenicity, Microsclerotial Formation, and Stress Adaptation

These data provide insights into the distinctive functions of VdSsk2 and VdSte11 in pathogenicity, stress adaptation, and microsclerotial formation in V. dahliae.

Verticillium dahliae causes destructive vascular wilt diseases on more than 200 plant species, including economically important crops and ornamental trees worldwide. The melanized microsclerotia enable the fungus to survive for years in soil and are crucial for its disease cycle. Previously, we found that the VdPbs2-VdHog1 (V. dahliae Pbs2-V. dahliae Hog1) module plays key roles in microsclerotial formation, stress responses, and virulence in V. dahliae. In this study, two mitogen-activated protein kinase kinase kinases (MAPKKKs) homologous to Ssk2p and Ste11p, which activate the Pbs2p-Hog1p module by phosphorylation in budding yeast, were identified in the genome of V. dahliae. Both ΔVdSsk2 (V. dahliaeSsk2) and ΔVdSte11 strains showed severe defects in microsclerotial formation and melanin biosynthesis, but the relative importance of these two genes in microsclerotial development was different. Deletion of VdSsk2, but not VdSte11, affected responses to osmotic stress, fungicidal response, and cell wall stressors. The ΔVdSsk2 strain exhibited a significant reduction in virulence, while the ΔVdSte11 strain was nonpathogenic due to failure to penetrate and form hyphopodia. Phosphorylation assays demonstrated that VdSsk2, but not VdSte11, can phosphorylate VdHog1 in V. dahliae. Moreover, VdCrz1, encoding a calcineurin-responsive zinc finger transcription factor and a key regulator of calcium signaling in fungi, was misregulated in the ΔVdSsk2, ΔVdPbs2, and ΔVdHog1 mutants.

IMPORTANCE These data provide insights into the distinctive functions of VdSsk2 and VdSte11 in pathogenicity, stress adaptation, and microsclerotial formation in V. dahliae.

A Homeobox Transcription Factor UvHOX2 Regulates Chlamydospore Formation, Conidiogenesis, and Pathogenicity in Ustilaginoidea virens

Rice false smut fungus (teleomorph: Villosiclava virens; anamorph: Ustilaginoidea virens) can generate chlamydospores and survive winter under field conditions. The chlamydospore is considered as an important infection source of the disease. However, little is known about the regulatory mechanism of the chlamydospore production. In this study, we identified a defective homeobox transcription factor (designated as UvHOX2) gene in a U. virens random insertional mutant B-766 that could not form chlamydospores. To confirm the regulatory function of UvHOX2, an Agrobacterium tumefaciens mediated transformation- and CRISPR/Cas9- based targeted gene replacement method was developed. The UvHox2 deletion mutants completely failed to produce chlamydospores, showed reduced conidia production and decreased virulence, and was hyper-sensitive to oxidative, osmotic, and cell wall stresses. We confirmed that UvHOX2 is located in the nuclei of U. virens, and the expression of UvHox2 was the strongest during the early stage of chlamydospore and conidium formation. Global transcription pattern of UvHOX2 was also determined by RNA-seq in this study, and several genes that might be down-stream of UvHOX2 regulation were identified. The results will better our understanding of the molecular mechanism of chlamydospore formation in U. virens as a model fungus.

Communicate and Fuse: How Filamentous Fungi Establish and Maintain an Interconnected Mycelial Network

