Nitrate reductase of Neurospora crassa: the functional role of individual amino acids in the heme domain as examined by site-directed mutagenesis

The enzyme nitrate reductase, which catalyzes the reduction of nitrate to nitrite, is a multi-redox center homodimeric protein. Each polypeptide subunit is approximately 100 kDa in size and contains three separate domains, one each for a flavin, a heme-iron, and a molybdopterin cofactor. The heme-iron domain of nitrate reductase has homology with the simple redox protein, cytochrome b5, whose crystal structure was used to predict a three-dimensional structure for the heme domain. Two histidine residues have been identified that appear to coordinate the iron of the heme moiety, while other residues may be important in the folding or the function of the heme pocket. Site-directed mutagenesis was employed to obtain mutants that encode nitrate reductase derivatives with eight different single amino acid substitutions within the heme domain, including the two central histidine residues. Replacement of one of these histidines by alanine resulted in a completely nonfunctional enzyme whereas replacement of the other histidine resulted in a stable and functional enzyme with a lower affinity for heme. Certain amino acid substitutions appeared to cause a rapid turnover of the heme domain, whereas other substitutions were tolerated and yielded a stable and fully active enzyme. Three different single amino acid replacements within the heme domain led to a dramatic change in regulation of nitrate reductase synthesis, with significant expression of the enzyme even in the absence of nitrate induction.     

Regulation of synthesis of ribosomal protein in Neurospora crassa

In Neurospora crassa during a nutritional shift-down transition of growth, the synthesis of rRNA is for about 2 h largely inhibited and the rate of protein synthesis is only partially reduced (by about 25 %). During this period the relative rate of synthesis of individual ribosomal proteins, measured irrespectively of their incorporation into ribosomes, is reduced by 70–80%. The ribosomal proteins synthesized during the shift are stable. Thus, the synthesis of ribosomal proteins appears in N. crassa to be coordinately regulated with that of rRNA.     

Nitrate reductase and its role in nitrate assimilation in plants

Nitrate reductase (EC 1.6.6.1) is an enzyme found in most higher plants and appears to be a key regulator of nitrate assimilation as a result of enzyme induction by nitrate. The biochemistry of nitrate reductase has been elucidated to a great extent and the role that nitrate reductase plays in regulation of nitrate assimilation is becoming understood.     

An EPR analysis of cyanide-resistant mitochondria isolated from the mutant poky strain of Neurospora crassa

An analysis of the paramagnetic components present in mitochondria isolated from the poky mutant of Neurospora crassa is described. The study was undertaken with a view to shedding light on the nature of the cyanide- and antimycin A-resistant alternative terminal oxidase which is present in these preparations.

Of the ferredoxin-type iron-sulfur centers, only Centers S-1 and S-2 of succinate dehydrogenase could be detected in significant quantities. Paramagnetic centers attributable to Site I were virtually absent. In the oxidized state, at least two ‘high potential iron sulfur’ centers could be distinguished and these were attributed to Center S-3 of succinate dehydrogenase and a second component analogous to that found in mammalian systems. Much of the Center S-3 signal was in a highly distorted state which was apparently dependent upon the presence of an accompanying free radical species. At lower field positions, a succinate-reducible signal peaking around g = 3.15 was found. This signal is caused by a low spin heme species, presumably the cytochrome c which is the only major cytochrome in these mitochondria. At even lower field positions, signals attributable to iron in a field of low symmetry at g = 4.3 and multiple high spin heme species around g = 6, could be distinguished.

The effects of salicylhydroxamic acid, an inhibitor of the alternative oxidase, were tested on these components. Effects could be seen on at least one high spin heme component and also partially upon the distorted Center S-3 signal converting part of it to a signal indistinguishable from Center S-3. Some increase in the g = 4.3 iron signal was also noted. No effects of the inhibitor on the ferredoxin-type centers were detected.

These results are interpreted with respect to the nature and location of the alternative oxidase and with respect to possible models for the nature of the alternative oxygen-consuming component.     

