Biochemical studies on the Nit mutants of Neurospora crassa

Summary One allele at each of the five nit loci in Neurospora crassa together with the wild type strain have been compared on various nitrogen sources with regard to (i) their growth characteristics (ii) the level of nitrate reductase and its associated activities (reduced benzyl viologen nitrate reductase and cytochrome c reductase) (iii) the level of nitrite reductase and (iv) their ability to take up nitrite from the surrounding medium. Results are consistent with the hypothesis that nit-3 is the structural gene for nitrate reductase, nit-1 specifies in part a molybdenum containing moiety which is responsible for the nit-3 gene product dimerising to form nitrate reductase, nit-4 and nit-5 are regulator genes whose products are involved in the induction of both nitrate reductase and nitrite reductase and nit-2 codes for a generalised ammonium activated repressor protein. Studies on the induction of nitrate reductase (and its associated activities) and nitrite reductase in wild type, nit-1 and nit-3 in the presence of either nitrate or nitrite suggest that each enzyme may be regulated independently of the other and that nitrite could be true co-inducer of the assimilatory pathway. Nitrite uptake experiments with nit-2, nit-4 and nit-5 strains show that whereas nit-4 and nit-5 are freely permeable to this molecule, it is unable to enter the nit-2 mycelium.     

Biochemical characterization of some nitrate reductase deficient mutants of Nicotiana plumbaginifolia

Four nitrate reductase deficient (NR⁻) mutants (Cnx 20, Cnx 103: impaired in the Mo-cofactor; Nia 26, NA 36: mutated in teh structural gene for the apoprotein) of Nicotiana plumbaginifolia were characterized biochemically. The phenotype of Cnx 20 (Mo repair in vitro, complementation of Neurospora nit-1, dimeric CcR) and Nia 26 (no Mo repair in vitro, complementation of Neurospora nit-1, absence of dimeric CcR) is similar to, respectively, other cnxA-(for Cnx 20) and nia mutants studied in Nicotiana. New Phenotypes were discovered in NA 36 and Cnx 103, the latter one belonging to complementation group cnxD. The mutant NR of Cnx 103 cannot be repaired by Mo in vitro and does not complement Neurospora nit-1. However, cytochrome-c reductase (CcR) suggests that at least some dimerization takes place. NA 36 lacks all nitrate reducing activities, irrespective of the electron donor (NADH, BVH, FADH₂) used, the Mo-cofactor is intact and CcR activity is present in the dimerized form. It is concluded, that two kinds of mutations (cnxD, NA 36) can result in the NR⁻ phenotype ‘dimeric nitrate-inducible CcR, not repairable by Mo’.     

Isolation of identical nitrilase genes from multiple bacterial strains and real-time PCR detection of the genes from soils provides evidence of horizontal gene transfer

Bacterial enzymes capable of nitrile hydrolysis have significant industrial potential. Microbacterium sp. AJ115, Rhodococcus erythropolis AJ270 and AJ300 were isolated from the same location in England and harbour identical nitrile hydratase/amidase gene clusters. Strain AJ270 has been well studied due to its nitrile hydratase and amidase activity. R. erythropolis ITCBP was isolated from Denmark and carries a very similar nitrile hydratase/amidase gene cluster. In this study, an identical nitrilase gene (nit1) was isolated from the four strains, and the nitrilase from strain AJ270 cloned and expressed in Escherichia coli. Analysis of the recombinant nitrilase has shown it to be functional with activity demonstrated towards phenylacetonitrile. A real-time PCR TaqMan^® assay was developed that allowed nit1 detection directly from soil enrichment cultures without DNA extraction, with nit1 detected in all samples tested. Real-time PCR screening of isolates from these soils resulted in the isolation of nit1 and also very similar nitrilase gene nit2 from a number of Burkholderia sp. The genes nit1 and nit2 have also been detected in many bacteria of different genera but are unstable in these isolates. It is likely that the genes were acquired by horizontal gene transfer and may be widespread in the environment.     

Xanthine dehydrogenase expression inNeurospora crassa does not require a functionalnit-2 regulatory gene

Xanthine dehydrogenase (XDH) is the initial enzyme in the purine catabolic pathway ofN. crassa. Secondary nitrogen sources such as purines are metabolized when preferred sources of reduced nitrogen (ammonium or glutamine) are unavailable. XDH synthesis is regulated by glutamine repression and uric acid induction. Thenit-2 locus is believed to encode atrans-acting positive regulator essential for the expression of genes encoding enzymes involved in secondary pathways of nitrogen acquisition, such as XDH and nitrate reductase. However, immunoblot analyses and enzyme assays reveal that XDH protein is synthesized and XDH activity is expressed innit-2 mutants. Nevertheless, XDH responds to nitrogen metabolite repression. The generality thatnit-2 is an obligate control element in nitrogen metabolite repression is questioned. Additionally, mutants defective in XDH activity, namely,xdh-1 and the molybdenum cofactor mutantsnit-1, -7, -8 and -9, are observed to grow on xanthine but not hypoxanthine.This research was supported in part by National Science Foundation Grant DMB 8516203.     

