Depression of uracil uptake by ammonium in Neurospora crassa

DNA affinity purification sequencing and transcriptional profiling reveal new aspects of nitrogen regulation in a filamentous fungus

Sensing available nutrients and efficiently utilizing them is a challenge common to all organisms. The model filamentous fungus Neurospora crassa is capable of utilizing a variety of inorganic and organic nitrogen sources. Nitrogen utilization in N. crassa is regulated by a network of pathway-specific transcription factors that activate genes necessary to utilize specific nitrogen sources in combination with nitrogen catabolite repression regulatory proteins. We identified an uncharacterized pathway-specific transcription factor, amn-1, that is required for utilization of the nonpreferred nitrogen sources proline, branched-chain amino acids, and aromatic amino acids. AMN-1 also plays a role in regulating genes involved in responding to the simple sugar mannose, suggesting an integration of nitrogen and carbon metabolism. The utilization of nonpreferred nitrogen sources, which require metabolic processing before being used as a nitrogen source, is also regulated by the nitrogen catabolite regulator NIT-2. Using RNA sequencing combined with DNA affinity purification sequencing, we performed a survey of the role of NIT-2 and the pathway-specific transcription factors NIT-4 and AMN-1 in directly regulating genes involved in nitrogen utilization. Although previous studies suggested promoter binding by both a pathway-specific transcription factor and NIT-2 may be necessary for activation of nitrogen-responsive genes, our data show that pathway-specific transcription factors regulate genes involved in the catabolism of specific nitrogen sources, while NIT-2 regulates genes involved in utilization of all nonpreferred nitrogen sources, such as nitrogen transporters. Together, these transcription factors form a nutrient sensing network that allows N. crassa cells to regulate nitrogen utilization.

A fungal transcription factor essential for starch degradation affects integration of carbon and nitrogen metabolism

In Neurospora crassa, the transcription factor COL-26 functions as a regulator of glucose signaling and metabolism. Its loss leads to resistance to carbon catabolite repression. Here, we report that COL-26 is necessary for the expression of amylolytic genes in N. crassa and is required for the utilization of maltose and starch. Additionally, the Δcol-26 mutant shows growth defects on preferred carbon sources, such as glucose, an effect that was alleviated if glutamine replaced ammonium as the primary nitrogen source. This rescue did not occur when maltose was used as a sole carbon source. Transcriptome and metabolic analyses of the Δcol-26 mutant relative to its wild type parental strain revealed that amino acid and nitrogen metabolism, the TCA cycle and GABA shunt were adversely affected. Phylogenetic analysis showed a single col-26 homolog in Sordariales, Ophilostomatales, and the Magnaporthales, but an expanded number of col-26 homologs in other filamentous fungal species. Deletion of the closest homolog of col-26 in Trichoderma reesei, bglR, resulted in a mutant with similar preferred carbon source growth deficiency, and which was alleviated if glutamine was the sole nitrogen source, suggesting conservation of COL-26 and BglR function. Our finding provides novel insight into the role of COL-26 for utilization of starch and in integrating carbon and nitrogen metabolism for balanced metabolic activities for optimal carbon and nitrogen distribution.

In nature, filamentous fungi sense nutrient availability in the surrounding environment and adjust their metabolism for optimal utilization, growth and reproduction. Carbon and nitrogen are two of major elements required for life. Within cells, signals from carbon and nitrogen catabolism are integrated, resulting in balanced metabolic activities for optimal carbon and nitrogen distribution. However, coordination of carbon and nitrogen metabolism is often missed in studies that are based on comparisons between single carbon or nitrogen sources. In this study, we performed systematic transcriptional profiling of Neurospora crassa on different components of starch and identified the transcription factor COL-26 to be an essential regulator for starch utilization and needed for coordinating carbon and nitrogen regulation and metabolism. Proteins with sequence similar to COL-26 widely exist among ascomycete fungi. Here we provide experimental evidence for shared function of a col-26 ortholog in Trichoderma reesei. Our finding provides novel insight into how the regulation of carbon and nitrogen metabolism can be integrated in filamentous fungi by the function of COL-26 and which may aid in the rational design of fungal strains for industrial purposes.