Uptake and efflux of sulfate in Neurospora crassa

Sulfate efflux from an intracellular pool was observed with both wild-type and cys-11 cells of Neurospora and apparently occurs by way of the sulfate transport system. Efflux requires the presence of external sulfate or the related ions, chromate, selenate, or thiosulfate, and probably occurs by an exchange reaction. The sulfur amino acids, cysteine or methionine, do not promote sulfate efflux. The K_m for efflux is much greater than the K_m for sulfate uptake, which permits the accumulation of a considerable intracellular pool before efflux becomes significant. Substantial transmembrane movement of sulfate both influx and exit, was found to occur in azidetreated cells, although the net uptake of sulfate was abolished by this inhibitor. Both sulfate uptake and efflux are inhibited by p-chloromercuribenzoate which suggests that the sulfate permease possesses an essential sulfhydryl group.     

Ribosomal DNA inheritance and recombination in Neurospora crassa

Summary The genetic segregation of ribosomal DNA (rDNA) in Neurospora crassa was analyzed by exploiting restriction fragment length polymorphisms in the nontranscribed spacer (NTS) sequences of nine laboratory wild-type strains and wild-collected strains. In an analysis of random spore progeny from seven crosses, and of ordered tetrads from two of those crosses the rDNA was shown to be inherited in a simple, stable Mendelian fashion, exhibiting an approximately 1:1 ratio of the two parental rDNA types. No meiotic recombinants were detected among the progeny, indicating that non-sister-chromatid crossing over is highly suppressed in the rDNA region. The basis for this suppression of meiotic recombination is not known.     

Molecular cloning and characterization of alc the gene encoding allantoicase of Neurospora crassa

Summary Purrtins can be utilized as a secondary nitrogen source by Neurospora crassa during conditions of nitrogen limitation. The expression of purine catabolic enzymes is governed by the nitrogen regulatory circuit and requires induction by uric acid. The major positive-acting nitrogen regulatory gene, nit-2, turns on the expression of the purine catabolic enzymes, which may also be subject to negative regulation by a second control gene, nmr. We have cloned alc, the structural gene which encodes allantoicase, an inducible enzyme of the purine degradative pathway. The identity of the alc clone was confirmed by restriction fragment length polymorphism analysis and by repeat-induced mutation. The alc gene is transcribed to give a single messenger RNA, approximately 1.2 kb in length. The negative-acting nmr gene affects the expression of alc in the expected manner. Both the nit-2 and the nmr control genes affect alc mRNA levels and allantoicase enzyme activity in both the induced and nitrogen-repressed conditions.     

Functional analysis by site-directed mutagenesis of individual amino acid residues in the flavin domain of Neurospora crassa nitrate reductase

Nitrate reductase of Neurospora crassa is a complex multi-redox protein composed of two identical subunits, each of which contains three distinct domains, an amino-terminal domain that contains a molybdopterin cofactor, a central heme-containing domain, and a carboxy-terminal domain which binds a flavin and a pyridine nucleotide cofactor. The flavin domain of nitrate reductase appears to have structural and functional similarity to ferredoxin NADPH reductase (FNR). Using the crystal structure of FNR and amino acid identities in numerous nitrate reductases as guides, site-directed mutagenesis was used to replace specific amino acids suspected to be involved in the binding of the flavin or pyridine nucleotide cofactors and thus important for the catalytic function of the flavin domain. Each mutant flavin domain protein was expressed in Escherichia coli and analyzed for NADPH: ferricyanide reductase activity. The effect of each amino acid substitution upon the activity of the complete nitrate reductase reaction was also examined by transforming each manipulated gene into a nit-3 ^– null mutant of N. crassa. Our results identify amino acid residues which are critical for function of the flavin domain of nitrate reductase and appear to be important for the binding of the flavin or the pyridine nucleotide cofactors.     

