Amber nonsense mutations in regulatory and structural genes of the nitrogen control circuit of Neurospora crassa

Summary Neurospora crassa possesses a set of nitrogen-regulated enzymes whose expression requires a lifting of nitrogen catabolite repression and specific induction. The nit-2 gene is a major regulatory locus which appears to act in a positive way to turn on the expression of these nitrogen-related enzymes whereas the nit-4 gene appears to mediate nitrate induction of nitrate and nitrite reductase. The nit-3 gene specifies nitrate reductase and is subject to control by both nit-2 and nit-4. Many new nit-2, nit-3, and nit-4 mutants were isolated in order to obtain amber nonsense mutations in these loci which were suppressible by the suppressor gene, Ssu-1. A nit-2 nonsense mutant was isolated which has altered regulatory properties for control of nitrate reductase, L-amino acid oxidase, and uricase, and which may encode a truncated regulatory protein. Four nit-3 nonsense mutations were isolated, each of which completely lacks nitrate reductase activity, which is restored to markedly different levels by suppression with Ssu-1. Studies of heat activation and thermal lability of nitrate reductase suggest a qualitative alteration of the enzyme occurs in two of the Ssu-1 nit-3 strains.     

Genetic analysis of nitrate reductase-deficient mutants in Chlamydomonas reinhardii

Summary Six mutants (305, 301, 203, 307, 104 and 102) of Chlamydomonas reinhardii, all defective in nitrate reductase (NR) activity, have been genetically analyzed. All except 102 carry single Mendelian mutations.Mutant 305, defective in diaphorase activity and mutant 301, defective in terminal enzyme activity, did not give rise to wild-type recombinants when crossed to each other or with the nit-1 mutant isolated from strain 137c (which is actually a double mutant nit-1 nit-2). Nit-1 was shown to lack both diaphorase and terminal activities. Whether the mutated sites in 305 and 301 are located in a unique cistron (nit-1) or in two adjacent cistrons (nit-1a and nit-1b) coding for a diaphorase subunit and a terminal subunit of NR is discussed in the light of previous biochemical findings.The 203 mutation affecting a regulatory gene did not recombine with nit-2, the other mutated locus present in strain 137c.Mutants 307, 104 and 102, all lacking molybdenum cofactor for both NR and xanthine dehydrogenase, where shown to be affected in different loci. The genes mutated in 307 and 104 have been designated nit-3 and nit-4, respectively. The 102 strain is mutated in two non-linked loci, nit-5 and nit-6, with both mutations required to confer the mutant phenotype. One of these cryptic mutations is present in the wild strain 21gr.The results indicate that at least six or seven loci are involved in the production of an active NR enzyme: one (nit-1) or two (nit-1a and nit-1b) cistrons to produce the NR apoproteins responsible for the partial activities diaphorase and terminal, one locus (nit-2) for the regulation of NR synthesis, and four loci (nit-3, nit-4, nit-5 and nit-6) to produce the molybdenum cofactor. The loci nit-1a and nit-2 seem to correspond to the nit-A and nit-B loci described by Nichols and Syrett (J Gen Microbiol 108:71–77, 1978).Abbreviations NR nitrate reductase - MNNG N-methyl-N-nitro-N-nitrosoguanidine - MoCo molybdenum-containing cofactor - PD parental ditype - NPD non-parental ditype - TT tetratype - WT wild type - BVH reduced benzyl viologen     

Molybdate repair of molybdopterin deficient mutants from Chlamydomonas reinhardtii

