Transcriptomic insights into the alternative splicing-mediated adaptation of the entomopathogenic fungus Beauveria bassiana to host niches: autophagy-related gene 8 as an example

Alternative splicing perspective to prey preference of environmentally friendly biological agent Cryptolaemus montrouzieri

BACKGROUND

Cryptolaemus montrouzieri (Coccinellidae) is widely utilized as biological control agents in modern agriculture. A comprehensive understanding of its food preference can help guide mass rearing and safety management during field application of pest control. Although some studies have paid attentions to the impacts of prey shift on C. montrouzieri, little is known regarding the role of post-transcriptional regulations in its acclimation to unnatural preys.

RESULTS

We performed a genome-wide investigation on alternative splicing dynamics in C. montrouzieri in response to the predation transition from natural prey to unnatural ones. When feeding on undesired diets, 402-764 genes were differentially alternative spliced in C. montrouzieri. It is noteworthy that the majority of these genes (> 87%) were not differentially expressed, and these differentially spliced genes regulated distinct biological processes from differentially expressed genes, such as organ development and morphogenesis, locomotory behavior, and homeostasis processes. These suggested the functionally nonredendant role of alternative splicing in modulating physiological and metabolic responses of C. montrouzieri to the shift to undesired preys. In addition, the individuals feeding on aphids were subject to a lower level of changes in splicing than other alternative diets, which might be because of the similar chemical and microbial compositions. Our study further suggested a putative coupling of alternative splicing and nonsense-mediated decay (AS-NMD), which may play an important role in fine-tuning the protein repertoire of C. montrouzieri, and promoting its acclimation to predation changes.

CONCLUSION

These findings highlight the key role of alternative splicing in modulating the acclimation of ladybirds to prey shift and provide new genetic clues for the future application of ladybirds in biocontrol.

Transcriptomic landscape of the interaction between the entomopathogenic fungus Beauveria bassiana and its tolerant host Tribolium castaneum revealed by dual RNA-seq

Entomopathogenic fungi such as Beauveria bassiana are the only insect pathogens able to start the infection process by penetrating through the host cuticle. However, some insects try to avoid fungal infection by embedding their cuticle with antifungal compounds. This is the case of the red flour beetle Tribolium castaneum, which generates economical loss of great significance in stored product environments worldwide. In this study, T. castaneum adults were fed during different time periods (from 3 to 72 h) on B. bassiana conidia-covered corn kernels. The progression of fungal infection was monitored using the dual RNA-seq technique to reconstruct the temporal transcriptomic profile and to perform gene enrichment analyses in both interacting organisms. After mapping the total reads with the B. bassiana genome, 904 genes were identified during this process. The more expressed fungal genes were related to carbon catabolite repression, cation binding, peptidase inhibition, redox processes, and stress response. Several immune-related genes from Toll, IMD, and JNK pathways, as well as genes related to chitin modification, were found to be differentially expressed in fungus-exposed T. castaneum. This study represents the first dual transcriptomic approach to help understand the interaction between the entomopathogenic fungus B. bassiana and its tolerant host T. castaneum.

Insight into the regulation of the Nrf2 pathway in response to ascovirus infection in Spodoptera exigua

BACKGROUND

Ascoviruses are a type of entomopathogenic microorganism with high biological pest control potential and are expected to contribute to the natural control of lepidopteran pests. However, knowledge of the molecular mechanism underlying the biocidal activity of ascovirus on its host insects remains limited.

RESULTS

In this study, the relative enzyme activity of superoxide dismutase and peroxidase, as well as the expression level of Spodoptera exigua peroxidase (SePOD), were found to be significantly increased at 6 h post infection with Heliothis virescens ascovirus 3h (HvAV-3h). H₂ O₂ accumulation and enhanced expression of NADPH Oxidase (SeNOX) were also observed. In addition, Nuclear Factor erythroid 2-Related Factor 2 (SeNrf2) and muscle aponeurosis fibromatosis (SeMaf) were overexpressed following infection with HvAV-3h. Silencing of SeNrf2 decreased the expression of SePOD, whereas the mortality of SeNrf2-silenced larvae and viral genome copy number also increased. Further RNA interference of SeNOX significantly decreased expression of SeNrf2 and SePOD and therefore increased the mortality and viral genome copy number of the ascovirus-infected host.

CONCLUSION

The HvAV-3h activated Nrf2/ARE pathway of S. exigua and reactive oxygen species were found to respond to ascovirus infection by regulating alterations in antioxidant enzyme genes mediated by the host Nrf2/ARE pathway. These findings enhance our knowledge of ascovirus-host interactions and lay the foundation for the application of ascoviruses in biological pest control. © 2022 Society of Chemical Industry.

