Terricoxanthones A-E, unprecedented dihydropyran-containing dimeric xanthones from the endophytic fungus Neurospora terricola HDF-Br-2 associated with the vulnerable conifer Pseudotsuga gaussenii

An investigation on the secondary metabolites from a rice culture broth of the endophytic fungus Neurospora terricola HDF-Br-2 derived from the vulnerable conifer Pseudotsuga gaussenii led to the isolation and characterization of 34 structurally diverse polyketides (1-34). Seven of them are previously undescribed, including five unprecedented dihydropyran-containing (terricoxanthones A-E, 1-5, resp.) and one rare tetrahydrofuran-containing (terricoxanthone F, 6) dimeric xanthones. The structures were elucidated by spectroscopic methods and single-crystal X-ray diffraction analyses. Terricoxanthones each were obtained as a racemic mixture. Their plausible biosynthetic relationships were briefly proposed. Compounds 6, aspergillusone A (8), and alatinone (27) displayed considerable inhibition against Candida albicans with MIC values of 8-16 μg/mL. 4-Hydroxyvertixanthone (12) and 27 exhibited significant inhibitory activities against Staphylococcus aureus, with MIC values of 4-8 μg/mL. Furthermore, compounds 8 and 27 could disrupt biofilm of S. aureus and C. albicans at 128 μg/mL. The findings not only extend the skeletons of xanthone dimers and contribute to the diversity of metabolites of endophytes associated with the endangered Chinese conifer P. gaussenii, but could further reveal the important role of protecting plant species diversity in support of chemical diversity and potential sources of new therapeutics.

Sensing of H2O2-induced oxidative stress by the UPF factor complex is crucial for activation of catalase-3 expression in Neurospora

UPF-1-UPF-2-UPF-3 complex-orchestrated nonsense-mediated mRNA decay (NMD) is a well-characterized eukaryotic cellular surveillance mechanism that not only degrades aberrant transcripts to protect the integrity of the transcriptome but also eliminates normal transcripts to facilitate appropriate cellular responses to physiological and environmental changes. Here, we describe the multifaceted regulatory roles of the Neurospora crassa UPF complex in catalase-3 (cat-3) gene expression, which is essential for scavenging H2O2-induced oxidative stress. First, losing UPF proteins markedly slowed down the decay rate of cat-3 mRNA. Second, UPF proteins indirectly attenuated the transcriptional activity of cat-3 gene by boosting the decay of cpc-1 and ngf-1 mRNAs, which encode a well-studied transcription factor and a histone acetyltransferase, respectively. Further study showed that under oxidative stress condition, UPF proteins were degraded, followed by increased CPC-1 and NGF-1 activity, finally activating cat-3 expression to resist oxidative stress. Together, our data illustrate a sophisticated regulatory network of the cat-3 gene mediated by the UPF complex under physiological and H2O2-induced oxidative stress conditions.

A case of Neurospora sitophila causing PD peritonitis

We describe a rare case of fungal peritoneal dialysis (PD) peritonitis caused by the ascomycete fungus Neurospora sitophila (N. sitophila). The patient had little response to initial antibiotics and PD catheter removal was necessary for source control. The fungal biomarker β-d-glucan (BDG) was positive prior to N. sitophila being cultured and remained positive for 6 months after discharge. Use of BDG early in the assessment of PD peritonitis may reduce time to definitive therapy in fungal peritonitis.

Cryptochrome 1 as a state variable of the circadian clockwork of the suprachiasmatic nucleus: Evidence from translational switching

The suprachiasmatic nucleus (SCN) of the hypothalamus is the principal clock driving circadian rhythms of physiology and behavior that adapt mammals to environmental cycles. Disruption of SCN-dependent rhythms compromises health, and so understanding SCN time keeping will inform management of diseases associated with modern lifestyles. SCN time keeping is a self-sustaining transcriptional/translational delayed feedback loop (TTFL), whereby negative regulators inhibit their own transcription. Formally, the SCN clock is viewed as a limit-cycle oscillator, the simplest being a trajectory of successive phases that progresses through two-dimensional space defined by two state variables mapped along their respective axes. The TTFL motif is readily compatible with limit-cycle models, and in Neurospora and Drosophila the negative regulators Frequency (FRQ) and Period (Per) have been identified as state variables of their respective TTFLs. The identity of state variables of the SCN oscillator is, however, less clear. Experimental identification of state variables requires reversible and temporally specific control over their abundance. Translational switching (ts) provides this, the expression of a protein of interest relying on the provision of a noncanonical amino acid. We show that the negative regulator Cryptochrome 1 (CRY1) fulfills criteria defining a state variable: ts-CRY1 dose-dependently and reversibly suppresses the baseline, amplitude, and period of SCN rhythms, and its acute withdrawal releases the TTFL to oscillate from a defined phase. Its effect also depends on its temporal pattern of expression, although constitutive ts-CRY1 sustained (albeit less stable) oscillations. We conclude that CRY1 has properties of a state variable, but may operate among several state variables within a multidimensional limit cycle.