Summary The phenotypically wild strain I₃ of Chlamydomonas reinhardtii, carrying a cryptic mutation at the nit-6 locus, was distinguished from strains 21gr (cryptic mutant at nit-5) and 6145c (wild type) because of the ability of I₃ to grow on nitrate media containing 2mM tungstate.Molybdopterin-cofactor (MoCo) mutants 102 (double mutant at nit-5 and nit-6) and 104 (mutant at nit-4) grew on nitrate media supplemented with high concentrations of molybdate, although final cell densities were 40–60% lower and generation times 3.5 to six fold longer than for wild type. Under these conditions, nitrate reductase (NR) activity of the mutants, when measured either in situ or in vitro, was practically undetectable. The MoCo defective mutant 307 (nit-3) was not molybdate repairable. Although NR activity was not restored in vitro by molybdate in any of the MoCo^– mutant strains, their extracts had free NR-diaphorase subunits together with NR-subunits assembled into high molecular weight species.Our results indicate that: a) nit-4, nit-5 and nit-6 loci are responsible for molybdate processing in the cell; b) nit-3 may encode a component of the pterin moiety biosynthetic route; c) NR subunits can assemble in the presence of an inactive MoCo; d) high concentrations of molybdate can replace partially in vivo but not in vitro the function of nit-4 and the combined function(s) of the nit-5 and nit-6 gene products.     

Biochemical characterization of the molybdenum cofactor mutants of Neurospora crassa: in vivo and in vitro reconstitution of NADPH-nitrate reductase activity

Summary Molybdenum cofactor (MoCo) mutants of Neurospora crassa lack both NADPH-nitrate reductase and xanthine dehydrogenase activity. In vivo and in vitro studies to further characterize these mutants are now reported. The MoCo mutants nit-9A and nit-9B are capable of growing, albeit poorly, with nitrate as the sole nitrogen source, provided high levels of molybdate are present. The MoCo mutants nit-9A, nit-9B and nit-9C, but not nit-1, nit-7 or nit-8, have significant levels of NADPH-nitrate reductase when grown in nitrate medium containing 30 mM molybdate. In vitro reconstitution experiments using cell free extracts of the N. crassa MoCo mutants and E. coli HB101 as a source of wild-type MoCo were performed. MoCo from E. coli was capable of reconstituting NADPH-nitrate reductase activity to nit-1, nit-7 and nit-8. Molybdate is required for the in vitro reconstitution of NADPH-nitrate reductase activity. It was not possible to in vitro reconstitute NADPH-nitrate reductase activity in the MoCo mutants nit-9A, nit-9B or nit-9C.     

Cloning and preliminary characterization of a molybdenum cofactor gene of Neurospora crassa

Summary A Neurospora crassa library, constructed in a derivative of the plasmid pBR322 (pRK9), was used to transform two E. coli ch1D molybdenum cofactor mutants (ch1D, ch1D::Mu). Subsequently, one transformant from each of three independent transformation experiments was restriction mapped. All three transformants had an identical N. crassa DNA insert (4.2 kb). Southern Blot analysis with one of the plasmids (pMoCo, 1:4) showed hybridization to a single band of N. crassa genomic DNA. When pMoCo plasmid (1:4) was used to transform various E. coli nitrate reductase mutants (ch1A, ch1B, ch1C, ch1D, ch1E, ch1G and ch1M), the pMoCo plasmid was capable of restoring E. coli nitrate reductase activity to only the ch1D mutant. In vitro reconstitution experiments using wild-type, ch1D and ch1D; pMoCo cell-free extracts as a source of molybdenum cofactor (MoCo) were performed with the N. crassa MoCo mutants nit-1, nit-7 and nit-8. MoCo from wild-type E. coli cell-free extracts was capable of reconstituting NADPH : nitrate reductase activity to all three N. crassa mutants. MoCo from ch1D; pMoCo cell-free extracts was capable of reconstituting more NADPH : nitrate reductase activity to the N. crassa mutants than cell-free extracts from the original ch1D mutant.     

Developmental analysis of GFAP immunoreactivity in the cerebellum of the meander tail mutant mouse

