Mutagenesis of a gene encoding a cytochrome o-like terminal oxidase of Azotobacter vinelandii: A cytochrome o mutant is aero-tolerant during nitrogen fixation

Abstract The amino acid sequence obtained by translating the nucleotide sequence of a 0.55 kb fragment, amplified from Azotobacter vinelandii chromosomal DNA by PCR, was 57% identical to part of the Escherichia coli cyoB gene, encoding subunit I of the cytochrome bo -type quinol oxidase. This fragment was mutated in vitro by insertion of a kanamycin-resistance cassette and introduced into the chromosome of A. vinelandii by homologous recombination. The mutant contained no spectrally detectable cytochrome o . However, in the stationary phase of growth, the level of the alternative oxidase (cytochrome bd ) was 11-fold higher than in the wild-type strain. Respiration of the mutant was insensitive to chlorpromazine, an inhibitor thought to act specifically on cytochrome o . Cytochrome o -deficient mutants fixed nitrogen in air, clearly distinguishing the role of this oxidase from that of cytochrome bd , which is required for respiratory protection of oxygen-labile nitrogenase.     

Effect of ammonium or nitrate on nitrogen fixation by a terrestrial Blue-green alga

Summary The effects of ammonium or nitrate-nitrogen on biological nitrogen fixation by an algal crust are compared. Nitrate-nitrogen up to 3.0 moles N g^–1 sand/algal crust at 60% water holding capacity did not affect fixation, whereas an ammonium-nitrogen concentration of 0.2 moles N g^–1 crust markedly depressed fixation. Consequences of these differential effects are considered.     

A Rhizobium meliloti mutant, lacking a functional γ-aminobutyrate (GABA) bypass, is defective in glutamate catabolism and symbiotic nitrogen fixation

Abstract A Rhizobium meliloti mutant, CMF1 2:38, was isolated which was specifically defective in the degradation of glutamate as sole carbon and nitrogen source. Biochemical analysis of CMF1 2:38 revealed a reduction in succinic semialdehyde dehydrogenase (SSDH) activity, the third enzyme of the γ-aminobutyrate (GABA) bypass. Evidence is presented which suggests that the Tn 5-induced mutation in CMF1 2:38 exists in a regulatory gene governing the expression of both NAD and NADP-linked SSDH activity. CMF1 2:38 nodulated alfalfa plants, but was reduced in its nitrogen fixation activity and biomass accumulating ability relative to the wild-type strain. The results presented in this study indicate that the GABA bypass is a major mechanism of glutamate degradation in R. meliloti CMF1 and that glutamate catabolism via this pathway may play an important role in the symbiotic nitrogen fixation process.     

Some characteristics of symbiotic nitrogen fixation,yield, protein and oil accumulation in irrigated peanuts (Arachis hypogaea L.)

Summary The potential of peanuts for symbiotic nitrogen fixation is considerable and under optimal edaphic and climatic conditions it reached 222 kg N₂/ha, which was 58% of the nitrogen accumulated in the plants. The effect of the Rhizobium inoculation on crude protein accumulation in the yield (kg/ha) was 3–4 times greater than its effect on the yield of pods and hay. There was an inverse relationship between the protein and oil content in the kernels.Seasonal changes in nitrogenase activity in the nodules were determined by the acetylene reduction method during two growing seasons. Under favorable conditions the specific activity of the nitrogenase reached a very high level (up to 975 moles C₂H₂ g dry wt nod/h) and the total activity (moles C₂H₄/plant/h) was also high in spite of the relatively poor nodulation (weight and number). The high activity was drastically reduced (to 75 moles C₂H₄ g dry wt nod/h) due to exceptionally hot and dry weather, which occurred in the middle of the second half of the growing season. It appears that N₂-fixation (nitrogenase activity) is more sensitive to these unfavorable conditions, than is nodule growth. Maximum nitrogenase activity was observed during the podfilling stage; until 50–60 days after planting, nitrogenase activity was very low.     