Landscape and regulation of alternative splicing and alternative polyadenylation in a plant pathogenic fungus

Alternative splicing (AS) and alternative polyadenylation (APA) contribute significantly to the regulation of gene expression in higher eukaryotes. Their biological impact in filamentous fungi, however, is largely unknown. Here we combine PacBio Isoform-Sequencing and strand-specific RNA-sequencing of multiple tissues and mutant characterization to reveal the landscape and regulation of AS and APA in Fusarium graminearum. We generated a transcript annotation comprising 51 617 isoforms from 17 189 genes. In total, 4997 and 11 133 genes are alternatively spliced and polyadenylated, respectively. Majority of the AS events alter coding sequences. Unexpectedly, the AS transcripts containing premature-termination codons are not sensitive to nonsense-mediated messenger RNA decay. Unlike in yeasts and animals, distal APA sites have strong signals, but proximal APA isoforms are highly expressed in F. graminearum. The 3'-end processing factors FgRNA15, FgHRP1, and FgFIP1 play roles in promoting proximal APA site usage and intron splicing. A genome-wide increase in intron inclusion and distal APA site usage and downregulation of the spliceosomal and 3'-end processing factors were observed in older and quiescent tissues, indicating intron inclusion and 3'-untranslated region lengthening as novel mechanisms in regulating aging and dormancy in fungi. This study provides new insights into the complexity and regulation of AS and APA in filamentous fungi.

The Entomopathogenic Fungus Beauveria bassiana Shows Its Toxic Side within Insects: Expression of Genes Encoding Secondary Metabolites during Pathogenesis

Entomopathogenic fungi are extensively used for the control of insect pests worldwide. Among them, Beauveria bassiana (Ascomycota: Hypocreales) produce a plethora of toxic secondary metabolites that either facilitate fungal invasion or act as immunosuppressive compounds. These toxins have different chemical natures, such as nonribosomal peptides and polyketides. Even though their precise role is poorly understood, they are usually linked to virulence. These fungal secondary metabolites are produced by the expression of gene clusters encoding the various proteins needed for their biosynthesis. Each cluster includes synthetases for nonribosomal peptides (NRPS), polyketides (PKS), or hybrid NRPS–PKS genes. The aim of this review is to summarize the information available from transcriptomics and quantitative PCR studies related to the expression of B. bassiana NRPS and PKS genes inside different insects as the infection progresses; as for the host immune response, to help understand the mechanisms that these toxins trigger as virulence factors, antimicrobials, or immunosuppressives within the context of a fungus–insect interaction.

Transcriptomic Analysis Reveals That Rho GTPases Regulate Trap Development and Lifestyle Transition of the Nematode-Trapping Fungus Arthrobotrys oligospora

Nematode-trapping (NT) fungi can form unique infection structures (traps) to capture and kill free-living nematodes and, thus, can play a potential role in the biocontrol of nematodes. Arthrobotrys oligospora is a representative species of NT fungi. Here, we performed a time course transcriptome sequencing (RNA-seq) analysis of transcriptomes to understand the global gene expression levels of A. oligospora during trap formation and predation. We identified 5,752 unique differentially expressed genes, among which the rac gene was significantly upregulated. Alternative splicing events occurred in 2,012 genes, including the rac and rho2 gene. Furthermore, we characterized three Rho GTPases (Rho2, Rac, and Cdc42) in A. oligospora using gene disruption and multiphenotypic analysis. Our analyses showed that AoRac and AoCdc42 play an important role in mycelium growth, lipid accumulation, DNA damage, sporulation, trap formation, pathogenicity, and stress response in A. oligospora. AoCdc42 and AoRac specifically interacted with components of the Nox complex, thus regulating the production of reactive oxygen species. Moreover, the transcript levels of several genes associated with protein kinase A, mitogen-activated protein kinase, and p21-activated kinase were also altered in the mutants, suggesting that Rho GTPases might function upstream from these kinases. This study highlights the important role of Rho GTPases in A. oligospora and provides insights into the regulatory mechanisms of signaling pathways in the trap morphogenesis and lifestyle transition of NT fungi. IMPORTANCE Nematode-trapping (NT) fungi are widely distributed in terrestrial and aquatic ecosystems. Their broad adaptability and flexible lifestyles make them ideal agents for controlling pathogenic nematodes. Arthrobotrys oligospora is a model species employed for understanding the interaction between fungi and nematodes. Here, we revealed that alternative splicing events play a crucial role in the trap development and lifestyle transition in A. oligospora. Furthermore, Rho GTPases exert differential effects on the growth, development, and pathogenicity of A. oligospora. In particular, AoRac is required for sporulation and trap morphogenesis. In addition, our analysis showed that Rho GTPases regulate the production of reactive oxygen species and function upstream from several kinases. Collectively, these results expand our understanding of gene expression and alternative splicing events in A. oligospora and the important roles of Rho GTPases in NT fungi, thereby providing a foundation for exploring their potential application in the biocontrol of pathogenic nematodes.