It is thought that Bergmann glial fibers assist in the inward migration of granule cells. Model systems in which there is a perturbation of either the migrating cells or the glial cell population have been useful in understanding the migratory process. In the meander tail mutant mouse, the anterior cerebellar region is agranular, whereas the posterior cerebellum is relatively unaffected by the mutation. This study presents a qualitative analysis of the development of cerebellar radial glia in mea/mea and +/mea mice aged from postnatal day 0 to adult, using an antibody against the glia specific antigen, glial fibrillary acidic protein. The results indicate a slight delay in the onset of immunoreactivity in the mea/mea cerebellum and abnormal glial formation in the anterior and posterior regions by postnatal day 5. At postnatal day 11, the full complement of labeled fibers appears to be present and although they appear abnormal in formation, they eventually reach the surface and terminate in oddly shaped and irregularly spaced endfeet. In adult mea/mea and +/mea mice, as compared to the early postnatal stages, there is a significant reduction in GFAP immunoreactive fibers. Cresyl violet stained adult mea/mea sections revealed the presence of ectopic granule cells in radial columns and small clumps at the surface of and within the molecular layer of the caudal cerebellum. Quantitative analyses revealed a 4- to 5-fold increase in the number of ectopic granule cells in lobule VIII of the mea/mea when compared with the +/mea cerebellum. These results suggest that the radial glia in the mea/mea cerebellum exhibit some uncharacteristic morphologies, but that these abnormalities are most likely the consequence of environmental alterations produced by the mutant gene.     

Developmental analysis of GFAP immunoreactivity in the cerebellum of the meander tail mutant mouse

It is thought that Bergmann glial fibers assist in the inward migration of granule cells. Model systems in which there is a perturbation of either the migrating cells or the glial cell population have been useful in understanding the migratory process. In the meander tail mutant mouse, the anterior cerebellar region is agranular, whereas the posterior cerebellum is relatively unaffected by the mutation. This study presents a qualitative analysis of the development of cerebellar radial glia in mea/mea and +/mea mice aged from postnatal day 0 to adult, using an antibody against the glia specific antigen, glial fibrillary acidic protein. The results indicate a slight delay in the onset of immunoreactivity in the mea/mea cerebellum and abnormal glial formation in the anterior and posterior regions by postnatal day 5. At postnatal day 11, the full complement of labeled fibers appears to be present and although they appear abnormal in formation, they eventually reach the surface and terminate in oddly shaped and irregularly spaced endfeet. In adult mea/mea and +/mea mice, as compared to the early postnatal stages, there is a significant reduction in GFAP immunoreactive fibers. Cresyl violet stained adult mea/mea sections revealed the presence of ectopic granule cells in radial columns and small clumps at the surface of and within the molecular layer of the caudal cerebellum. Quantitative analyses revealed a 4- to 5-fold increase in the number of ectopic granule cells in lobule VIII of the mea/mea when compared with the +/mea cerebellum. These results suggest that the radial glia in the mea/mea cerebellum exhibit some uncharacteristic morphologies, but that these abnormalities are most likely the consequence of environmental alterations produced by the mutant gene.     

Transformants of Neurospora crassa with the nit-4 nitrogen regulatory gene: copy number,growth rate and enzyme activity

Summary nit-4 is a pathway-specific regulatory gene which controls nitrate assimilation in Neurospora crassa, and appears to mediate nitrate induction of nitrate and nitrite reductase. The NIT4 protein consists of 1090 amino-acid residues and possesses a single GAL4-like putative DNA-binding domain plus acidic, glutaminerich, and polyglutamine regions. Several mutants with amino-acid substitutions in the putative DNA-binding domain and a nit-4 deletion mutant, which encodes a truncated NIT4 protein lacking the polyglutamine region, are functional, i.e., they are capable of transforming a nit-4 mutant strain. However, transformants obtained with most of these nit-4 mutant genes possess a markedly reduced level of nitrate reductase and grow only slowly on nitrate, emphasizing the need to examine quantitatively the affects of in vitro-manipulated genes. The possibility that some mutant genes could yield transformants only if multiple copies were integrated was examined. The presence of multiple copies of wild-type or mutant nit-4 genes did not generally lead to increased enzyme activity or growth rate, but instead frequently appeared to be detrimental to nit-4 function. A hybrid nit-4-nirA gene transforms nit-4 mutants but only allows slow growth on nitrate and has a very low level of nitrate reductase.     

A single mutation leads to loss of glutamine synthetase and relief of ammonium repression in Aspergillus

Summary Glutamine synthetase activity in the ascomycete fungus Aspergillus nidulans is regulated by nitrogen source. The lowest activities are obtained when the fungus is grown on L-glutamine, and the highest activities when grown on L-glutamate + arabinose. Glutamine auxotrophs of the fungus have been isolated, and one of these mutant strains, glnA-1, has been shown to lack the enzyme glutamine synthetase. The mutation is recessive, and is located on the right arm of chromosome II. In addition to abolishing glutamine synthetase activity, the mutation results in the relief of repression for several enzyme activities normally subject to repression by ammonium. These include nitrate reductase, asparaginase, proline uptake and urea uptake.     

