Phenotypic instability in fungi

TOR Signaling Tightly Regulated Vegetative Growth, Conidiation, Oxidative Stress Tolerance and Entomopathogenicity in the Fungus Beauveria bassiana

Beauveria bassiana degenerates after repeated subcultures, demonstrating declined conidiation and insect virulence. The target of rapamycin (TOR) kinase conserved among eukaryotes is the master regulator of cellular physiology and is likely involved in culture degeneration. Indeed, the levels of TOR-associated proteins increase over successive subcultures. Here, CRISPR/Cas9 locus engineering introduced the inducible Tet-On promoter upstream of the TOR kinase 2 gene tor2 in B. bassiana. The mutant PTet-Ontor2 'T41' was verified for the Tet-On integration via PCR analyses and provided a model for evaluating the fungal phenotypes according to the tor2 expression levels, induced by doxycycline (Dox) concentrations. At 0 µg·mL-1 of Dox, T41 had 68% of the wild type's (WT) tor2 expression level, hampered radial growth and relatively lower levels of oxidative stress tolerance, conidiation and virulence against Spodoptera exigua, compared to those under the presence of Dox. A low dose of Dox at 0.1-1 µg·mL-1 induced tor2 upregulation in T41 by up to 91% compared to 0 µg·mL-1 of Dox, resulting in significant increases in radial growth by 8-10% and conidiation by 8-27%. At 20 µg·mL-1 of Dox, which is 132% higher than T41's tor2 expression level at 0 µg·mL-1 of Dox, T41 showed an increased oxidative stress tolerance and a decrease in growth inhibition under iron replete by 62%, but its conidiation significantly dropped by 47% compared to 0 µg·mL-1 of Dox. T41 at 20 µg·mL-1 of Dox had a strikingly increased virulence (1.2 day lower LT50) against S. exigua. The results reflect the crucial roles of TOR kinase in the vegetative growth, conidiation, pathogenicity and oxidative stress tolerance in B. bassiana. Since TOR upregulation is correlated with culture degeneration in multiple subcultures, our data suggest that TOR signaling at relatively low levels plays an important role in growth and development, but at moderate to high levels could contribute to some degenerated phenotypes, e.g., those found in successive subcultures.

The phenomenon of strain degeneration in biotechnologically relevant fungi

Fungi are widely exploited for large-scale production in the biotechnological industry to produce a diverse range of substances due to their versatility and relative ease of growing on various substrates. The occurrence of a phenomenon-the so-called fungal strain degeneration-leads to the spontaneous loss or decline of production capacity and results in an economic loss on a tremendous scale. Some of the most commonly applied genera of fungi in the biotechnical industry, such as Aspergillus, Trichoderma, and Penicillium, are threatened by this phenomenon. Although fungal degeneration has been known for almost a century, the phenomenon and its underlying mechanisms still need to be understood. The proposed mechanisms causing fungi to degenerate can be of genetic or epigenetic origin. Other factors, such as culture conditions, stress, or aging, were also reported to have an influence. This mini-review addresses the topic of fungal degeneration by describing examples of productivity losses in biotechnical processes using Aspergillus niger, Aspergillus oryzae, Trichoderma reesei, and Penicillium chrysogenum. Further, potential reasons, circumvention, and prevention methods are discussed. This is the first mini-review which provides a comprehensive overview on this phenomenon in biotechnologically used fungi, and it also includes a collection of strategies that can be useful to minimize economic losses which can arise from strain degeneration. KEY POINTS: • Spontaneous loss of productivity is evident in many fungi used in biotechnology. • The properties and mechanisms underlying this phenomenon are very versatile. • Only studying these underlying mechanisms enables the design of a tailored solution.

A Nuclei-Based Conceptual Model of (Eco)evolutionary Dynamics in Fungal Heterokaryons

Filamentous fungi are characterised by specific features, such as multinuclearity, coexistence of genetically different nuclei and nuclear movement across the mycelial network. These attributes make them an interesting, yet rather underappreciated, system for studying (eco)evolutionary dynamics. This is especially noticeable among theoretical studies, where rather few consider nuclei and their role in (eco)evolutionary dynamics. To encourage such theoretical approaches, we here provide an overview of existing research on nuclear genotype heterogeneity (NGH) and its sources, such as mutations and vegetative non-self-fusion. We then discuss the resulting intra-mycelial nuclear dynamics and the potential consequences for fitness and adaptation. Finally, we formulate a nuclei-based conceptual framework, which considers three levels of selection: a single nucleus, a subpopulation of nuclei and the mycelium. We compare this framework to other concepts, for example those that consider only the mycelium as the level of selection, and outline the benefits of our approach for studying (eco)evolutionary dynamics. Our concept should serve as a baseline for modelling approaches, such as individual-based simulations, which will contribute greatly to our understanding of multilevel selection and (eco)evolutionary dynamics in filamentous fungi.