斯氏假单胞菌A1501固氮新基因PST1305的功能分析

摘要：【目的】研究斯氏假单胞菌A1501基因组“固氮岛”中PST1305基因在A1501生物固氮过程中所起的作用。【方法】利用同源重组与三亲接合的方法构建PST1305的非极性突变株。乙炔还原法测定固氮酶活。RT-PCR分析PST1305基因与其周围基因转录单元的关系,Real-Time PCR比较PST1305在最佳固氮与非固氮条件下表达水平的差异。【结果】突变株np1305的固氮酶活显著降低,功能互补菌株np1305Comp能基本恢复细胞的固氮作用。PST1305与其上游的nifB、fdxN、下游的nifQ等基因位于同一个转录单元,组成一个操纵子。基因芯片表明,PST1305基因在固氮比非固氮条件下表达量显著上调（约38.7倍）,Real-Time PCR验证支持这一结果。【结论】PST1305基因参与固氮过程,其突变会影响固氮酶的活性,该基因可能通过参与A1501固氮酶电子传递或者固氮酶的氧保护过程影响固氮效率。     

Backbone 1H, 13C, and 15N NMR assignments for the Cyanothece 51142 protein cce_0567: a protein associated with nitrogen fixation in the DUF683 family

Cyanothece 51142 contains a 78-residue protein, cce_0567, that falls into the DUF683 family of proteins associated with nitrogen fixation. Here we report the assignment of most of the main chain and ¹³C^β side chain resonances of the ∼40 kDa homo-tetramer.     

The effect of nutrient enrichment on nitrogen fixation activity in the Bay of Quinte,Lake Ontario

Nitrogen fixation was measured in situ by the ¹⁵N tracer technique in the Bay of Quinte, Lake Ontario, and three lake enclosures with different nutrient enrichment. The fixation rates in the Bay were low but detectable during the summer season. The fixation activities were found to be correlated with the presence of nitrogen-fixing blue-green algae and the distribution of the algal species in the water was affected by nitrate enrichment. The study showed that, with the addition of nitrate, species not able to fix atmospheric nitrogen became predominant. However, in the absence of external nitrogen (i.e., nitrate), species able to fix nitrogen became dominant. Phosphorus enrichment alone did result in higher N-fixation rates in the water and, without the addition of phosphorus, the fixation rates are lower and fluctuate throughout the season, presumably dependent on the availability of phosphorus in the water.A comparison between the ¹⁵N-isotopic method and the acetylene reduction method is reported and the factors involved in the variations between these two methods are discussed.     

根瘤菌共生固氮能力的进化模式

根瘤菌-豆科植物共生固氮体系对农业的可持续性发展至关重要,也是研究原核与真核生物互利共生的模式体系之一。长期以来,根瘤菌共生固氮相关研究主要集中在结瘤因子与固氮酶合成及调控等少数关键基因,但仅获得这些关键基因却不能保证细菌获得结瘤固氮能力。随着比较和功能基因组学的快速发展和应用,越来越多的研究发现根瘤菌使用了很多系统发育分支特异的遗传机制与豆科植物建立有效的共生关系,进一步揭示了双方互利共生的复杂性。本综述总结了近年来比较基因组学、遗传学以及实验进化等方面的相关研究进展,在此基础上讨论根瘤菌共生固氮能力的进化模式。     

The human RD protein is closely related to nuclear RNA-binding proteins and has been highly conserved

We have isolated cDNA clones encoding the human RD protein, which is closely related to several known nuclear RNA-binding proteins. The RD protein contains a 60-amino acid (aa) tract almost entirely of alternating basic and acidic aa, (RD)_n, primarily arginine (Arg; R) and aspartic acid (Asp; D). The protein also contains an ‘RNP sequence domain’. Arg-rich tracts and the RNP sequence domain are both features of nuclear RNA-binding proteins. However, we have been unable to detect RNA-binding by the human RD protein. The very strong evolutionary conservation of the mammalian RD protein as sequence suggests that it plays an important role in the cell.     