for improving ammonia production during thermophilic composting of organic sludge

Recent attempts have been made to develop a thermophilic composting process for organic sludge to not only produce organic fertilizers and soil conditioners, but to also utilize the generated ammonia gas to produce high value-added algae. The hydrolysis of organic nitrogen in sludge is a bottleneck in ammonia conversion, and its improvement is a major challenge. The present study aimed to elucidate the effects of inoculated Neurospora sp. on organic matter decomposition and ammonia conversion during thermophilic composting of two organic sludge types: anaerobic digestion sludge and shrimp pond sludge. A laboratory-scale sludge composting experiment was conducted with a 6-day pretreatment period at 30 °C with Neurospora sp., followed by a 10-day thermophilic composting period at 50 °C by inoculating the bacterial community. The final organic matter decomposition was significantly higher in the sludge pretreated with Neurospora sp. than in the untreated sludge. Correspondingly, the amount of non-dissolved nitrogen was also markedly reduced by pretreatment, and the ammonia conversion rate was notably improved. Five enzymes exhibiting high activity only during the pretreatment period were identified, while no or low activity was observed during the subsequent thermophilic composting period, suggesting the involvement of these enzymes in the degradation of hardly degradable fractions, such as bacterial cells. The bacterial community analysis and its function prediction suggested the contribution of Bacillaceae in the degradation of easily degradable organic matter, but the entire bacterial community was highly incapable in degrading the hardly degradable fraction. To conclude, this study is the first to demonstrate that Neurospora sp. decomposes those organic nitrogen fractions that require a long time to be decomposed by the bacterial community during thermophilic composting.

Starch and protein recovery from brewer's spent grain using hydrothermal pretreatment and their conversion to edible filamentous fungi - A brewery biorefinery concept

This study aimed at recovering a highly concentrated starch and protein stream from the brewer's spent grain (BSG). The effect of pretreatment temperature and retention time on the solubilization of starch and protein; and the generation of fermentation inhibitors were studied. Then, the application of recovered streams for fungal cultivation was evaluated using different edible fungi Aspergillus oryzae, Neurospora intermedia, and Rhizopus delemar. The hydrothermal pretreatment resulted in the highest solubilized starch concentration, 43 g/L, corresponding to 83% solubilization of initial BSG starch content. The highest protein concentration was 27 g/L (48% solubilization of initial BSG protein content). Cultivation with Neurospora intermedia on the recovered streams from the two best pretreatment conditions, 140 ℃ for 4 h and 180 ℃ for 30 min, resulted in pure fungal biomass with the highest protein content 59.62% and 50.42% w/w, respectively. Finally, a brewery biorefinery was proposed for the valorization of BSG.

Occupational exposure to fungi on recyclable paper pots and growing media and associated health effects - A review of the literature

Different types of pots and growing and casing media, including biodegradable materials, are used for plant and mushroom production. The fungus Peziza ostracoderma has gained attention for its visible growth on growing media for plants and casing media for mushrooms. Through a review of the literature we aim to evaluate whether exposure to fungi from recyclable pots and different growing and casing media occurs and causes occupational health effects. Based on the published papers, specific fungal species were not related to a specific medium. Thus P. ostracoderma has been found on paper pots, peat, sterilized soil, vermiculite, and rockwool with plants, and on peat, pumice, and paper casing for mushrooms. It has been found in high concentrations in the air in mushroom farms. Also Acremonium spp., Aspergillus niger, A. fumigatus, Athelia turficola, Aureobasidium pullulans, Chaetomium globosum, Chrysonilia sitophila, Cladosporium spp., Cryptostroma corticale, Lecanicillium aphanocladii, Sporothrix schenckii, Stachybotrys chartarum, and Trichoderma spp. have been found on different types of growing or casing media. Most of the fungi have also been found in the air in greenhouses, but the knowledge about airborne fungal species in mushroom farms is very limited. Eight publications describe cases of health effects associated directly with exposure to fungi from pots or growing or casing media. These include cases of hypersensitivity pneumonitis caused by exposure to: A. fumigatus, A. niger, Au. pullulans, Cr. corticale, P. ostracoderma, and a mixture of fungi growing on different media. Different approaches have been used to avoid growth of saprophytes including: chemical fungicides, the formulation of biodegradable pots and growing media and types of peat. To increase the sustainability of growing media different types of media are tested for their use and with the present study we highlight the importance of also considering the occupational health of the growers who may be exposed to fungi from the media and pots.