A gene cluster with positive and negative elements controls bistability and hysteresis of the Crippled versus Normal growth in the fungus Podospora anserina

The Crippled Growth (CG) cell degeneration of the model ascomycete Podospora anserina (strain S) is controlled by a prion-like element and has been linked to the self-activation of the PaMpk1 MAP kinase cascade. Here, we report on the identification of the "86-11" locus containing twelve genes, ten of which are involved either in setting up the self-activation loop of CG or in inhibiting this loop, as demonstrated by targeted gene deletion. Interestingly, deletion of the whole locus results only in the elimination of CG and in no detectable additional physiological defect. Sequence comparison shows that these ten genes belong to four different families, each one endowed with a specific activity: two encode factors activating the loop, a third one encodes a factor crucial for inhibition of the loop and the fourth one participates in inhibiting the loop in a pathway parallel to the one controlled by the previously described PDC1 gene. Intriguingly, a very distant homologue of this "86-11" locus is present at the syntenic position in Podospora comata (strain T) that do not present Crippled Growth. Introgression of the P. comata strain T locus in P. anserina strain S and the P. anserina strain S in P. comata strain T showed that both drive CG in the P. anserina strain S genetic background, but not in the genetic background of strain P. comata T, indicating that genetic determinants outside the twelve-gene locus are responsible for lack of CG in P. comata strain T. Our data question the role of this twelve-gene locus in the physiology of P. anserina.

Quantification and Isolation of Spontaneous Colony Growth Variants

The appearance of colony growth sectors on solid medium plates has been described in many fungi. Although the molecular bases of this phenomenon remain largely unknown, possible relationships with genetic or epigenetic changes have been reported. Here we present a method to quantify the frequency of colony growth sectors in Fusarium oxysporum, which can be used to compare different fungal strains and to infer their genetic instability.

Coinfection of domestic felines by distinct Sporothrix brasiliensis in the Brazilian sporotrichosis hyperendemic area

Microbial interactions may impact patient's diagnosis, prognosis and treatment. Sporotrichosis is a hyperendemic neglected zoonosis in Brazil, caused by Sporothrix brasiliensis. Four pairs of clinical isolates of Sporothrix were recovered from four diseased cats (CIM01-CIM04, two isolates per animal) raising the possibility of coinfection in a sporotrichosis hyperendemic area, Brazil. Each isolate of the pair had distinct pigmentation in mycological culture, and was designated as "Light" or "Dark", for low and high pigmentation, respectively. Dark isolates reacted strongly with monoclonal antibodies to melanin (p ≤ 0.05) by both ELISA and FACS quantitation, and displayed a ring pattern with some regions exhibiting higher punctuated labeling at cell wall by immunofluorescence. In turn, Light isolates reacted less intensely, with few and discrete punctuated labeling at the cell wall. PCR identified all isolates as S. brasiliensis, MAT1-2 idiomorph. Sequencing of β-tubulin and calmodulin genes followed by phylogenetic analysis placed all eight isolates within the same cluster as others from the Brazilian hyperendemic area. The ability of these strains to stimulate cytokine production by human PBMCs (Peripheral blood mononuclear cells) was also analyzed. CIM01 and CIM03 Light and Dark isolates showed similar cytokine profiles to the control strain, while CIM02 and CIM04 behaved differently (p < 0.001), suggesting that differences in the surface of the isolates can influence host-fungus interaction. MICs for amphotericin B, terbinafine, caspofungin, micafungin, itraconazole, fluconazole, and voriconazole were obtained (CLSI M38-A2/M27-A3). Pairwise comparisons showed distinct MICs between Sporothrix Light and Dark isolates, higher than at least two-fold dilutions, to at least one of the antifungals tested. Isolates from the same pair displayed discrepancies in relation to fungistatic or fungicidal drug activity, notably after itraconazole exposure. Since S. brasiliensis Light and Dark isolates show disparate phenotypic parameters it is quite possible that coinfection represents a common occurrence in the hyperendemic area, with potential clinical implications on feline sporotrichosis dynamics. Alternatively, future studies will address if this specie may have, as reported for other fungi, broad phenotypic plasticity.