A conserved regulator controls asexual sporulation in the fungal pathogen Candida albicans

Impact of TaFtsZ2 overexpression and mutation on wheat starch granule characteristics and quality

Starch granule size is strongly related to the physicochemical properties and quality of starch. This study used genetic engineering techniques to obtain mutants and overexpressing lines of the wheat amyloplast-division gene TaFtsZ2, to regulate the size and physicochemical properties of wheat starch granules. The results showed that the gene TaFtsZ2 was localized to the chloroplasts of wheat leaves. Although mutation of this gene did not result in unfavorable agronomic traits, it caused abnormal amyloplast division, leading to irregular starch morphology and increased granule size and number of micropores. Simultaneously, the mutation also led to a down-regulation in the expression of sucrose metabolism-related genes and starch-branching enzyme genes. As a result, the total starch content, amylopectin content, starch branching degree, and crystallinity all decreased compared with those of the non-mutated lines, and the contents of amylose, resistant starch, and proteins increased. The starch also exhibited lower peak viscosity and a higher gelatinization temperature. In contrast, overexpression of TaFtsZ2 promoted amyloplast division, increasing the number of small starch granules. It also up-regulated the expression of genes related to starch and sucrose metabolism, leading to an increase in starch-branching degree, amylopectin content, peak viscosity and a decrease in gelatinization temperature, ultimately improving the quality of wheat starch. This study will provide a new method for regulating the size and physicochemical properties of wheat starch granules by controlling amyloplast division and novel germplasm resources for the production of wheat starch with specific functions.

When HSFs bring the heat-mapping the transcriptional circuitries of HSF-type regulators in Candida albicans

Heat shock factor (HSF)-type regulators are stress-responsive transcription factors widely distributed among eukaryotes, including fungi. They carry a four-stranded winged helix-turn-helix DNA-binding domain considered as the signature domain for HSFs. The genome of the opportunistic yeast Candida albicans encodes four HSF members, namely, Sfl1, Sfl2, Skn7, and the essential regulator, Hsf1. C. albicans HSFs do not only respond to heat shock and/or temperature variation but also to CO2 levels, oxidative stress, and quorum sensing, acting this way as central decision makers. In this minireview, I follow on the heels of my mSphere of Influence commentary (2020) to provide an overview of the repertoire of HSF regulators in Saccharomyces cerevisiae and C. albicans and describe how their genetic perturbation in C. albicans, coupled with genome-wide expression and location analyses, allow to map their transcriptional circuitry. I highlight how they can regulate, in common, a crucial developmental program: filamentous growth.

Strain-limited biofilm regulation through the Brg1-Rme1 circuit in Candida albicans

Prominent virulence traits of Candida albicans include its ability to produce filamentous hyphal cells and grow as a biofilm. These traits are under control of numerous transcription factors (TFs), including Brg1 and Rme1. In the reference strain SC5314, a brg1Δ/Δ mutant has reduced levels of biofilm/filament production; a brg1Δ/Δ rme1Δ/Δ double mutant has wild-type levels of biofilm/filament production. Here, we asked whether this suppression relationship is preserved in four additional strain backgrounds: P76067, P57055, P87, and P75010. These strains represent diverse clades and biofilm/filament production abilities. We find that a rme1Δ/Δ mutation restores biofilm/filament production in a brg1Δ/Δ mutant of P76067, but not in brg1Δ/Δ mutants of P57055, P87, and P75010. We speculate that variation in activities of two functionally related TFs, Nrg1, and Ume6, may cause the strain-limited impact of the rme1Δ/Δ mutation.

IMPORTANCE

Candida albicans is a widespread fungal pathogen. The regulatory circuitry underlying virulence traits is well studied in the reference strain background, but not in other clinical isolate backgrounds. Here, we describe a pronounced example of strain variation in the control of two prominent virulence traits, biofilm formation and filamentation.

A Brg1-Rme1 circuit in Candida albicans hyphal gene regulation

Major Candida albicans virulence traits include its ability to make hyphae, to produce a biofilm, and to damage host cells. These traits depend upon expression of hypha-associated genes. A gene expression comparison among clinical isolates suggested that transcription factor Rme1, established by previous studies to be a positive regulator of chlamydospore formation, may also be a negative regulator of hypha-associated genes. Engineered RME1 overexpression supported this hypothesis, but no relevant rme1Δ/Δ mutant phenotype was detected. We reasoned that Rme1 may function within a specific regulatory pathway. This idea was supported by our finding that an rme1Δ/Δ mutation relieves the need for biofilm regulator Brg1 in biofilm formation. The impact of the rme1Δ/Δ mutation is most prominent under static or "biofilm-like" growth conditions. RNA sequencing (RNA-seq) of cells grown under biofilm-like conditions indicates that Brg1 activates hypha-associated genes indirectly via repression of RME1: hypha-associated gene expression levels are substantially reduced in a brg1Δ/Δ mutant and partially restored in a brg1Δ/Δ rme1Δ/Δ double mutant. An rme1Δ/Δ mutation does not simply bypass Brg1, because iron homeostasis genes depend upon Brg1 regardless of Rme1. Rme1 thus connects Brg1 to the targets relevant to hypha and biofilm formation under biofilm growth conditions.IMPORTANCECandida albicans is a major fungal pathogen of humans, and its ability to grow as a surface-associated biofilm on implanted devices is a common cause of infection. Here, we describe a new regulator of biofilm formation, RME1, whose activity is most prominent under biofilm-like growth conditions.