Biochemical characterization of a shikimic acid-resistant mutant of Nostoc linckia

The growth of Nostoc linckia was significantly inhibited by shikimic acid concentrations greater than 4.0 μg ml^?1 and was completely inhibited at 10.0μg ml^?1. Shikimic acid increased the duration of the lag phase and the doubling time and hastened the onset of the retardation phase of growth. A mutant (NL_shi) capable of growing in presence of 50 μg ml^?1 shikimic acid, was isolated by nitrosoguanidine mutagenesis from the wild type population at a frequency of about 1 × 10^?5 to 1 × 10^?6. The mutant grew slower than the wild type. Both the wild type and the mutant strain grew photoheterotrophically in light, with and without 3 (3–4 dichlorophenyl) 1,1-dimethyl urea (DCMU) and in darkness when provided with glucose. Glucose supplementation promoted ammonium uptake from the medium, when wild type and mutant were grown in an ammonium-supplemented medium. Glucose stimulated heterocyst production and nitrogenase activity in both the strains. As compared to wild type, this mutant showed higher heterocyst frequency and nitrate reductase activity but its ammonium uptake activity was lower. No significant difference in glutamine synthetase and nitrogenase activities of the mutant were observed. The mutant was stable and retained its resistance even after several subcultures through medium free of shikimic acid.     

Assimilatory nitrate reductase in a chlorate-resistant mutant of Escherichia coli

Nitrate reductase was investigated in extracts from cells of a chlorate-resistant mutant strain of E. coli which grew anaerobically on nitrate as the sole source of nitrogen. The nitrate reductase was of particulate nature and reduced chlorate like the nitrate reductase from the wild strain, but in contrast was inhibited only weakly by azide or cyanide. Nitrate reductase activity was found in extracts from the mutant cells grown on nitrate as the sole source of nitrogen, but not in extracts from cells grown in complex nutrient medium. Addition of ammonia also caused a decrease in activity. Accordingly, the nitrate reductase in the chlorateresistant mutant is of the assimilatory type.     

Nitrogen metabolite repression in Hansenula polymorpha: the nmr1-1 mutation

In Hansenula polymorpha, the expression of the nitrate assimilation metabolism is subjected to re-pression-derepression mechanisms triggered by reduced nitrogen compounds such as ammonium. To further our knowledge on the genetics of these regulatory mechanisms, a screening strategy for the isolation of mutants exhibiting nitrate reductase activities in the presence of reduced nitrogen compounds was set up. This strategy makes use of a nitrate+ methylamine mutant to isolate suppressors of its characteristic phenotype--the inability to grow on a nitrate plus methylamine medium. A total of 21 regulatory mutants were isolated with this strategy and grouped into five complementation classes. One of these mutants harbours the recessive mutation nmr1-1, which determines the derepression of the nitrate assimilation metabolism in media containing nitrate plus a repressing nitrogen source (ammonium, methylamine, glutamate, urea or aspartate). Therefore, nitrate reductase activities are detected in the presence of reduced nitrogen sources, as long as nitrate is also in the medium. Our data indicate that the processes of repression-derepression and induction are controlled by elements which are distinct. Furthermore, they indicate that Nmrlp is involved in repressing circuits which control not only the nitrate-utilisation pathway, but also other pathways which are necessary for the utilisation of nitrogen sources alternative to ammonium. Of considerable interest is the fact that our nmr1-1 mutant is derepressed in glutamate but not in glutamine. Since the phenotype of this mutant seems to exclude a glutamine synthetase defect, we suggest that glutamate (or a derivative of this compound) might be involved in signalling nitrogen metabolite repression in H. polymorpha. Thus, in H. polymorpha, a glutamine-dependent circuit may co-exist with a glutamine-independent circuit.     