Salmonella typhimurium nit Is nadE: Defective Nitrogen Utilization and Ammonia-Dependent NAD Synthetase

S. typhimurium nit mutants are defective in nitrogen assimilation, despite having normal levels of assimilatory enzymes. Complementation, enzyme assays, and genetic mapping show that nit is nadE. We present evidence that ammonia, not glutamine, is the physiological substrate for eubacterial NAD synthetases and that low activity completely accounts for the mutant phenotype.     

In vitro restoration of nitrate reductase: Investigation of Aspergillus nidulans and Neurospora crassa nitrate reductase mutants

Extracts of Aspergillus nidulans wild type (bi-1) and the nitrate reductase mutant niaD-17 were active in the in vitro restoration of NADPH-dependent nitrate reductase when mixed with extracts of Neurospora crassa, nit-1. Among the A. nidulans cnx nitrate reductase mutants tested, only the molybdenum repair mutant, cnxE-14 grown in the presence of 10⁻³ M Na₂MoO₄ was active in the restoration assay.Aspergillus extracts contained an inhibitor(s) which was measured by the decrease in NADPH-dependent nitrate reductase formed when extracts of Rhodospirillum rubrum and N. crassa, nit-1 were incubated at room temperature. The inhibition by extracts of A. nidulans, bi-1, cnxG-4 and cnxH-3 was a linear function of time and a logarithmic function of the protein concentration in the extract.The molybdenum content of N. crassa wild type and nit-1 mycelia were found to be similar, containing approx. 10 μg molybdenum/mg dry mycelium. The NADPH-dependent cytochrome c reductase associated with nitrate reductase was purified from both strains. The enzyme purified from wild-type N. crassa contained more than 1 mol of molybdenum per mol of enzyme, whereas the enzyme purified from nit-1 contained negligible amounts of molybdenum.     

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.     

Release of molybdenum co-factor from nitrate reductase and xanthine oxidase by heat treatment

Heat treatment (90 sec at 70°) is shown to convert the bound molybdenum co-factor of tobacco cell-free extracts and bovine milk xanthine oxidase into a form capable of complementing the Neurospora crassa mutant nit-1.In the presence of 1 mM ascorbic acid, 25 mM molybdate and, for plant extracts, sulphydryl group protecting agents, the molybdenum co-factor can survive incubations up to 100° whilst maintaining its biological activity. Especially with plant extracts, the efficiency of heat treatment is considerably higher than that of the acidification procedure which is often utilized for releasing molybdenum co-factor.     

Biochemical analysis of mutants defective in nitrate assimilation in Neurospora crassa: evidence for autogenous control by nitrate reductase

Summary A biochemical analysis of mutants altered for nitrate assimilation in Neurospora crassa is described. Mutant alleles at each of the nine nit (nitrate-nonutilizing) loci were assayed for nitrate reductase activity, for three partial activities of nitrate reductase, and for nitrite reductase activity. In each case, the enzyme deficiency was consistent with data obtained from growth tests and complementation tests in previous studies. The mutant strains at these nit loci were also examined for altered regulation of enzyme synthesis. Such exeriments revealed that mutations which affect the structural integrity of the native nitrate reductase molecule can result in constitutive synthesis of this enzyme protein and of nitrite reductase. These results provide very strong evidence that, as in Aspergillus nidulans, nitrate reductase autogenously regulates the pathway of nitrate assimilation. However, only mutants at the nit-2 locus affect the regulation of this pathway by nitrogen metabolite repression.     