Growth, nutrition, and nitrogen fixation in grey alder at varied rate of nitrogen addition

Seedlings of grey alder (Alnus incana Moench), nodulated or unnodulated, were investigated at varied relative addition rate of nitrogen. Nitrogen fixation alone, without addition of mineral nitrogen, resulted in an almost optimum nitrogen status but only about half the maximum relative growth rate, probably mainly because of energy costs of nodulation and fixation. The growth deficit due to nodulation was much more than can be explained by the theoretical energy requirement for the amount of nitrogen fixed. Thus, the nitrogen fixation process was not very efficiently used. The nitrogen fixation rate was strongly stimulated by increasing nitrogen addition rate up to high levels. The fixation rate decreased rapidly close to optimum (maximum relative growth rate) and was negligible at maximum growth. A feed-back of mineral nitrogen on photosynthesis increased fixation rate with time, and the relative importance of fixation over mineral nitrogen nutrition increased. However, nitrogen fixation, also at maximum rate, supplied only a small proportion of the nitrogen amount required for maximum growth. The optimum nutrient solutions contained comparatively high nitrogen concentrations to secure free access to nitrogen. The nodules were damaged by this treatment, and it is concluded that the nitrogen additions must be adjusted to the current consumption of the plants to avoid an increased external nitrogen concentration. Strong linear regressions were found between relative growth rate, nitrogen status expressed as percentage content of fresh weight, and relative growth rate in unnodulated seedlings. There was a greater variability in nodulated seedlings than in unnodulated ones, because of the nitrogen fixation. The reactions of unnodulated grey alder were largely the same as previously reported for birch seedlings, but the maximum growth capacity was lower in grey alder. During an initial period of change in the internal nitrogen status, deficiency symptoms appeared, especially in unnodulated seedlings. As in birch, the leaves turned green again at stable nitrogen status, independent of level. The results are in sharp contrast to data from the literature where the external nitrogen concentration was used as the driving variable for the internal nitrogen status. The measured fixation rates for grey alder are much higher than those previously reported. Still, the maximum fixation rate observed is small compared to the total nitrogen uptake rate required for maximum growth, in contrast to reported relationships. These comparisons indicate that increased external nitrogen concentration obscures the real relations between mineral and fixed nitrogen, on one hand because of rapid inhibition of nitrogen fixation and, on the other hand, because of failure to obtain stable optimum nutrition and maximum growth by means of this treatment variable.     

A study of nodulation and nitrogen fixation of alder on the purplish soils in China

Summary The alder has a perennial nodule cluster. The nodule amount on the roots increases with tree age. The N₂-fixing activity of nodules decreases with nodule age. Purple coloured soils with various soil pHs and CaCO₃ contents are, in the main, the ones which influence nodulation and N₂-fixing. Higher N₂-fixing capacity existed in the neutral and low calcium soils. High calcium soils and acid soils can restrain nodulation and the N₂-fixing rate significantly. On the slope, where calcarous light loams are found, the annual nitrogen fixation capacity of alder and cypress mixed plantations, less than 10 years old, is 16 or 17 kg/ha yr, but in the valley, a pure alder plantation can reach 40 kg/ha yr.     

高寒草地珠芽蓼内生拮抗固氮菌Z19的鉴定及其固氮功能

【目的】从东祁连山高寒草地珠芽蓼内生细菌中筛选和鉴定具有固氮能力和拮抗能力的内生细菌。【方法】采用16S rRNA基因序列同源性分析和生理生化指标测定方法对该菌株进行鉴定。【结果】从珠芽蓼中分离获得的21株内生细菌中6株内生菌具有固氮能力,76.2%具有抑菌能力,其中5株内生细菌对5种以上的病原菌有抑制作用;菌株Z19具有较强固氮能力和分解纤维素的能力,其纤维素溶解圈直径与菌落直径比达3.33,产生的纤维素酶活性为0.31 U,且对辣椒立枯丝核病菌(Rhizoctonia solani)、油菜菌核病菌(Sclerotinia sclerotiorum)、番茄灰霉病菌(Botrytis cinerea)、小麦根腐病菌(Bipolaris sorokiniana)和番茄早疫病菌(Alternaria solani)具有较强拮抗能力;经PCR扩增和测序,获得了菌株Z19的固氮基因(nifH)序列和16S rRNA基因序列,在GenBank中的登录号分别为EU693340和EU236746;菌株Z19呈革兰氏阳性,杆状,产芽孢。【结论】结合生理生化特征及16S rRNA基因序列同源性比较,鉴定其为枯草芽孢杆菌(Bacillus subtilis)。     

