Mark Arentshorst

Expanding the ku70 toolbox for filamentous fungi: establishment of complementation vectors and recipient strains for advanced gene analyses

Mutants with a defective non-homologous-end-joining (NHEJ) pathway have boosted functional genomics in filamentous fungi as they are very efficient recipient strains for gene-targeting approaches, achieving homologous recombination frequencies up to 100%. For example, deletion of the ku70 homologous gene kusA in Aspergillus niger resulted in a recipient strain in which deletions of essential or non-essential genes can efficiently be obtained. To verify that the mutant phenotype observed is the result of a gene deletion, a complementation approach has to be performed. Here, an intact copy of the gene is transformed back to the mutant, where it should integrate ectopically into the genome. However, ectopic complementation is difficult in NHEJ-deficient strains, and the gene will preferably integrate via homologous recombination at its endogenous locus. To circumvent that problem, we have constructed autonomously replicating vectors useful for many filamentous fungi which contain either the pyrG allele or a hygromycin resistance gene as selectable markers. Under selective conditions, the plasmids are maintained, allowing complementation analyses; once the selective pressure is removed, the plasmid becomes lost and the mutant phenotype prevails. Another disadvantage of NHEJ-defective strains is their increased sensitivity towards DNA damaging conditions such as radiation. Thus, mutant analyses in these genetic backgrounds are limited and can even be obscured by pleiotropic effects. The use of sexual crossings for the restoration of the NHEJ pathway is, however, impossible in imperfect filamentous fungi such as A. niger. We have therefore established a transiently disrupted kusA strain as recipient strain for gene-targeting approaches.

Fungal gene expression on demand: An inducible, tunable and metabolism-independent expression system for Aspergillus niger

ABSTRACT Filamentous fungi are the cause of serious human and plant diseases but are also exploited in biotechnology as production platforms. Comparative genomics has documented their genetic diversity, and functional genomics and systems biology approaches are under way to understand the functions and interaction of fungal genes and proteins. In these approaches, gene functions are usually inferred from deletion or overexpression mutants. However, studies at these extreme points give only limited information. Moreover, many overexpression studies use metabolism-dependent promoters, often causing pleiotropic effects and thus limitations in their significance. We therefore established and systematically evaluated a tunable expression system for Aspergillus niger that is independent of carbon and nitrogen metabolism and silent under noninduced conditions. The system consists of two expression modules jointly targeted to a defined genomic locus. One module ensures constitutive expression of the tetracycline-dependent transactivator rtTA2S-M2, and one module harbors the rtTA2S-M2-dependent promoter that controls expression of the gene of interest (the Tet-on system). We show here that the system is tight, responds within minutes after inducer addition, and allows fine-tuning based on the inducer concentration or gene copy number up to expression levels higher than the expression levels of the gpdA promoter. We also validate the Tet-on system for the generation of conditional overexpression mutants and demonstrate its power when combined with a gene deletion approach. Finally, we show that the system is especially suitable when the functions of essential genes must be examined.

Functional characterization of Rho GTPases in Aspergillus niger uncovers conserved and diverged roles of Rho proteins within filamentous fungi

Rho GTPases are signalling molecules regulating morphology and multiple cellular functions including metabolism and vesicular trafficking. To understand the connection between polarized growth and secretion in the industrial model organism Aspergillus niger, we investigated the function of all Rho family members in this organism. We identified six Rho GTPases in its genome and used loss‐of‐function studies to dissect their functions. While RhoA is crucial for polarity establishment and viability, RhoB and RhoD ensure cell wall integrity and septum formation respectively. RhoC seems to be dispensable for A. niger. RacA governs polarity maintenance via controlling actin but not microtubule dynamics, which is consistent with its localization at the hyphal apex. Both deletion and dominant activation of RacA (RacG18V) provoke an actin localization defect and thereby loss of polarized tip extension. Simultaneous deletion of RacA and CftA (Cdc42) is lethal; however, conditional overexpression of RacA in this strain can substitute for CftA, indicating that both proteins concertedly control actin dynamics. We finally identified NoxR as a RacA‐specific effector, which however, is not important for apical dominance as reported for A. nidulans but for asexual development. Overall, the data show that individual Rho GTPases contribute differently to growth and morphogenesis within filamentous fungi.