Vegetative Compatibility,Pathogenicity and Virulence Diversity of Fusarium oxysporum f. sp. melongenae Recovered from Eggplant

Fusarium oxysporum (Schlechtend.: Fr.) f. sp. melongenae (Fomg) recovered from symptomatic eggplants from five eggplant‐growing areas in Turkey, including the south, west, north‐west, north and south‐east regions. The objective of this study was to investigate the genetic diversity of the Fomg isolates from different geographical location by pathogenicity and VCG tests. Three hundred and seventy‐four Fomg isolates were classified as highly virulent, virulent, moderately virulent and low virulent through pathogenicity assays. No correlation was observed between virulence of Fomg isolates and their locations. The nitrate non‐utilizing mutants (nit) were generated as nit1, nit3 and NitM, based on phenotyping of Fomg growth characteristics of the Fomg isolates on diagnostic media with various sources of nitrogen. The majority of nit mutants (39.4%) recovered were nit1 from minimal medium (MM) containing of 2.0% potassium chlorate (MMC). The most of Fomg isolates were identified as heterokaryon self‐compatible (HSC) based on their ability to form a stable heterokaryon, while four isolates were classified as heterokaryon self‐incompatible (HSI). A large amount of Fomg isolates were vegetatively compatible and assigned as members of the same VCG, whereas nit mutants of 10 Fomg isolates that did not complement with tester strains only paired by themselves (HSC), these isolates were termed vegetative incompatible (vic). The complementation of 33 isolates with tester strains was slow and quite weak, but not paired with themselves even though they are HSC. About 96.3% of the Fomg isolates were assigned to VCG 0320, while the remaining 3.7% were classified as vegetative incompatible group.     

Presence of the molybdenum-cofactor in nitrate reductase-deficient mutant cell lines of Nicotiana tabacum

Summary Nicotiana tabacum mutant cell cultures lacking nitrate reductase activity were assayed for the presence of the molybdenum-cofactor using its ability to restore NADPH-nitrate reductase activity in extracts of Neurospora crassa nit-1 mycelia. The molybdenum-cofactor of the tobacco wild-type line was shown to complement efficiently the N. crassa nit-1 mutant in vitro. The molybdenum-cofactor seems to exist in a bound form, as acid-treatment was required for release of cofactor activity. Molybdate (5–10 mM), ascorbic acid, and anaerobic conditions greatly increased the activity of the cofactor, demonstrating its high lability and sensitivity to oxygen. Similar results were obtained with two tobacco nia mutants, which are defective in the apoprotein of nitrate reductase. The four cnx mutants studied were shown to contain exclusively an inactive form of the molybdenum-cofactor. This inactive cofactor could be reactivated in vitro and in vivo by unphysiologically high concentrations of molybdate (1–10 mM), thereby converting the cnx cells into highly active cofactor sources in vitro, and restoring nitrate reductase and xanthine dehydrogenase in vivo to partial acitivity. Thus the defect of the cnx mutants resides in a lack of molybdenum as a catalytically active ligand metal for the cofactor, while the structural moiety of the cofactor seems not to be impaired by the mutation. The subunit assembly of the nitrate reductase was found to be independent of the molybdenum content of the cofactor.     

Occurrence of xanthine dehydrogenase in Chlamydomonas reinhardii: A common cofactor shared by xanthine dehydrogenase and nitrate reductase

Wild-type Chlamydomonas reinhardii cells have xanthine dehydrogenase activity when grown with nitrate, nitrite, urea, or amino acid media. Mutant strains 102, 104, and 307 of Chlamydomonas, lacking both xanthine dehydrogenase and nitrate reductase activities, were incapable of restoring the NADPH-nitrate reductase activity of the mutant nit-1 of Neurospora crassa, whereas wild type cells and mutants 203 and 305 had xanthine dehydrogenase and were able to reconstitute the nitrate reductase activity of nit-1 of Neurospora. Therefore, it is concluded that in Chlamydomonas a common cofactor is shared by xanthine dehydrogenase and nitrate reductase. Xanthine dehydrogenase is repressed by ammonia and seems to be inessential for growth of Chlamydomonas.     

Vegetative compatibility groups and sexual reproduction among Spanish Monilinia fructicola isolates obtained from peach and nectarine orchards,but not Monilinia laxa

The frequency of occurrence of Monilinia fructicola in the Ebro Valley, Spain has increased since its first appearance in 2006, and M. fructicola has displaced Monilinia laxa, the native species which is the main cause of brown rot in peaches in this valley. In order to determine the characteristics that may be related to the displacement, we studied the capacity to generate new genotypic combinations of M. fructicola under laboratory conditions. The morphology and parasitic ability from ten field isolates of M. fructicola and M. laxa collected from three different orchards in the valley, and sampling from five different lesions were studied. Nitrate-non-utilising (nit) mutants were generated in order to test the isolates for vegetative compatibility which was done by assessing their colony growth when cultured singly or in pairs on media that contained different nitrogen sources. For the M. fructicola isolates, five vegetative compatibility groups (VCGs) were identified using the nit mutants and six VCGs were identified when they were grown on potato dextrose agar dishes. In all instances, the vegetatively compatible M. fructicola isolates came mainly from the same orchard. Only one VCG displays the same morphological and competition characteristics. No VCGs were identified among the M. laxa isolates. We did not find any apothecia of M. laxa and M. fructicola isolates in the soil of the three orchards, but we were able to produce apothecia of M. fructicola in the laboratory. Our finding of sexual reproduction and VCGs in the M. fructicola isolates suggests that the genetic variability of M. fructicola could be maintained by sexual and/or parasexual recombination.     