Properties of uracil transport by vegetative mycelium of Trichoderma viride

The transport of radioactively labelled uracil into submerged mycelium of T. viride was measured by means of a membrane filtration technique. It was found to be time-dependent (up to 90 min) and concentration-dependent (up to 8 mmol l-1). Its concentration dependence was biphasic and consisted from the saturatable part (at the uracil concentration below 0.2 mmol l-1) with KM = 0.08 +/- 0.02 mmol l-1 and Vmax = 1.74 +/- 0.3 nmol (mg dry wt.)-1 h-1, and from the region at higher uracil concentration which showed only a weak saturatability with the substrate. The transport measured in the saturatable part of the curve was also pH- and temperature-dependent. The optimal pH was between 5.4 and 6.4 and the optimal temperature was at 37 degrees C. The activation energy of 54 kJ mol-1 and the temperature quotient of Q10 = 2.1 could be calculated from the temperature dependence. The entry of uracil was in part inhibited by nucleobases and their analogues, nucleosides, nucleotides and amino acids. The inhibitors had similar inhibitory efficiency about 50% at 0.2 mmol l-1. 3,3',4',5-tetrachlorosalicylanilide (TCS), the uncoupling agent, significantly inhibited the uracil transport, but its inhibitory efficiency decreased upon increasing the uracil concentration. Ionophore antibiotics valinomycin and monensin also inhibited the uracil transport. Inhibitors of RNA-polymerase, rifamycin and rifampicin were without effect. The results suggest that at low uracil concentrations (below 0.2 mmol l-1), its transport is mediated by a carrier and is driven by the electrochemical potential of protons. At higher uracil concentrations, the transport may be driven by the concentration difference of uracil with the contribution of the protonmotive force. It is feasible that inhibitors of uracil transport tested exert their inhibition by the dissipation of the driving force rather than by the direct competition with the substrate-binding site.

Nitrogen metabolite repression of fluoropyrimidine resistance and pyrimidine uptake in Neurospora crassa

Wild type Neurospora crassa was shown to be more resistant to 5-fluoro-uracil, 5-fluoro-uridine and 5-fluoro-2'-deoxyuridine in the presence of ammonia than in its absence. This differential resistance may in part be accounted for by the observation that both uracil and uridine uptake in germinating conidia is under nitrogen metabolite regulation. The uptake of uracil and uridine is increased on poor nitrogen sources in wild type, is unaffected by nitrogen source in a nit-2 mutant strain while a gln-1 mutant strain showed intermediate behaviour. Wild type also showed increased resistance to all three fluoropyrimidines with increased temperature and both uracil and uptake in the wild type increased with temperature and both uracil and uridine uptake in the wild type increased with temperature.

Specificity of uracil uptake in Neurospora crassa

The specificity of uracil uptake was investigated in germinating wild-type conidia of Neurospora crassa. From comparative inhibition studies, several generalizations concerning the specificity of uracil uptake can be made. (i) The tautomeric forms of uracil analogs is an important determinant of recognition by the uptake system. (ii) Substituents at the 5 position of the pyrimidine ring may impose steric constraints on binding. (iii) The presence of a negative charge results in the loss of recognition. (iv) The double bond between the 5 and 6 carbons appears to be important for recognition. (v) Purine bases do not inhibit uracil uptake. Crude extracts of the transport-deficient mutant strain uc-5 pyr-1 were shown to have uridine 5'-monophosphate pyrophosphorylase activity comparable to that of the wild-type strain, suggesting that uracil uptake in Neurospora does not occur by a group translocation mechanism involving phosphoribosylation. Specificity studies of uridine 5'-monophosphate pyrophosphorylase indicated that phosphoribosylation was not an important determinant of the specificity of uracil uptake.

Pyrimidine metabolism in microplasmodia of Physarum polycephalum

If microplasmodia of Physarum polycephalum are exposed to 14C-labelled pyrimidine nucleosides or bases, an unusual pattern of metabolism is found. Only the nucleosides are taken up. Analysis of the distribution of the radioactivity in the cells revealed that ribonucleosides and deoxyribonucleosides are incorporated into nucleotides; however, a substantial catabolism takes place. Thus incubation with [2-14C]pyrimidine nucleosides readily gives rise to [14C]O2, particularly in the case of [2-14C]thymidine. Due to this a significant part of the trichloroacetic-acid-insoluble radioactivity from exogenously supplied [2-14C]thymidine is not associated with DNA. The pattern of labelling of nucleoside triphosphates from exogenously supplied nucleosides indicated that the de novo synthesis of nucleotides was only partly repressed. An unusual conversion of deoxycytidine into cytidine was noted. Enzyme analysis on cell-free extracts revealed that pyrimidine nucleosides can be salvaged by kinases and that their initial catabolism is initiated by hydrolases. Incubation of microplasmodia with pyrimidine analogues showed that only nucleoside analogues are toxic. The experimental results have led us to propose a scheme for the metabolism of pyrimidine nucleosides and bases in Physarum polycephalum.