Transcriptomic analyses reveal comprehensive responses of insect hemocytes to mycopathogen Beauveria bassiana, and fungal virulence-related cell wall protein assists pathogen to evade host cellular defense

Entomopathogenic fungi naturally infect insect hosts in environment. Fungal invasion and host immune defense are still in the progress of co-evolution. In this study, entomopathogenic fungus Beauveria bassiana and lepidopteran insect Galleria mellonella were used to investigate host cellular immunity and fungal strategy to evade host defense. First of all, genome-wide expression revealed the transcriptomic responses of hemocytes to insect mycopathogen, which dynamically varied during infection process. Enrichment analysis indicated that differentially expressed genes were primarily involved in metabolism, cellular process and immune system. Notably, cellular response involved a series of hydrolytic enzyme and antimicrobial peptide genes which were sorted together in clustering analysis. In B. bassiana, a cell-wall protein gene (BbCwp) contributes to fungal development in host hemocoel and virulence. RT-qPCR analyses indicated that infection by ΔBbCwp mutant strain caused the up-regulated expression of a series of immunity-related genes, including β-1, 3-glucan recognition protein, hydrolytic enzyme and antimicrobial peptide genes. Disruption of BbCwp resulted in a significant change in conidial lectin-binding feature and the enhanced encapsulation by the host hemocytes. After being treated with hydrolytic enzymes, ΔBbCwp mutant displayed a significantly enhanced sensitivity to osmotic and oxidative stresses. In conclusion, fungal invasion initiates comprehensive physiological responses in the host hemocytes. For mycopathogen, cell-wall protein plays an important role in fungal evasion of immunity defense and colonization in host. Our studies provide an initial framework for exploring more mechanistic details about the fungus–host interaction.

Swi6B, an alternative splicing isoform of Swi6, mediates the cell wall integrity of Ganoderma lucidum

The cell wall integrity (CWI) signaling activates the transcription factor Swi6 through a MAPK signaling cascade in response to cell wall stresses. In this study, we observed two different mRNA variants of swi6 (GlSwi6A and GlSwi6B) existed, due to alternative splicing. Besides, the expression level of GlSwi6B was higher than that of the GlSwi6A mRNA variant. The co-silencing of GlSwi6A and GlSwi6B was more sensitive to cell wall stress compared with WT, resulting in a decrease of 78% and 76% in chitin and β-1,3-d-glucan content respectively. However, only the overexpression of GlSwi6B decreased the sensitivity to cell wall stress and increased the content of chitin and β-1,3-d-glucan compared with the WT strain. Furthermore, Y1H, EMSA and BLI assays revealed that the GlSwi6B could bind to the promoters of chitin and glucan synthesis genes (GL24454 and GL18134). However, the binding phenome has not been observed in the isoform GlSwi6A. Taken together, our results found two different transcripts generated from Swi6, in which the alternative splice isoform of GlSwi6B participates in regulating the CWI of G. lucidum. This study provides the first insight into the alternative splicing isoform of GlSwi6B in the regulation of CWI signaling in fungi.

Transcriptional Responses of Beauveria bassiana Blastospores Cultured Under Varying Glucose Concentrations

Culturing the entomopathogenic fungus, Beauveria bassiana, under high glucose concentrations coupled with high aeration results in a fungal developmental shift from hyphal growth to mostly blastospores (yeast-like cells). The underlying molecular mechanisms involved in this shift remain elusive. A systematic transcriptome analysis of the differential gene expression was preformed to uncover the fungal transcriptomic response to osmotic and oxidative stresses associated with the resulting high blastospore yield. Differential gene expression was compared under moderate (10% w/v) and high (20% w/v) glucose concentrations daily for three days. The RNAseq-based transcriptomic results depicted a higher proportion of downregulated genes when the fungus was grown under 20% glucose than 10%. Additional experiments explored a broader glucose range (4, 8, 12, 16, 20% w/v) with phenotype assessment and qRT-PCR transcript abundance measurements of selected genes. Antioxidant, calcium transport, conidiation, and osmosensor-related genes were highly upregulated in higher glucose titers (16-20%) compared to growth in lower glucose (4-6%) concentrations. The class 1 hydrophobin gene (Hyd1) was highly expressed throughout the culturing. Hyd1 is known to be involved in spore coat rodlet layer assembly, and indicates that blastospores or another cell type containing hydrophobin 1 is expressed in the haemocoel during the infection process. Furthermore, we found implications of the HOG signaling pathway with upregulation of homologous genes Ssk2 and Hog1 for all fermentation time points under hyperosmotic medium (20% glucose). These findings expand our knowledge of the molecular mechanisms behind blastospore development and may help facilitate large-scale industrial production of B. bassiana blastospores for pest control applications.