The relationship of Mo,molybdopterin, and the cyanolyzable sulfur in the Mo cofactor

Reconstitution of the apoprotein of the molybdoenzyme nitrate reductase in extracts of the Neurospora crassa mutant nit-1 with molybdenum cofactor released by denaturation of purified molybdoenzymes is efficient in the absence of exogenous MoO₄^2? under defined conditions. Evidence is presented that this molybdate-independent reconstitution is due to transfer of intact Mo cofactor, a complex of Mo and molybdopterin (MPT), the organic constituent of the cofactor. This complex can be separated from denatured protein by gel filtration, and from excess MoO₄^2? by reverse-phase HPLC. Sulfite oxidase, native xanthine dehydrogenase, and cyanolyzed xanthine dehydrogenase are equipotent Mo cofactor donors. Other well-studied inactive forms of xanthine dehydrogenase are also shown to be good cofactor sources. Using xanthine dehydrogenase specifically radiolabeled in the cyanolyzable sulfur, it is shown that this terminal ligand of Mo is rapidly removed from Mo cofactor under the conditions used for reconstitution.     

In situ soil net nitrogen mineralization in coastal salt marshes (Suaeda salsa) with different flooding periods in a Chinese estuary

Flooding periods can be one of the most important factors influencing nitrogen (N) biogeochemical processes in wetlands ecosystem. We conducted a field study using in situ incubation method to investigate the seasonal dynamics of soil net N mineralization in three coastal salt marshes (Suaeda salsa) with different flooding periods (i.e., short-term (STF), seasonal (SF), and tidal (TF) flooding wetland) in the Yellow River Delta. Selected soil inorganic N pools (ammonium, nitrate and inorganic N) and N transformation (mineralization, nitrification and ammonification) rates in the top 0–10 cm soils were repeatedly quantified from April to October. Clear seasonal patterns in inorganic N pools and transformation rates were observed in accord with the seasonal variations of temperature and moisture. Generally, higher levels of soil inorganic nitrogen, ammonium nitrogen (NH₄⁺-N) and nitrate nitrogen (NO₃^－-N) occurred in the early-growing season (April), and NH₄⁺-N contents got a small accumulative peak in midsummer (September). The lower rates (negative) of net mineralization (R_min), nitrification (R_nit) and ammonification (R_amm) were observed in the early-growing season (April–June) and fall (September–October), whereas higher values (positive) in midsummer (August–September). Flooding had a significant influence on inorganic N pools (except for NH₄⁺-N) and transformation rates (p < 0.05). R_min values in SF wetland were significantly higher in the August-September period than those in other incubation periods. R_nit values in TF wetland exhibited a small variation and the highest value occured in the June–August period. The results of principal component analysis showed that soil samples were clearly divided into two groups before and after flow-sediment regulation. After flooding events, the R_min and R_amm values generally increased in the three wetlands, whereas a significant decrease in R_nit values was observed in SF wetland (p < 0.05), thus the differences in NO₃^－-N among these wetlands were eliminated. These results suggested that seasonal variations in temperature and moisture are important factors influencing inorganic N pools and transformation rates.     

High‐Throughput Assessment and Genetic Investigation of Vegetative Compatibility in Verticillium dahliae

Classification of isolates into vegetative compatibility groups (VCGs) using nitrate‐non‐utilizing (nit) mutants has been widely used for the characterization of Verticillium dahliae populations. However, certain methodological limitations prevent its application on a large scale. Furthermore, systematic investigations into the genetics underlying complementation tests between nit mutants of fungal isolates (i.e. heterokaryon formation) are lacking for Verticillium species. In this work, a diverse collection of 27 V. dahliae isolates – including representatives of all VCGs, both mating types, and heterokaryon self‐incompatible isolates – was employed for the development and optimization of (i) a protocol for the rapid generation of nit mutants of V. dahliae isolates using UV‐irradiation and (ii) a reproducible high‐throughput procedure for complementation tests between nit mutants in liquid cultures using 96‐well microplates. The genetic analysis of selected heterokaryons demonstrated that the frequently encountered ‘weak’ cross‐reactions between VCGs and their subgroups can be actually heterokaryotic, implying the absence of strict genetic barriers between VCGs. In conclusion, we provide in this work an optimized method for the high‐throughput VCG assignment of V. dahliae populations and a genetic analysis of heterokaryons that may have serious implications for the interpretation of VCG classification data. These advancements in the available methodology and the genetic background of vegetative compatibility grouping may contribute to a better understanding of the population biology of V. dahliae and possibly other mitosporic fungi.     