Genetic recombination in Neurospora crassa and N. sitophila

Mutant genes in linkage groups I (mating-type chromosome), VI and VII have been transferred from Neurospora crassa to N. sitophila by hybridization and repeated backcrossing. Recombination between these genes has been studied from five-point crosses involving linkage group I and three-point crosses involving linkage groups VI and VII of the two species.

The results show significant differences in the amount of recombination between some of the genes in the proximal regions of the mating-type chromosomes of the two species. They indicate proximal localization of crossovers in the mating-type chromosome of N. sitophila. The results also show significant differences in recombination frequency between the genes in linkage group VI and a close similarity in linkage group VII. They further show that the centromere in the two species may not be interfering with crossing-over in its vicinity to such an extent as to be of any evolutionary significance.

An ATP gate controls tubulin binding by the tethered head of kinesin-1

Kinesin-1 is a two-headed molecular motor that walks along microtubules, with each step gated by adenosine triphosphate (ATP) binding. Existing models for the gating mechanism propose a role for the microtubule lattice. We show that unpolymerized tubulin binds to kinesin-1, causing tubulin-activated release of adenosine diphosphate (ADP). With no added nucleotide, each kinesin-1 dimer binds one tubulin heterodimer. In adenylyl-imidodiphosphate (AMP-PNP), a nonhydrolyzable ATP analog, each kinesin-1 dimer binds two tubulin heterodimers. The data reveal an ATP gate that operates independently of the microtubule lattice, by ATP-dependent release of a steric or allosteric block on the tubulin binding site of the tethered kinesin-ADP head.

Conformational coupling between the cytoplasmic carboxylic acid and the retinal in a fungal light-driven proton pump

Many fungal rhodopsins, eukaryotic structural homologues of the archaeal light-driven proton pump bacteriorhodopsin, have been discovered in the course of genome sequencing projects. Recently, two fungal rhodopsins were characterized in vitro and exhibited very different photochemical behavior. Neurospora rhodopsin possesses a slow photocycle and shows no ion transport, reminiscent of sensory rhodopsins, while Leptosphaeria rhodopsin has a fast bacteriorhodopsin-like photocycle and pumps protons light-dependently. Such a dramatic difference is surprising considering the very high degree of sequence homology of the two proteins. In this paper, we investigate whether the chemical structure of a cytoplasmic carboxylic acid, the homologue of Asp-96 of bacteriorhodopsin serving as a proton donor for the retinal Schiff base, can define the photochemical properties of fungal rhodopsins. We studied mutants of Leptosphaeria rhodopsin in which this aspartic acid was replaced with Glu or Asn using spectroscopy in the infrared and visible ranges. We show that Glu at this position is inefficient as a proton donor similar to a nonprotonatable Asn. Moreover, this replacement induces long-range structural perturbations of the retinal environment, as evidenced by changes in the vibrational bands of retinal (especially, hydrogen-out-of-plane modes) and neighboring aspartic acids and water molecules. The conformational coupling of the mutation site to the retinal may be mediated by helical rearrangements as suggested by the changes in amide and proline vibrational bands. We conclude that the difference in the photochemical behavior of fungal rhodopsins from Leptosphaeria and Neurospora may be ascribed, to some extent, to the replacement of the cytoplasmic proton donor Asp with Glu.

Circadian rhythms and molecular noise

Circadian rhythms, characterized by a period of about 24 h, are the most widespread biological rhythms generated autonomously at the molecular level. The core molecular mechanism responsible for circadian oscillations relies on the negative regulation exerted by a protein on the expression of its own gene. Deterministic models account for the occurrence of autonomous circadian oscillations, for their entrainment by light-dark cycles, and for their phase shifting by light pulses. Stochastic versions of these models take into consideration the molecular fluctuations that arise when the number of molecules involved in the regulatory mechanism is low. Numerical simulations of the stochastic models show that robust circadian oscillations can already occur with a limited number of mRNA and protein molecules, in the range of a few tens and hundreds, respectively. Various factors affect the robustness of circadian oscillations with respect to molecular noise. Besides an increase in the number of molecules, entrainment by light-dark cycles, and cooperativity in repression enhance robustness, whereas the proximity of a bifurcation point leads to less robust oscillations. Another parameter that appears to be crucial for the coherence of circadian rhythms is the binding/unbinding rate of the inhibitory protein to the promoter of the clock gene. Intercellular coupling further increases the robustness of circadian oscillations.