Cloning of the nitrate reductase gene of Stagonospora (Septoria) nodorum and its use as a selectable marker for targeted transformation

The nitrate reductase gene (NIA1) of the phytopathogenic fungus Stagonospora (Septoria) nodorum has been cloned from a cosmid library by homologous hybridisation with a PCR-generated probe. A 6.7-kb fragment carrying the NIA1 gene was subcloned and partially characterised by restriction mapping. Sequencing of the gene indicated a high degree of homology, both at the nucleotide and amino-acid levels, with nitrate reductase genes of other filamentous fungi. Furthermore, consensus regulatory signals thought to be involved in the control of nitrogen metabolism are present in the 5′ flanking region. The cloned NIA1 gene has been used to develop a gene-transfer system based on nitrate assimilation. Stable nia1 mutants of S. nodorum defective in nitrate reductase were isolated by virtue of their resistance to chlorate. These were transformed back to nitrate utilisation with the wild-type S. nodorum NIA1 gene. Southern analyses revealed that transformation occurred as a result of the integration of transforming DNA into the fungal genome; in all cases examined, integration was targeted to the homologous sequence. Received: 30 March / 9 June 1998     

NIT2, the nitrogen regulatory protein of Neurospora crassa,binds upstream of nia,the tomato nitrate reductase gene,in vitro

Summary The nit-2 gene of Neurospora crassa encodes a trans-acting regulatory protein that activates the expression of a number of structural genes which code for nitrogen catabolic enzymes, including nitrate reductase. The NIT2 protein contains a Cys2/Cys2-type zinc-finger DNA-binding domain that recognizes promoter regions of the Neurospora nitrogen-related genes. The NIT2 zincfinger domain/-Gal fusion protein was shown to recognize and bind in a specific manner to two upstream fragments of the nia gene of Lycopersicon esculentum (tomato) in vitro, whereas two mutant NIT2 proteins failed to bind to the same fragments. The dissociation kinetics of the complexes formed between the NIT2 protein and the Neurospora nit-3 and the tomato nia gene promoters were examined; NIT2 binds more strongly to the nit-3 promoter DNA fragment than it does to fragments derived from the plant nitrate reductase gene itself. The observed specificity of the binding suggests the existence of a NIT2-like homolog which regulates the expression of the nitrate assimilation pathway of higher plants.     

Glucosamine-resistant mutations in yeast affecting the glucose repression sensitivity of electron transport enzymes

Summary We have isolated two mutant strains, GSA^r-4 and GSA^r-5, which are able to grow on lactate in the presence of D-glucosamine. The glucosamine-resistant phenotype results from the cooperative effects of mutations in three loci, GAR1, GAR2 and GAR3. Both glucosamine resistant mutant strains were doubly mutant at gar1 gar2 (GSA^r-4) or gar1 gar3 (GSA^r-5). The mutants were also shown to exhibit glucose repression insensitive synthesis of NADH-cytochrome c reductase and cytochrome c oxidase. Glucose-repressible synthesis of the following enzymes was seen: succinic dehydrogenase, succinic: cytochrome c reductase, maltase (PNPGase), galactokinase, -galactokinase. The glucose-repression insensitivity segregates in association with the glucosamine resistance.     

Cloning and biochemical characterization of LYS5 gene of Saccharomyces cerevisiae

Summary In Saccharomyces cerevisiae, the functions of two unlinked genes (LYS2 and LYS5) are required for the synthesis of the lysine biosynthetic enzyme, -aminoadipate reductase. The LYS5 gene of S. cerevisiae was cloned by functional complementation of a lys5 mutant, X4004-3A, using a YEp24 plasmid library. The cloned LYS5 gene was contained within a 7.5 kb DNA insert of the recombinant plasmid pSC5. Cloning of LYS5 gene was confirmed by second cycle transformation of a lys5 mutant with the pSC5 plasmid, growth response studies, and plasmid loss experiments with Lys5 ⁺ transformants. Analysis of restriction digests of the pSC5 plasmid revealed 3 EcoRI, 5 PvuII, 1 PstI, 1 BglII and 2 HpaI sites in the 7.5 kb insert. A 3.9 kb internal pSC5 fragment hybridized only to the plasmid pSC5, but no homology was observed with LYS2 DNA or the YEp24 vector. The pSC5 transformed Lys5 ⁺ cells and the wild-type strain exhibited same level of -aminoadipate reductase activity, whereas lys5 mutant and plasmid-cured transformed strain exhibited none. Lys2 ⁺ transformants consistently had five times greater -aminoadipate reductase activity when compared with the wildtype and the Lys5 ⁺ transformant. The -aminoadipate reductase activity was repressed in lysine-grown wildtype and Lys5 ⁺ transformed cells but not in Lys2 ⁺ transformed cells. A Lys2 ⁺ and Lys5 ⁺ double transformant exhibited higher a-aminoadipate reductase activity than lys2 ⁺ or lys5 ⁺ transformant.     