nit 7: A New Locus for Molybdopterin Cofactor Biosynthesis in the Green Alga Chlamydomonas reinhardtii

Two new nitrate reductase-deficient mutants from Chlamydomonas reinhardtii have been genetically and biochemically characterized. Both H1 and F23 mutants carry single recessive allelic mutations that map at a new locus designated nit-7. This locus is unlinked to the other six nit loci related to the nitrate assimilation pathway in C. reinhardtii. Both mutant alleles H1 and F23 lack an active molybdopterin cofactor, the activity of which is restored neither in vitro nor in vivo by high concentrations of molybdate. Nitrate reductase subunits in these mutants seem to assemble, although not in a stable form, in a high molecular weight complex and, as in other molybdenum cofactor-defective mutants of C. reinhardtii, they cannot reconstitute nitrate reductase activity with an active molybdenum cofactor source from extracts of ammonium-grown cells. The results suggest that nit-7 mutants are defective in molybdopterin biosynthesis. They do produce some precursor(s) that are capable of binding to nitrate reductase subunits.     

重度放牧对欧亚温带草原东缘生态样带土壤氮矿化及其温度敏感性的影响

以欧亚温带草原东缘生态样带为平台,以样带上未放牧和重度放牧配对样地为研究对象,开展重度放牧对欧亚温带典型草原土壤氮矿化及其温度敏感性的影响研究。结果表明:(1)在室内培养条件下,土壤氮积累量和土壤净氮矿化速率呈现出干燥度指数较大的样点显著大于干燥度指数最低的样点(P0.05)。在相对湿润的样点,土壤氮素矿化周转速率较快;(2)重度放牧对不同样点土壤氮积累量和土壤氮矿化速率的影响是不同的。在干燥度指数较高样点,重度放牧样地土壤铵态氮减少量和速率较未放牧样地低(P0.05),重度放牧显著降低了土壤硝态氮积累量、无机氮积累量、硝化速率、净氮矿化速率(P0.05);在干燥度指数较低样点,重度放牧样地土壤铵态氮减少量和速率较未放牧样地高(P0.05),重度放牧对土壤硝态氮积累量、无机氮积累量、硝化速率、净氮矿化速率影响不大(P0.05);(3)土壤氮矿化作用温度敏感性(Q_(10))变化范围在1.61—2.06,重度放牧对Q_(10)无显著影响。随着纬度的升高,Q_(10)呈升高趋势。Q_(10)与基质质量指数以及表观活化能与基质质量指数均呈显著的负相关关系(P0.05);(4)土壤硝态氮积累量、无机氮积累量、硝化速率、净氮矿化速率对重度放牧的响应比与干燥度指数呈极显著负相关(P0.01),重度放牧对欧亚温带典型草原土壤氮矿化的影响受气候条件(温度和降水)的调控。     

Nitrate-nonutilizing mutants ofGibberella zeae (Fusarium graminearum) and their use in determining vegetative compatibility

Twenty-four single-spore isolates ofFusarium graminearum were obtained from scabby wheat seeds or glumes collected from 23 locations in Kansas in 1990. All isolates were sexually fertile and homothallic. Nitrate-nonutilizing (nit) mutants of each isolate were generated on a medium amended with 1.5% KCIO₃. Of 378 mutants, 161 were able to utilize nitrite and hypoxanthine (nit1), 165 utilized hypoxanthine but not nitrite (nit3), 47 utilized nitrite but not hypoxanthine (NitM), and 5 appeared to be global nitrogen regulatory mutants similar to the previously describednnu mutant. Complementation was tested by pairingnit1 mutants of each isolate with either a NitM or anit3 mutant from each isolate on media containing nitrate as the sole nitrogen source. Complementation was more pronounced whennit1 and NitM mutants were paired. Mutants were only able to complement with other mutants from the same wild-type isolate. Therefore, each wild-type isolate belonged to a genetically distinct vegetative compatibility group. The genetic diversity suggests that sexual genetic recombination may be important in the field.