AfSwi6 Regulates the Stress Response, Chlamydospore Production, and Pathogenicity in the Nematode-Trapping Fungus Arthrobotrys flagrans

Nematode-trapping (NT) fungi are a major resource for controlling parasitic nematodes. Arthrobotrys flagrans, as a typical NT fungus, can capture nematodes by producing three-dimensional nets. The APSES transcription factor Swi6 plays a vital role in fungal growth and the pathogenicity of pathogens. In this study, we characterized AfSwi6 via gene disruption using the homologous recombinant method and transcriptome sequencing. Knockout of the AfSwi6 gene caused defects in mycelial growth, trap formation and pathogenicity, chlamydospore production, and stress response. Moreover, the transcriptome data indicated that AfSwi6 was related to DNA repair, stress response, and plasma membrane fusion. The result showed that AfSwi6 has a significant effect on trap development and chlamydospore production in A. flagrans.

AfLaeA, a Global Regulator of Mycelial Growth, Chlamydospore Production, Pathogenicity, Secondary Metabolism, and Energy Metabolism in the Nematode-Trapping Fungus Arthrobotrys flagrans

Arthrobotrys flagrans (Duddingtonia flagrans) is a typical nematode-trapping fungus which has been used for nematode biocontrol. The global regulator LaeA is widely distributed in filamentous fungi and plays a crucial role in secondary metabolism and development in addition to pathogenicity in fungal pathogens. In this study, the chromosome-level genome of A. flagrans CBS 565.50 was sequenced and homologous sequences of LaeA were identified in A. flagrans. A. flagrans LaeA (AfLaeA) knockout resulted in slower hyphal growth and a smoother hyphal surface. Importantly, deletion of AfLaeA resulted in the absence of chlamydospores and attenuated glycogen and lipid accumulation in hyphae. Similarly, disruption of the AfLaeA gene led to fewer traps and electron-dense bodies, lower protease activity, and a delay in capturing nematodes. The AfLaeA gene had a large effect on the secondary metabolism of A. flagrans, and both the deletion and overexpression of AfLaeA could yield new compounds, whereas some compounds were lost due to the absence of the AfLaeA. Protein-protein interactions between AfLaeA and another eight proteins were detected. Furthermore, transcriptome data analysis showed that 17.77% and 35.51% of the genes were influenced by the AfLaeA gene on days 3 and 7, respectively. AfLaeA gene deletion resulted in the higher expression level of the artA gene cluster, and multiple differentially expressed genes involved in glycogen and lipid synthesis and metabolism showed opposite expression patterns in wild-type and ΔAfLaeA strains. In summary, our results provide novel insights into the functions of AfLaeA in mycelial growth, chlamydospore production, pathogenicity, secondary metabolism, and energy metabolism in A. flagrans. IMPORTANCE The regulation of biological functions, such as the secondary metabolism, development, and pathogenicity of LaeA, has been reported in multiple fungi. But to date, no study on LaeA in nematode-trapping fungi has been reported. Moreover, it has not been investigated whether or not LaeA is involved in energy metabolism and chlamydospore formation has not been investigated. Especially in the formation mechanism of chlamydospores, several transcription factors and signaling pathways are involved in the production of chlamydospores, but the mechanism of chlamydospore formation from an epigenetic perspective has not been revealed. Concurrently, an understanding of protein-protein interactions will provide a broader perspective on the regulatory mechanism of AfLaeA in A. flagrans. This finding is critical for understanding the regulatory role of AfLaeA in the biocontrol fungus A. flagrans and establishes a foundation for developing high-efficiency nematode biocontrol agents.