Control of nucleotide and erythroascorbic acid pools by cyclic AMP in Neurospora crassa

UDPglucuronic acid and erythroascorbic acid were identified in extracts of the fungus Neurospora crassa. The concentrations of these two compounds are estimated, in growing wild type N. crassa, to be about 0.10 and 0.28 μmol/ml of cell water, respectively. The pools of these two compounds are regulated by cyclic AMP in Neurospora, both being elevated in the cr-1, adenylate cyclase deficient mutant and both being lowered by exogenous cyclic AMP. The pools of these two compounds are also elevated on nitrogen deprivation. The pools of a large number of other nucleotides are not influenced by cyclic AMP. Possible relationships between the metabolism of UDPglucuronic acid and erythroascorbic acid are discussed. It was found that exogenous cyclic AMP was much more effective in influencing cultures grown at 30–37°C than those grown at 25°C. We suggest that higher temperatures may render Neurospora more permeable to a variety of different compounds.     

Regulation of RNA synthesis in Neurospora crassa : An analysis of a shift-up

A shift-up transition of growth from acetate to glucose is analyzed in Neurospora crassa. The rates of DNA and of protein accumulations remain at the preshift values for about 2 h, afterwards they increase to the rate characteristic of the new medium. The rate of RNA accumulation increases markedly 30 min after glucose addition initially at a rate greater than that of the new exponential growth which is achieved later on. An increase of the level of ribosomal proteins accompanies the increase of the rRNA content of the shifting cells, and 2–2.5 h after the shift the ribosomal level has reached the value characteristic of the new steady state of growth. The rate of rRNA methylation, which is strictly proportional to rRNA synthesis, remains almost unchanged in the 30 min following the shift; thereafter it increases to values greater than the final rate. It is interesting that the rate of rRNA synthesis is enhanced above the value typical of the new steady state as long as the ribosome level in the cells is below that characteristic of the new steady state, as if a compensatory mechanism were active.     

Isolation and characterization of a new gene, sre , which encodes a GATA-type regulatory protein that controls iron transport in Neurospora crassa

Multiple GATA factors – regulatory proteins with consensus zinc finger motifs that bind to DNA elements containing a GATA core sequence – exist in the filamentous fungus Neurospora crassa. One GATA factor, NIT2, controls nitrogen metabolism, whereas two others, WC-1 and WC-2, regulate genes responsive to blue light induction. A gene encoding a new GATA factor, named SRE, was isolated from Neurospora using a PCR-mediated method. Sequence analysis of the new GATA factor gene revealed an ORF specifying 587 amino acids, which is interrupted by two small introns. Unlike all previously known Neurospora GATA factors, which possess a single zinc-finger DNA-binding motif, SRE contains two GATA-type zinc fingers. The deduced amino acid sequence of SRE shows significant similarity to URBS1 of Ustilago and SREP of Penicillium. A loss-of-function mutation was created by the RIP procedure. Analysis of sre ⁺ and sre ⁻ strains revealed that SRE acts as a negative regulator of iron uptake in Neurospora by controlling the synthesis of siderophores. Siderophore biosynthesis is repressed by high iron concentrations in the wild-type strain but not in sre ⁻ mutant cells. The sre promoter contains a number of GATA sequences; however, expression of sre mRNA occurs in a constitutive fashion and is not regulated by the concentration of iron available to the cells. Received: 20 January 1998 / Accepted: 23 April 1998     

Nit-3, the structural gene of nitrate reductase in Neurospora crassa: nucleotide sequence and regulation of mRNA synthesis and turnover

Summary The nit-3 gene of the filamentous fungus Neurospora crassa encodes the enzyme nitrate reductase, which catalyzes the first reductive step in the highly regulated nitrate assimilatory pathway. The nucleotide sequence of nit-3 was determined and translates to a protein of 982 amino acid residues with a molecular weight of approximately 108 kDa. Comparison of the deduced nit-3 protein sequence with the nitrate reductase protein sequences of other fungi and higher plants revealed that a significant amount of homology exists, particularly within the three cofactor-binding domains for molybdenum, heme and FAD. The synthesis and turnover of the nit-3 mRNA were also examined and found to occur rapidly and efficiently under changing metabolic conditions.