The Aspergillus niger MADS‐box transcription factor RlmA is required for cell wall reinforcement in response to cell wall stress

In Aspergillus niger, the genes coding for glutamine:fructose‐6‐phosphate amidotransferase (gfaA) and α‐1,3‐glucan synthase (agsA) are induced in response to cell wall stress. In silico analysis of the promoter region of the two genes revealed the presence of putative DNA binding sites for transcription factors involved in stress responses, including sites identical to the Saccharomyces cerevisiae Rlm1p and Msn2p/Msn4p transcription factors. Promoter analysis indicated that the induction of the agsA gene in response to cell wall stress is fully dependent on a putative Rlm1p binding site in its promoter region. Database searches revealed the presence of S. cerevisiae Rlm1p homologues in most filamentous fungi examined, including A. niger. Deletion of the RLM1 homologue, named rlmA in A. niger, completely eliminated the induction of agsA and resulted in a twofold reduced induction of gfaA during Calcofluor White‐induced cell wall stress. The rise in cell wall chitin in the presence of Calcofluor White was also affected in the rlmA deletion strain. In addition, the deletion strain was more sensitive towards cell wall stress agents. Our results indicate that A. niger responds to cell wall stress by transcriptional activation of cell wall reinforcing genes including agsA and gfaA through an Rlm1p‐like transcription factor. We propose that such a cell wall salvage mechanism is wide spread in filamentous fungi.

Survival in the Presence of Antifungals GENOME-WIDE EXPRESSION PROFILING OF ASPERGILLUS NIGER IN RESPONSE TO SUBLETHAL CONCENTRATIONS OF CASPOFUNGIN AND FENPROPIMORPH

How yeast cells respond to cell wall stress is relatively well understood; however, how filamentous fungi cope with cell wall damage is largely unexplored. Here we report the first transcriptome analysis of Aspergillus niger exposed to the antifungal compounds caspofungin, an inhibitor of β-1,3-glucan synthesis, and fenpropimorph, which inhibits ergosterol synthesis. The presence of sublethal drug concentrations allowed A. niger to adapt to the stress conditions and to continue growth by the establishment of new polarity axes and formation of new germ tubes. By comparing the expression profile between caspofungin-exposed and nonexposed A. niger germlings, we identified a total of 172 responsive genes out of 14,509 open reading frames present on the Affymetrix microarray chips. Among 165 up-regulated genes, mainly genes predicted to function in (i) cell wall assembly and remodeling, (ii) cytoskeletal organization, (iii) signaling, and (iv) oxidative stress response were affected. Fenpropimorph modulated expression of 43 genes, of which 41 showed enhanced expression. Here, genes predicted to function in (i) membrane reconstruction, (ii) lipid signaling, (iii) cell wall remodeling, and (iv) oxidative stress response were identified. Northern analyses of selected genes were used to confirm the microarray analyses. The results further show that expression of the agsA gene encoding an α-1,3-glucan synthase is up-regulated by both compounds. Using two PagsA-GFP reporter strains of A. niger and subjecting them to 16 different antifungal compounds, including caspofungin and fenpropimorph, we could show that agsA is specifically activated by compounds interfering directly or indirectly with cell wall biosynthesis.

A novel screening method for cell wall mutants in Aspergillus niger identifies UDP-galactopyranose mutase as an important protein in fungal cell wall biosynthesis

To identify cell wall biosynthetic genes in filamentous fungi and thus potential targets for the discovery of new antifungals, we developed a novel screening method for cell wall mutants. It is based on our earlier observation that the Aspergillus niger agsA gene, which encodes a putative α-glucan synthase, is strongly induced in response to cell wall stress. By placing the agsA promoter region in front of a selectable marker, the acetamidase (amdS) gene of A. nidulans, we reasoned that cell wall mutants with a constitutively active cell wall stress response pathway could be identified by selecting mutants for growth on acetamide as the sole nitrogen source. For the genetic screen, a strain was constructed that contained two reporter genes controlled by the same promoter: the metabolic reporter gene PagsA-amdS and PagsA-H2B-GFP, which encodes a GFP-tagged nuclear protein. The primary screen yielded 161 mutants that were subjected to various cell wall-related secondary screens. Four calcofluor white-hypersensitive, osmotic-remediable thermosensitive mutants were selected for complementation analysis. Three mutants were complemented by the same gene, which encoded a protein with high sequence identity with eukaryotic UDP-galactopyranose mutases (UgmA). Our results indicate that galactofuranose formation is important for fungal cell wall biosynthesis and represents an attractive target for the development of antifungals.