The secretory Candida effector Sce1 licenses fungal virulence by masking the immunogenic β-1,3-glucan and promoting apoptosis of the host cells

Candida albicans deploys a variety of mechanisms such as morphological switch and elicitor release to promote virulence. However, the intricate interactions between the fungus and the host remain poorly understood, and a comprehensive inventory of fungal virulence factors has yet to be established. In this study, we identified a C. albicans secretory effector protein Sce1, whose induction and secretion are associated with vagina-simulative conditions and chlamydospore formation. Sequence alignment showed that Sce1 belongs to a Pir family in C. albicans, which is conserved across several fungi and primarily characterized as a β-glucan binding protein in the Saccharomyces cerevisiae. Mechanically, Sce1 is primarily localized to the cell wall in a cleaved form as an alkali-labile β-1,3-glucan binding protein and plays a role in masking β-glucan in acidic environments and chlamydospores, a feature that might underline C. albicans' ability to evade host immunity. Further, a cleaved short form of Sce1 protein could be released into extracellular compartments and presented in bone marrow-derived macrophages infected with chlamydospores. This cleaved short form of Sce1 also demonstrated a unique ability to trigger the caspases-8/9-dependent apoptosis in various host cells. Correspondingly, genetic deletion of SCE1 led to dampened vaginal colonization of C. albicans and diminished fungal virulence during systemic infection. The discovery of Sce1 as a versatile virulence effector that executes at various compartments sheds light on the fungus-host interactions and C. albicans pathogenesis.

Nitrogen addition enhanced Per-fluoroalkyl substances' microbial availability in a wheat soil ecosystem

Per-fluoroalkyl substances (PFASs) have been widely detected in farmland soils and are understood to pose toxicological threats to soil microbiomes and crop safety. Meanwhile, farmland ecosystems have experienced increasing nitrogen loading caused by soil fertilization. Yet it is still unclear how nitrogen additions affect soil's microbial responses to PFASs. In this study, using a laboratory-based ecological experiment, we assessed the microbial availability of PFASs in soils receiving ammonium, nitrate, and urea nitrogen amendments by quantifying the translocation factors of PFASs from soil particle to soil extracellular polymeric substances (EPS). Our results showed that nitrogen, specifically ammonium, significantly increased the PFASs' microbial availability (p < 0.05). Second, nitrogen fertilization in PFASs-polluted soils decreased the microbial community diversity and stability at the structural, species, and functional levels (p < 0.05). For soil microbial activities, nitrogen enhanced the activity of superoxide dismutase (SOD) while it inhibited the catalase (CAT) and peroxidase (POD) (p < 0.01). Congruently, PFASs, as well as the nitrate and nitrite nitrogen, were shown to be the predominant abiotic drivers regulating the soil fungal succession (p < 0.05), while bacteria were mostly regulated by dissolved organic carbon (DOC) (p < 0.01). Furthermore, we revealed that the nitrogen cycling gene hmp (dominates the transformation from NO to NO₃^-) was the hub gene integrating the microbially available PFASs and the soil nitrogen cycling processes (p < 0.01), indicating that hmp could be the core regulator affecting the accumulation of PFASs in soil EPS. Our study highlighted that decreasing ammonia's amendments could mitigate China's national initiatives to reduce nitrogen fertilization in farmlands, reduce the PFASs' availability to the soil microbiome, and protect the microbial community stability in soil.

Secondary Metabolism Gene Clusters Exhibit Increasingly Dynamic and Differential Expression during Asexual Growth, Conidiation, and Sexual Development in Neurospora crassa

Secondary metabolite clusters (SMCs) encode the machinery for fungal toxin production. However, understanding their function and analyzing their products requires investigation of the developmental and environmental conditions in which they are expressed. Gene expression is often restricted to specific and unexamined stages of the life cycle. Therefore, we applied comparative genomics analyses to identify SMCs in Neurospora crassa and analyzed extensive transcriptomic data spanning nine independent experiments from diverse developmental and environmental conditions to reveal their life cycle-specific gene expression patterns. We reported 20 SMCs comprising 177 genes-a manageable set for investigation of the roles of SMCs across the life cycle of the fungal model N. crassa-as well as gene sets coordinately expressed in 18 predicted SMCs during asexual and sexual growth under three nutritional and two temperature conditions. Divergent activity of SMCs between asexual and sexual development was reported. Of 126 SMC genes that we examined for knockout phenotypes, al-2 and al-3 exhibited phenotypes in asexual growth and conidiation, whereas os-5, poi-2, and pmd-1 exhibited phenotypes in sexual development. SMCs with annotated function in mating and crossing were actively regulated during the switch between asexual and sexual growth. Our discoveries call for attention to roles that SMCs may play in the regulatory switches controlling mode of development, as well as the ecological associations of those developmental stages that may influence expression of SMCs. IMPORTANCE Secondary metabolites (SMs) are low-molecular-weight compounds that often mediate interactions between fungi and their environments. Fungi enriched with SMs are of significant research interest to agriculture and medicine, especially from the aspects of pathogen ecology and environmental epidemiology. However, SM clusters (SMCs) that have been predicted by comparative genomics alone have typically been poorly defined and insufficiently functionally annotated. Therefore, we have investigated coordinate expression in SMCs in the model system N. crassa, and our results suggest that SMCs respond to environmental signals and to stress that are associated with development. This study examined SMC regulation at the level of RNA to integrate observations and knowledge of these genes in various growth and development conditions, supporting combining comparative genomics and inclusive transcriptomics to improve computational annotation of SMCs. Our findings call for detailed study of the function of SMCs during the asexual-sexual switch, a key, often-overlooked developmental stage.