Cell-to-cell communication and cell fusion are fundamental biological processes across the tree of life. Survival is often dependent upon being able to identify nearby individuals and respond appropriately. Communication between genetically different individuals allows for the identification of potential mating partners, symbionts, prey, or predators. In contrast, communication between genetically similar (or identical) individuals is important for mediating the development of multicellular organisms or for coordinating density-dependent behaviors (i.e., quorum sensing). This review describes the molecular and genetic mechanisms that mediate cell-to-cell communication and cell fusion between cells of Ascomycete filamentous fungi, with a focus on Neurospora crassa. Filamentous fungi exist as a multicellular, multinuclear network of hyphae, and communication-mediated cell fusion is an important aspect of colony development at each stage of the life cycle. Asexual spore germination occurs in a density-dependent manner. Germinated spores (germlings) avoid cells that are genetically different at specific loci, while chemotropically engaging with cells that share identity at these recognition loci. Germlings with genetic identity at recognition loci undergo cell fusion when in close proximity, a fitness attribute that contributes to more rapid colony establishment. Communication and cell fusion also occur between hyphae in a colony, which are important for reinforcing colony architecture and supporting the development of complex structures such as aerial hyphae and sexual reproductive structures. Over 70 genes have been identified in filamentous fungi (primarily N. crassa) that are involved in kind recognition, chemotropic interactions, and cell fusion. While the hypothetical signal(s) and receptor(s) remain to be described, a dynamic molecular signaling network that regulates cell-cell interactions has been revealed, including two conserved MAP-Kinase cascades, a conserved STRIPAK complex, transcription factors, a NOX complex involved in the generation of reactive oxygen species, cell-integrity sensors, actin, components of the secretory pathway, and several other proteins. Together these pathways facilitate the integration of extracellular signals, direct polarized growth, and initiate a transcriptional program that reinforces signaling and prepares cells for downstream processes, such as membrane merger, cell fusion and adaptation to heterokaryon formation.

Mycovirus Fusarium oxysporum f. sp. dianthi Virus 1 Decreases the Colonizing Efficiency of Its Fungal Host

Mycoviruses that induce hypovirulence in phytopathogenic fungi are interesting because their potential use as biological control agents of the plant diseases caused by their fungal hosts. The recently identified chrysovirus Fusarium oxysporum f. sp. dianthi virus 1 (FodV1) has been associated to the induction of hypovirulence in Fusarium oxysporum f. sp. dianthi, the forma specialis of F. oxysporum that causes vascular wilt in carnation (Dianthus caryophyllus). In this work, we have used confocal laser scanner microscopy and two isogenic GFP-labeled strains of F. oxysporum f. sp. dianthi infected (V⁺) and not infected (V^-) with the Fusarium oxysporum f. sp. dianthi virus 1, respectively, to analyze the effect of mycovirus FodV1 on the plant colonization pattern of its fungal host. Results demonstrate that FodV1-viral infection affects the speed and spatial distribution of fungal colonization into the plant. Initial stages of external root colonization were similar for both strains, but the virus-free strain colonized the internal plant tissues faster than the virus-infected strain. In addition, other differences related to the specific zone colonized and the density of colonization were observed between both F. oxysporum f. sp. dianthi strains. The hyphae of both V^- and V⁺ strains progressed up through the xylem vessels but differences in the number of vessels colonized and of hyphae inside them were found. Moreover, as colonization progressed, V^- and V⁺ hyphae propagated horizontally reaching the central medulla but, while the virus-free strain V^- densely colonized the interior of the medulla cells, the virus-infected strain V⁺ appeared mainly in the intercellular spaces and with a lower density of colonization. Finally, the incidence of FodV1-viral infections in a collection of 221 isolates sampled between 2008 and 2012 in the geographic area where the originally infected isolate was obtained has been also analyzed. The very low (<2%) incidence of viral infections is discussed here. To the best of our knowledge, this work provides the first microscopic evidence about the effect of a hypovirulence-inducing mycovirus on the pattern of plant colonization by its fungal host.

Integration of Self and Non-self Recognition Modulates Asexual Cell-to-Cell Communication in Neurospora crassa

Cells rarely exist alone, which drives the evolution of diverse mechanisms for identifying and responding appropriately to the presence of other nearby cells. Filamentous fungi depend on somatic cell-to-cell communication and fusion for the development and maintenance of a multicellular, interconnected colony that is characteristic of this group of organisms. The filamentous fungus Neurospora crassa is a model for investigating the mechanisms of somatic cell-to-cell communication and fusion. N. crassa cells chemotropically grow toward genetically similar cells, which ultimately make physical contact and undergo cell fusion. Here, we describe the development of a Pprm1-luciferase reporter system that differentiates whether genes function upstream or downstream of a conserved MAP kinase (MAPK) signaling complex, by using a set of mutants required for communication and cell fusion. The vast majority of these mutants are deficient for self-fusion and for fusion when paired with wild-type cells. However, the Δham-11 mutant is unique in that it fails to undergo self-fusion, but chemotropic interactions and cell fusion are restored in Δham-11 + wild-type interactions. In genetically dissimilar cells, chemotropic interactions are regulated by genetic differences at doc-1 and doc-2, which regulate prefusion non-self recognition; cells with dissimilar doc-1 and doc-2 alleles show greatly reduced cell-fusion frequencies. Here, we show that HAM-11 functions in parallel with the DOC-1 and DOC-2 proteins to regulate the activity of the MAPK signaling complex. Together, our data support a model of integrated self and non-self recognition processes that modulate somatic cell-to-cell communication in N. crassa.