Transcriptomic analysis of Sur7-mediated response of Beauveria bassiana to different nutritional conditions

Integrity of the cell wall is requisite for fungal growth and function. Sur7 governs cell wall composition, and affects conidial sporulation and germination in Beauveria bassiana, a filamentous entomopathogenic fungus. The role of Sur7 in fungal growth on various nutrients remains unclear. We have previously reported that Sur7 deletion results in the attenuation of B. bassiana growth on supplemented Sabouraud dextrose agar (SDAY) and minimal Czapek-Dox agar (CDA) compared to wild type (WT). Here, we used transcriptomic analysis to compare WT and Sur7 mutant (ΔSur7) responses to CDA and SDAY. Growth on CDA, compared with that on SDAY, affected the expression of more genes in the WT than in the mutant. Differentially expressed genes were enriched for transportation process terms in the ΔSur7 mutant and metabolic process terms in the WT. Different processes were repressed in the ΔSur7 (metabolic process) and WT (ribosome synthesis) cells. Despite the shared enrichment of nitrogen metabolism genes, differentially expressed genes were enriched in distinct saccharide-energy metabolism terms in each strain. We conclude that Sur7 ensures the growth of B. bassiana in a minimal medium by influencing the expression of genes involved in the consumption of sucrose via specific energy metabolism pathways.

Autophagy-related gene ATG7 participates in the asexual development, stress response and virulence of filamentous insect pathogenic fungus Beauveria bassiana

Autophagy is a sophisticated mechanism for maintaining cellular homeostasis, in which E1-like enzyme (ATG7) controls the activation of ubiquitin-like conjugation system in the autophagy pathway. In the insect pathogenic fungus Beauveria bassiana, a yeast ortholog of ATG7 was identified and functionally analyzed. Ablation of BbATG7 gene blocks the autophagic process under starvation stress. The mutant ΔBbATG7 exhibited impaired growth on the media with chitin as single nitrogen source. On rich media, gene loss did not cause notable effect on vegetative growth, but resulted in a considerable reduction in conidiation (71.6%) and blastospore yield (61.1%) in the mutant. In addition, the ΔBbATG7 mutant displayed increased sensitivity to stress caused by menadione and Congo red. The virulence of ΔBbATG7 mutant was significantly attenuated as indicated in topical and intrahemocoel injection assays. Our study indicates that BbATG7 contributes to B. bassiana virulence via regulating autophagy pathway and playing non-autophagic functions in the infection cycle.

Insight into vital role of autophagy in sustaining biological control potential of fungal pathogens against pest insects and nematodes

Autophagy is a conserved self-degradation mechanism that governs a large array of cellular processes in filamentous fungi. Filamentous insect and nematode mycopthogens function in the natural control of host populations and have been widely applied for biological control of insect and nematode pests. Entomopathogenic and nematophagous fungi have conserved “core” autophagy machineries that are analogous to those found in yeast but also feature several proteins involved in specific aspects of the autophagic pathways. Here, we review the functions of autophagy in protecting fungal cells from starvation and stress cues and sustaining cell differentiation, asexual development and virulence. An emphasis is placed upon the regulatory mechanisms involved in autophagic and non-autophagic roles of some autophagy-related genes. Methods used for monitoring conserved or specific autophagic events in fungal pathogens are also discussed.

Autophagy-related gene BbATG11 is indispensable for pexophagy and mitophagy, and contributes to stress response, conidiation and virulence in the insect mycopathogen Beauveria bassiana

Autophagy is a conserved degradation system in eukaryotic cells that includes non-selective and selective processes. Selective autophagy functions as a selective degradation mechanism for specific substrates in which autophagy-related protein 11 (ATG11) acts as an essential scaffold protein. In B. bassiana, there is a unique ATG11 family protein, which is designated as BbATG11. Disruption of BbATG11 resulted in significantly reduced conidial germination under starvation stress. The mutant ΔBbATG11 displayed enhanced sensitivity to oxidative stress and impaired asexual reproduction. The conidial yield was reduced by approximately 75%, and this defective phenotype could be repressed by increasing exogenous nutrients. The virulence of the ΔBbATG11 mutant strain was significantly impaired as indicated in topical and intra-hemocoel injection bioassays, with a greater reduction in topical infection. Notably, BbATG11 was involved in pexophagy and mitophagy, but these two autophagic processes appeared in different fungal physiological aspects. Both pexophagy and mitophagy were associated with nutrient shift, starvation stress and growth in the host hemocoel, but only pexophagy appeared in both oxidation-stressed cells and aerial mycelia. This study highlights that BbATG11 mediates pexophagy and mitophagy in B. bassiana and links selective autophagy to the fungal stress response, conidiation and virulence.