Analysis of codon usage in genes for nitrogen fixation from phylogenetically diverse diazotrophs

Summary A cluster analysis based on codon usage in genes for biological nitrogen fixation (nif genes) grouped diazotrophs into three distinct classes: anaerobes, cyanobacteria, and aerobes. In thenif genes ofKlebsiella pneumoniae there was no evidence for selection pressure in favor of highly translatable codons. However, in the nitrogen regulatory operonglnAntrBntrC of enteric bacteria the stoichiometrically high level of glutamine synthetase may be facilitated by the presence of efficiently translatable codons inglnA. Thenif genes of the cyanobacteriumAnabaena showed codon selection in favor of translational efficiency. Computation of codon adaptation indices for expression in heterologous systems indicated that the reading frames most suitable for expression ofnif genes inEscherichia coli, Bacillus subtilis, andSaccharomyces cerevisiae were present in azotobacters, clostridia, and cyanobacteria, respectively. In codon-usage-based cluster analysis, type 3 nitrogenase genes ofAzotobacter vinelandii grouped along with type 1 and type 2 genes. This is in contrast to the nucleotide sequence-based multiple alignment in which type 3 nitrogenase genes ofA. vinelandii have been reported to cluster with entirely unrelated diazotrophs such as methanogens and clostridia. This may be indicative of lateral transfer ofnif genes among widely divergent taxons. The chromosomal- and plasmid-locatednif genes of rhizobia also cluster separately in nucleotide sequence-based analysis but showed similar codon usage. These analyses suggested that the phylogeny ofnif genes drawn on the basis of nucleotide sequence homology was not masked by the taxon-specific pressure on codon usage.     

The relationship between hydrogen metabolism,sulfate reduction and nitrogen fixation in sulfate reducers

Summary Hydrogenase and nitrogenase activities of sulfate-reducing bacteria allow their adaptation to different nutritional habits even under adverse conditions. These exceptional capabilities of adaptation are important factors in the understanding of their predominant role in problems related to anaerobic metal corrosion. Although the D₂–H⁺ exchange reaction indicated thatDesulfovibrio desulfuricans strain Berre-Sol andDesulfovibrio gigas hydrogenases were reversible, the predominant activity in vivo was hydrogen uptake. Hydrogen production was restricted to some particular conditions such as sulfate or nitrogen starvation. Under diazotrophic conditions, a transient hydrogen evolution was followed by uptake when dinitrogen was effectively fixed. In contrast, hydrogen evolution proceeded when acetylene was substituted as the nitrogenase substrate. Hydrogen can thus serve as an electron donor in sulfate reduction and nitrogen metabolism.     

Heterotrophic nitrogen fixation (acetylene reduction) associated to flooded rice: A modified measurement technique in the field

A modifiedin situ technique for measuring heterotrophic nitrogen fixing (acetylene reducing) activity associated to rice is proposed. Ethylene evolution rates measured in opaque cylinders covering the stems of rice plants which have been cut 10 cm over the water level were found independent of the diurnal cycle. Cutting of the leaves resulted in decreased variation between plants and suppression of the acceleration of ethylene evolution rate after 12 h incubation as compared to intact plants. In both systems ethylene evolved was swept by a current of methane and the molar ratio between methane and ethylene was stabilized after 12 h. Methane evolution rates remained stable during 12 h and more than 24 h in whole plants and cut plants respectively. It is suggested that alteration in the active gas transport system after 12 h incubation under 10% acetylene may lead to erroneous evaluation of the actual ethylene production in the root's environment. The average values of ethylene evolution rates by cut plants between 12 and 24 h of incubation may be used for comparative studies of nitrogen fixing activity associated to flooded rice.     