Transcriptomic Insights into the Physiology of Aspergillus niger Approaching a Specific Growth Rate of Zero

ABSTRACT The physiology of filamentous fungi at growth rates approaching zero has been subject to limited study and exploitation. With the aim of uncoupling product formation from growth, we have revisited and improved the retentostat cultivation method for Aspergillus niger. A new retention device was designed allowing reliable and nearly complete cell retention even at high flow rates. Transcriptomic analysis was used to explore the potential for product formation at very low specific growth rates. The carbon- and energy-limited retentostat cultures were highly reproducible. While the specific growth rate approached zero (<0.005 h−1), the growth yield stabilized at a minimum (0.20 g of dry weight per g of maltose). The severe limitation led to asexual differentiation, and the supplied substrate was used for spore formation and secondary metabolism. Three physiologically distinct phases of the retentostat cultures were subjected to genome-wide transcriptomic analysis. The severe substrate limitation and sporulation were clearly reflected in the transcriptome. The transition from vegetative to reproductive growth was characterized by downregulation of genes encoding secreted substrate hydrolases and cell cycle genes and upregulation of many genes encoding secreted small cysteine-rich proteins and secondary metabolism genes. Transcription of known secretory pathway genes suggests that A. niger becomes adapted to secretion of small cysteine-rich proteins. The perspective is that A. niger cultures as they approach a zero growth rate can be used as a cell factory for production of secondary metabolites and cysteine-rich proteins. We propose that the improved retentostat method can be used in fundamental studies of differentiation and is applicable to filamentous fungi in general.

Reconstruction of Signaling Networks Regulating Fungal Morphogenesis by Transcriptomics

ABSTRACT Coordinated control of hyphal elongation and branching is essential for sustaining mycelial growth of filamentous fungi. In order to study the molecular machinery ensuring polarity control in the industrial fungus Aspergillus niger, we took advantage of the temperature-sensitive (ts) apical-branching ramosa-1 mutant. We show here that this strain serves as an excellent model system to study critical steps of polar growth control during mycelial development and report for the first time a transcriptomic fingerprint of apical branching for a filamentous fungus. This fingerprint indicates that several signal transduction pathways, including TORC2, phospholipid, calcium, and cell wall integrity signaling, concertedly act to control apical branching. We furthermore identified the genetic locus affected in the ramosa-1 mutant by complementation of the ts phenotype. Sequence analyses demonstrated that a single amino acid exchange in the RmsA protein is responsible for induced apical branching of the ramosa-1 mutant. Deletion experiments showed that the corresponding rmsA gene is essential for the growth of A. niger, and complementation analyses with Saccharomyces cerevisiae evidenced that RmsA serves as a functional equivalent of the TORC2 component Avo1p. TORC2 signaling is required for actin polarization and cell wall integrity in S. cerevisiae. Congruently, our microscopic investigations showed that polarized actin organization and chitin deposition are disturbed in the ramosa-1 mutant. The integration of the transcriptomic, genetic, and phenotypic data obtained in this study allowed us to reconstruct a model for cellular events involved in apical branching.

Characterization of the T-Cell–Mediated Immune Response Against the Aspergillus fumigatus Proteins Crf1 and Catalase 1 in Healthy Individuals

Invasive aspergillosis is a serious infectious complication after allogeneic stem cell transplantation. One of the strategies to improve the management of aspergillosis is the adoptive transfer of antigen-specific T cells, the success of which depends on the development of a broad repertoire of antigen-specific T cells. In this study, we identified CD4+ T cells specific for the Aspergillus proteins Crf1 and catalase 1 in 18 of 24 healthy donors by intracellular staining for interferon γ and CD154. Crf1- and catalase 1-specific T cells were selected on the basis of CD137 expression and underwent single-cell expansion. Aspergillus-specific T-cell clones mainly exhibited a T-helper cell 1 phenotype and recognized a broad variety of T-cell epitopes. Five novel Crf1 epitopes, 2 previously described Crf1 epitopes, and 30 novel catalase 1 epitopes were identified. Ultimately, by using overlapping peptides of Aspergillus fumigatus proteins, Aspergillus-specific T-cell lines that have a broad specificity and favorable cytokine profile and are suitable for adoptive T-cell therapy can be generated in vitro.

Using Non-homologous End-Joining-Deficient Strains for Functional Gene Analyses in Filamentous Fungi

Fungal strains deficient in the non-homologous end-joining (NHEJ) pathway are excellent recipient strains for gene targeting approaches. In addition, NHEJ-deficiency can facilitate the formation of heterokaryons which allows rapid identification of essential genes. However, the use of NHEJ-deficient strains can also pose some limitations for gene function analyses. For example, lack of the NHEJ pathway can interfere with phenotypic analyses and complicate complementation studies. Moreover, heterokaryons are difficult to propagate and re-transform. We describe here strategies and methods to circumvent these problems and to better exploit the power of NHEJ-deficient strains. We provide methods for the establishment of transiently deficient NHEJ strains, for improved complementation analyses using AMA1-based vectors and for fast identification and propagation of heterokaryons. The methods described are applicable for a wide range of filamentous fungi.