The Fusarium Circinatum Gene Fcrho1, Encoding a Putative Rho1 GTPase, Is Involved in Vegetative Growth but Dispensable for Pathogenic Development

Fusarium circinatum is the causal agent of pine pitch canker (PPC), one of the most devastating forest diseases worldwide. This fungus causes severe damping-off in pine seedlings and growth reduction, wilting and the development of cankers in pine forests and plantations. A draft of the complete genome sequence of this phytopathogen was recently made available. This information was used to annotate in silico the gene Fcrho1 as a putative homolog of Rho1 GTPase genes. In this study, we generated Fcrho1 deletion mutants in two F. circinatum wildtype strains isolated from damaged trees in northern Spain. For that, we used a modified version of the OSCAR methodology, an approach not previously used in F. circinatum that allows the generation of deletion constructs in a single cloning step. The conidiation and spore germination of the resulting deletion mutants were not affected, neither the hyphal morphology. However, the mutant strains showed significantly reduced growth in vitro and more foamy macroscopic hyphal morphology than their corresponding ectopic and wildtype strains. Finally, an in vivo virulence assay showed that the reduced in vitro growth rate characteristic to the deletion mutants does not impact their pathogenicity.

VdPLP, A Patatin-Like Phospholipase in Verticillium dahliae, Is Involved in Cell Wall Integrity and Required for Pathogenicity

The soil-borne ascomycete fungus Verticillium dahliae causes vascular wilt disease and can seriously diminish the yield and quality of important crops. Functional analysis of growth- and pathogenicity-related genes is essential for revealing the pathogenic molecular mechanism of V. dahliae. Phospholipase is an important virulence factor in fungi that hydrolyzes phospholipids into fatty acid and other lipophilic substances and is involved in hyphal development. Thus far, only a few V. dahliae phospholipases have been identified, and their involvement in V. dahliae development and pathogenicity remains unknown. In this study, the function of the patatin-like phospholipase gene in V. dahliae (VdPLP, VDAG_00942) is characterized by generating gene knockout and complementary mutants. Vegetative growth and conidiation of VdPLP deletion mutants (ΔVdPLP) were significantly reduced compared with wild type and complementary strains, but more microsclerotia formed. The ΔVdPLP mutants were very sensitive to the cell-wall-perturbing agents: calcofluor white (CFW) and Congo red (CR). The transcriptional level of genes related to the cell wall integrity (CWI) pathway and chitin synthesis were downregulated, suggesting that VdPLP has a pivotal role in the CWI pathway and chitin synthesis in V. dahliae. ΔVdPLP strains were distinctly impaired in in their virulence and ability to colonize Nicotiana benthamiana roots. Our results demonstrate that VdPLP regulates hyphal growth and conidial production and is involved in stabilizing the cell wall, thus mediating the pathogenicity of V. dahliae.

Verticillium dahliae-Arabidopsis Interaction Causes Changes in Gene Expression Profiles and Jasmonate Levels on Different Time Scales

Verticillium dahliae is a soil-borne vascular pathogen that causes severe wilt symptoms in a wide range of plants. Co-culture of the fungus with Arabidopsis roots for 24 h induces many changes in the gene expression profiles of both partners, even before defense-related phytohormone levels are induced in the plant. Both partners reprogram sugar and amino acid metabolism, activate genes for signal perception and transduction, and induce defense- and stress-responsive genes. Furthermore, analysis of Arabidopsis expression profiles suggests a redirection from growth to defense. After 3 weeks, severe disease symptoms can be detected for wild-type plants while mutants impaired in jasmonate synthesis and perception perform much better. Thus, plant jasmonates have an important influence on the interaction, which is already visible at the mRNA level before hormone changes occur. The plant and fungal genes that rapidly respond to the presence of the partner might be crucial for early recognition steps and the future development of the interaction. Thus they are potential targets for the control of V. dahliae-induced wilt diseases.