RNA silencing in fungi: Mechanisms and applications

Two RNA silencing-related phenomena, quelling and meiotic silencing by unpaired DNA (MSUD) have been identified in the fungus Neurospora crassa. Similar to the case with the siRNA and miRNA pathways in Drosophila, different sets of protein components including RNA-dependent RNA polymerase, argonaute and dicer, are used in the quelling and MSUD pathways. Orthologs of the RNA silencing components are found in most, but not all, fungal genomes currently available in the public databases, indicating that the majority of fungi possess the silencing machinery. Advantage and disadvantage of RNA silencing as a tool to explore gene function in fungi are discussed.

Insight into mitochondrial structure and function from electron tomography

In recent years, electron tomography has provided detailed three-dimensional models of mitochondria that have redefined our concept of mitochondrial structure. The models reveal an inner membrane consisting of two components, the inner boundary membrane (IBM) closely apposed to the outer membrane and the cristae membrane that projects into the matrix compartment. These two components are connected by tubular structures of relatively uniform size called crista junctions. The distribution of crista junction sizes and shapes is predicted by a thermodynamic model based upon the energy of membrane bending, but proteins likely also play a role in determining the conformation of the inner membrane. Results of structural studies of mitochondria during apoptosis demonstrate that cytochrome c is released without detectable disruption of the outer membrane or extensive swelling of the mitochondrial matrix, suggesting the formation of an outer membrane pore large enough to allow passage of holo-cytochrome c. The possible compartmentation of inner membrane function between the IBM and the cristae membrane is also discussed.

Rapid formation of a solvent-inaccessible core in the Neurospora Varkud satellite ribozyme

We have used hydroxyl radicals generated by decomposition of peroxynitrous acid to study Mg(2+)-dependent structure and folding of the Varkud satellite (VS) ribozyme. Protection from radical cleavage shows the existence of a solvent-inaccessible core, which includes nucleotides near two three-helix junctions, the kissing interaction between stem-loops I and V and other nucleotides, most of which have also been implicated as important for folding or activity. Kinetic folding experiments showed that the ribozyme folds very quickly, with the observed protections completely formed within 2 s of addition of MgCl(2). In mutants that disrupt the kissing interaction or entirely remove stem-loop I, which contains the cleavage site, nucleotides in the three-helix junctions and a subset of those elsewhere remain protected. Unlike smaller ribozymes, the VS ribozyme retains a significant amount of structure in the absence of its substrate. Protections that depend on proper interaction between the substrate and the rest ribozyme map to a region previously proposed as the active site of the ribozyme and along both sides of helix II, identifying candidate sites of docking for the substrate helix.

Modeling circadian oscillations with interlocking positive and negative feedback loops

Both positive and negative feedback loops of transcriptional regulation have been proposed to be important for the generation of circadian rhythms. To test the sufficiency of the proposed mechanisms, two differential equation-based models were constructed to describe the Neurospora crassa and Drosophila melanogaster circadian oscillators. In the model of the Neurospora oscillator, FRQ suppresses frq transcription by binding to a complex of the transcriptional activators WC-1 and WC-2, thus yielding negative feedback. FRQ also activates synthesis of WC-1, which in turn activates frq transcription, yielding positive feedback. In the model of the Drosophila oscillator, PER and TIM are represented by a "lumped" variable, "PER." PER suppresses its own transcription by binding to the transcriptional regulator dCLOCK, thus yielding negative feedback. PER also binds to dCLOCK to de-repress dclock, and dCLOCK in turn activates per transcription, yielding positive feedback. Both models displayed circadian oscillations that were robust to parameter variations and to noise and that entrained to simulated light/dark cycles. Circadian oscillations were only obtained if time delays were included to represent processes not modeled in detail (e.g., transcription and translation). In both models, oscillations were preserved when positive feedback was removed.

Circadian photoperception

The circadian clock is intrinsically linked to the daily cycle of day and night. A capacity for entrainment to light-dark cycles has proven to be a universal feature of the clock in all organisms examined. Here we review a wealth of recent advances that reveal more about the light input mechanisms by which the circadian clock is set to the correct time in a range of different systems. Now that we are identifying more of the molecular components of both the light input pathway and the clock mechanism itself, we are becoming increasingly less able to distinguish between the two.

Efficient method for selection of auxotrophic mutants of Neurospora

A technique for the selection of induced and spontaneous auxotrophic mutants of Neurospora in relatively high frequency is described. The method takes advantage of the reduced rate of death of germinating conidia of an inositol-requiring strain when a secondary mutation is imposed.