Nodulation and biological nitrogen fixation of 80 soybean cultivars in symbiosis with indigenous rhizobia

Eighty soybean cultivars were assessed for their potential for nodulation and nitrogen fixation with indigenous rhizobia in a Nigerian soil. Seventy-six days after planting (DAP) 87%, 3% and 10% of the soybean cultivars had from 0 to 30, 31 to 60 and over 61 nodules/plant, respectively. Only 8% had a nodule dry weight of 600 to 1100 mg/plant. At 84 DAP the proportion of nitrogen derived from the atmosphere (Ndfa) ranged from 0 to 65% 16% of the cultivars derived 51 to 65% of their N₂ from the atmosphere. The diversity of soybean germplasm and the variation in nodulation and N₂ fixation permitted the selection of the five best cultivars in terms of their compatibility with indigenous rhizobia, % Ndfa and the amount of N₂ which they fixed.     

Microclimatic parameters influencing nitrogen fixation in the phyllosphere in a Costa Rican premontane rain forest

The acetylene reduction method was used to measure nitrogen fixation in the phyllosphere of attached leaves of different phorophytes under natural conditions in a premontane rain forest in Costa Rica. Maximum rates of nitrogen fixation (26 ng N · cm⁻² leaf area · h⁻¹) – mainly due to the activity of two species of Scytonema (Cyanobacteria) – were measured in the rainy season in bright sunlight. Rates of nitrogen fixation were correlated with the leaf area covered by Scytonema. In periods without precipitation the fixation activity decreased to zero within 2–3 days. As long as the epiphylls were sufficiently supplied with water, other microclimatic factors like temperature and light intensity also influenced nitrogen fixation rates, but to a lesser extent. Relative humidity and species of phorophyte showed no direct influence. It was concluded that the most important factor for nitrogen fixation in the phyllosphere was the availability of liquid water. Linking these results to meteorological data, the input of nitrogen by biological nitrogen fixation in the phyllosphere in the investigation area was estimated to be as much as 1.6 ± 0.8 kg N · ha⁻¹ · year⁻¹ per unit of leaf area index (LAI). For an LAI of 2 for the understory the nitrogen input would vary between 2 and 5 kg N · ha⁻¹ · year⁻¹. This work also demonstrates the importance of detailed knowledge of variation in microclimate throughout the year as a basis for extrapolation of the annual nitrogen input. Received: 21 December 1997 / Accepted: 14 June 1998     

Deep placement: A method of nitrogen fertilizer application compatible with algal nitrogen fixation in wetland rice soils

Summary The effect of different methods of nitrogen fertilizer application on the algal flora and biological nitrogen fixation (Acetylene-reducing activity) in a wetland rice soil was studied in pot and field experiments. Broadcast application of urea inhibited nitrogen fixation and favored the growth of green algae. In contrast, deep placement of urea supergranules (1–2 g urea granules) did not suppress the growth of N₂-fixing blue-green algae and permitted acetylene-reducing activity on the soil surface to continue virtually uninhibited.     

The natural history of nitrogen fixation

In recent years, our understanding of biological nitrogen fixation has been bolstered by a diverse array of scientific techniques. Still, the origin and extant distribution of nitrogen fixation has been perplexing from a phylogenetic perspective, largely because of factors that confound molecular phylogeny such as sequence divergence, paralogy, and horizontal gene transfer. Here, we make use of 110 publicly available complete genome sequences to understand how the core components of nitrogenase, including NifH, NifD, NifK, NifE, and NifN proteins, have evolved. These genes are universal in nitrogen fixing organisms-typically found within highly conserved operons-and, overall, have remarkably congruent phylogenetic histories. Additional clues to the early origins of this system are available from two distinct clades of nitrogenase paralogs: a group composed of genes essential to photosynthetic pigment biosynthesis and a group of uncharacterized genes present in methanogens and in some photosynthetic bacteria. We explore the complex genetic history of the nitrogenase family, which is replete with gene duplication, recruitment, fusion, and horizontal gene transfer and discuss these events in light of the hypothesized presence of nitrogenase in the last common ancestor of modern organisms, as well as the additional possibility that nitrogen fixation might have evolved later, perhaps in methanogenic archaea, and was subsequently transferred into the bacterial domain.