Peering Into Candida albicans Pir Protein Function and Comparative Genomics of the Pir Family

The fungal cell wall, comprised primarily of protein and polymeric carbohydrate, maintains cell structure, provides protection from the environment, and is an important antifungal drug target. Pir proteins (proteins with internal repeats) are linked to cell wall β-1,3-glucan and are best studied in Saccharomyces cerevisiae. Sequential deletion of S. cerevisiae PIR genes produces strains with increasingly notable cell wall damage. However, a true null mutant lacking all five S. cerevisiae PIR genes was never constructed. Because only two PIR genes (PIR1, PIR32) were annotated in the Candida albicans genome, the initial goal of this work was to construct a true Δpir/Δpir null strain in this species. Unexpectedly, the phenotype of the null strain was almost indistinguishable from its parent, leading to the search for other proteins with Pir function. Bioinformatic approaches revealed nine additional C. albicans proteins that share a conserved Pir functional motif (minimally DGQ). Examination of the protein sequences revealed another conserved motif (QFQFD) toward the C-terminal end of each protein. Sequence similarities and presence of the conserved motif(s) were used to identify a set of 75 proteins across 16 fungal species that are proposed here as Pir proteins. The Pir family is greatly expanded in C. albicans and C. dubliniensis compared to other species and the orthologs are known to have specialized function during chlamydospore formation. Predicted Pir structures showed a conserved core of antiparallel beta-sheets and sometimes-extensive loops that contain amino acids with the potential to form linkages to cell wall components. Pir phylogeny demonstrated emergence of specific ortholog groups among the fungal species. Variation in gene expression patterns was noted among the ortholog groups during growth in rich medium. PIR allelic variation was quite limited despite the presence of a repeated sequence in many loci. Results presented here demonstrate that the Pir family is larger than previously recognized and lead to new hypotheses to test to better understand Pir proteins and their role in the fungal cell wall.

Overexpression approaches to advance understanding of Candida albicans

Candida albicans is an opportunistic fungal pathogen that is responsible for infections linked to high mortality. Loss‐of‐function approaches, taking advantage of gene knockouts or inducible down‐regulation, have been successfully used in this species in order to understand gene function. However, overexpression of a gene provides an alternative, powerful tool to elucidate gene function and identify novel phenotypes. Notably, overexpression can identify pathway components that might remain undetected using loss‐of‐function approaches. Several repressible or inducible promoters have been developed which allow to shut off or turn on the expression of a gene in C. albicans upon growth in the presence of a repressor or inducer. In this review, we summarize recent overexpression approaches used to study different aspects of C. albicans biology, including morphogenesis, biofilm formation, drug tolerance, and commensalism.

A Conserved Machinery Underlies the Synthesis of a Chitosan Layer in the Candida Chlamydospore Cell Wall

The polysaccharide chitosan is found in the cell wall of specific cell types in a variety of fungal species where it contributes to stress resistance, or in pathogenic fungi, virulence. Under certain growth conditions, the pathogenic yeast Candida dubliniensis forms a cell type termed a chlamydospore, which has an additional internal layer in its cell wall compared to hyphal or yeast cell types. We report that this internal layer of the chlamydospore wall is rich in chitosan. The ascospore wall of Saccharomyces cerevisiae also has a distinct chitosan layer. As in S. cerevisiae, formation of the chitosan layer in the C. dubliniensis wall requires the chitin synthase CHS3 and the chitin deacetylase CDA2 In addition, three lipid droplet-localized proteins-Rrt8, Srt1, and Mum3-identified in S. cerevisiae as important for chitosan layer assembly in the ascospore wall are required for the formation of the chitosan layer of the chlamydospore wall in C. dubliniensis These results reveal that a conserved machinery is required for the synthesis of a distinct chitosan layer in the walls of these two yeasts and may be generally important for incorporation of chitosan into fungal walls.IMPORTANCE The cell wall is the interface between the fungal cell and its environment and disruption of cell wall assembly is an effective strategy for antifungal therapies. Therefore, a detailed understanding of how cell walls form is critical to identify potential drug targets and develop therapeutic strategies. This study shows that a set of genes required for the assembly of a chitosan layer in the cell wall of S. cerevisiae is also necessary for chitosan formation in a different cell type in a different yeast, C. dubliniensis Because chitosan incorporation into the cell wall can be important for virulence, the conservation of this pathway suggests possible new targets for antifungals aimed at disrupting cell wall function.