Inhibition of nitrite reductase and urease by arginine and proline in the cyanobacterium Anabaena cycadeae

The arginine and proline inhibition of nitrite reductase and urease activities have been studied in the cyanobacterium Anabaena cycadeae and its mutant strain lacking glutamine synthetase (GS)¹) activity. Arginine and proline inhibited the nitrite reductase and urease activities in the parent strain, however, they could not do so in the mutant strain. The level of arginine- and proline-dependent NH production in the outer medium was several fold higher in the mutant strain as compared to its parent strain. These results suggest that (1) nitrite reductase and urease activities are arginine- and proline-repressible; (2) the catalytic function of GS is necessarily required for the arginine and proline inhibition of nitrite reductase and urease systems; and (3) the NH resulting from the catabolism of arginine and proline should be metabolized via GS for repression of nitrite reductase and urease to occur.     

Assimilatory reduction of nitrate in Rhizobium meliloti

Nitrate and nitrite reductases in the crude extract of aerobically grown Rhizobium meliloti were determined with methylviologen as electron donor at pH 7. Nitrate reductase was detected in the cells grown in the medium that did not contain nitrate, and in the presence of nitrate the specific activity increased about 2-fold. Nitrite reductase was induced by nitrate and produced ammonia from nitrite. In nitrate reducing cells, two kinds of O₂ labile nitrate reductase were found. One enzyme had optimal pH at 7 and was stabilized to O₂ by treating with DEAE-Toyopearl 650M. The other had optimal pH at 9 and was stabilized by the addition of dithiothreitol and EDTA. Nitrate reductase stabilized by DEAE-Toyopearl 650M treatment was purified 3,360-fold from crude extract. The purified enzyme showed a single protein band in polyacrylamide gel electrophoresis, and there was no absorption peak in the visible region. It had a molecular weight of 64,000 in SDS PAGE and 58,000 on Sephadex G-100 gel filtration. K_m for nitrate was 0.9 mM. It was inhibited by p-chloromercuribenzoate, cyanide, and α,α'-dipyridyl.     

The expression profile of the <Emphasis Type="Italic">Tuber borchii</Emphasis> nitrite reductase suggests its positive contribution to host plant nitrogen nutrition

Ectomycorrhizal symbiosis is a ubiquitous association between plant roots and numerous fungal species. One of the main aspects of the ectomycorrhizal association are the regulation mechanisms of fungal genes involved in nitrogen acquisition. We report on the genomic organisation of the nitrate gene cluster and functional regulation of tbnir1, the nitrite reductase gene of the ectomycorrhizal ascomycete Tuber borchii. The sequence data demonstrate that clustering also occurs in this ectomycorrhizal fungus. Within the TBNIR1 protein sequence, we identified three functional domains at conserved positions: the FAD box, the NADPH box and the two (Fe/S)-siroheme binding site signatures. We demonstrated that tbnir1 presents an expression pattern comparable to that of nitrate transporter. In fact, we found a strong down-regulation in the presence of primary nitrogen sources and a marked tbnir1 mRNA accumulation following transfer to either nitrate or nitrogen limited conditions. The real-time PCR assays of tbnir1 and nitrate transporter revealed that both nitrate transporter and nitrite reductase expression levels are about 15-fold and 10-fold higher in ectomycorrhizal tissues than in control mycelia, respectively. The results reported herein suggest that the symbiotic fungus Tuber borchii contributes to improving the host plant’s ability to make use of nitrate/nitrite in its nitrogen nutrition.