Molecular cloning and characterization of a cDNA encoding nitrate reductase from Chlorella ellipsoidea (Chlorophyta)

Nitrate reductase (NR) genes have beencloned from higher plants, fungi and algae.Based on seven of the amino acid residuesmost strongly conserved between Chlorella vulgaries and Chlamydomonasreinhardtii NR gene, a degenerate primerwas designed. This degenerate primer wasused to amplify the corresponding homologyin Chlorella ellipsoidea. A 3304 bpfull-length cDNA was cloned by rapidamplification of cDNA ends (RACE). Thededuced amino acid sequence of this cDNAhas a high degree of similarity withpreviously identified members of the NRgene. This suggests that the amplified cDNAencodes a functional NR. Northern blotexpression analysis suggests that this geneis strongly induced by nitrate, but isrepressed by ammonium. The nucleotidesequence data reported in this paper willappear in the DDBJ/EMBL/GeneBank databasesunder accession number AY275834.     

Schistosoma mansoni: ferredoxin-NADP(H) oxidoreductase and the metabolism of reactive oxygen species

Mitochondrial-type ferredoxin-NADP(H) oxidoreductases (FNR) catalyze the electron transport between NADPH and substrates such as ferredoxins. Even though enzymes belonging to this family are present in several organisms, including prokaryotes, their biological function is not clearly understood. In a previous work, we reported the existence of a mitochondrial-type FNR in the trematode Schistosoma mansoni (SmFNR). This enzyme conferred tolerance to oxidative stress conditions when tested in an heterologous system. In this work, we demonstrate that the SmFNR can be imported to mitochondria in mammal cells and show that its expression is induced in parasite cultures by reactive oxygen species (ROS). The results reported herein give further support to the involvement of SmFNR in ROS metabolism.     

Enzymes of assimilatory sulfate reduction in leaves of Pisum sativum: Activity changes during ontogeny and in vivo regulation by H2S and cyst(e)ine

Enzyme activities of assimilatory sulfate reduction were measured in leaves of Pisum sativum L., cv. Vatters Frühbusch, during their ontogenetic development, and during treatment with H₂S and cyst(e)ine. Ribulose bisphosphate (RuBP) carboxylase (EC 4.1.1.39) and ferredoxin-dependent nitrite reductase (Fd-NiR, EC 1.7.7.1) were measured for comparison. In etiolated pea leaves, ATP-sulfurylase (ATPase, EC 2.7.7.4), adenosine 5'-phosphosulfate sulfotransferase (APSSTase), ferredoxin-dependent sulfite reductase (Fd-SiR, EC 1.8.7.1) and O-acetyl-L-serine sulfhydrylase (OASSase, EC 4.2.99.8) activities were measured in appreciable rates, while neither RuBP carboxylase nor Fd-NiR activities could be detected.
During the first 2–7 days after transfer into the light all enzyme activities increased. After reaching maximal activities, ATPase, APSSTase, and Fd-SiR activities decreased in all leaves to low or indetectable levels during the following 3–6 days. RuBP carboxylase, Fd-NiR and OASSase, on the other hand, decreased slowly and were still at high levels of activity at the end of the experiment.
Fumigation of pea plants with 1.5 μl l⁻¹ H₂S delayed the initial increase and the subsequent decrease of ATPase activity by 1–3 days. APSSTase activity decreased for 1–2 days, increased rapidly during the next 4–6 days and retained a high level of activity until the end of the experiment as did Fd-SiR. One to two days after the beginning of fumigation the leaves started to accumulate high amounts of cyst(e)ine.
When pea plants with excised roots were placed on a nutrient solution containing cyst(e)ine, APSSTase activity decreased more on 0.2 and 0.5 m M than on 1.0 m M. Fd-SiR activity was only slightly decreased on 1.0 m M cyst(e)ine. Neither Fd-NiR nor RuBP carboxylase activities were affected.     

Asymmetric Dimeric Structure of Ferredoxin-NAD(P) Oxidoreductase from the Green Sulfur Bacterium Chlorobaculum tepidum: Implications for Binding Ferredoxin and NADP

Ferredoxin-NAD(P)⁺ oxidoreductase (FNR) catalyzes the reduction of NAD(P)⁺ to NAD(P)H with the reduced ferredoxin (Fd) during the final step of the photosynthetic electron transport chain. FNR from the green sulfur bacterium Chlorobaculum tepidum is functionally analogous to plant-type FNR but shares a structural homology to NADPH-dependent thioredoxin reductase (TrxR). Here, we report the crystal structure of C. tepidum FNR to 2.4 Å resolution, which reveals a unique structure-function relationship. C. tepidum FNR consists of two functional domains for binding FAD and NAD(P)H that form a homodimer in which the domains are arranged asymmetrically. One NAD(P)H domain is present as the open form, the other with the equivalent NAD(P)H domain as the relatively closed form. We used site-directed mutagenesis on the hinge region connecting the two domains in order to investigate the importance of the flexible hinge. The asymmetry of the NAD(P)H domain and the comparison with TrxR suggested that the hinge motion might be involved in pyridine nucleotide binding and binding of Fd. Surprisingly, the crystal structure revealed an additional C-terminal sub-domain that tethers one protomer and interacts with the other protomer by π-π stacking of Phe337 and the isoalloxazine ring of FAD. The position of this stacking Phe337 is almost identical with both of the conserved C-terminal Tyr residues of plant-type FNR and the active site dithiol of TrxR, implying a unique structural basis for enzymatic reaction of C. tepidum FNR.     

Identification of the green alga, Chlorella vulgaris (SDC1) using cyanobacteria derived 16S rDNA primers: targeting the chloroplast

We have tested a set of oligonucleotide primers originally developed for the specific amplification of 16S rRNA gene segments from cyanobacteria, in order to determine their versatility as an identification tool for phototrophic eucaryotes. Using web-based bioinformatics tools we determined that these primers not only targeted cyanobacterium sequences as previously described, but also 87% of sequences derived from phototrophic eucaryotes. In order to qualify our finding, a type culture and environmental strain from the freshwater unicellular, green algae genus Chlorella Beijerinck, were selected for further study. Subsequently, we sequenced a 578-bp fragment of the 16S rRNA gene, which proved to be present within the chloroplast genome, performed sequence analysis and positively identified our solvent-degrading environmental strain (SDC1) as Chlorella vulgaris.     

Physiological and Biochemical Role of Brassinosteroids and Their Structure-Activity Relationship in the Green Alga Chlorella vulgaris Beijerinck (Chlorophyceae)

This paper studies the influence of the 7-oxalactone type of brassinosteroids (BRs) and 6-ketone upon the biological activity of the alga Chlorella vulgaris (Chlorophyceae). The results of the study indicate significant differences in the growth and metabolism of C. vulgaris cells caused by the different chemical structures of the BRs used. The most significant differences in the stimulation of the growth of the biomass and metabolites contained in it were caused by structural differences in the B ring of BRs. It was found that in C. vulgaris 7-oxalactone type of BRs [brassinolide (BL) and its derivatives] are more active than 6-ketone type of BRs [castasterone (CS) and its derivatives]. It was found that BRs used within the range of concentration of 10⁻¹² to 10⁻⁸ m stimulate two- to threefold the growth and division of C. vulgaris cells. The most stimulating influence upon the number of the algal cells and the phosphorus, chlorophyll, and monosaccharides contained in the alga, as well as the intensity of the photosynthesis, and sugar and glycolate excretion was demonstrated by BL at a concentration 10⁻⁸ m in the 36th h of cultivation. HomoCS was characterized by the lowest biological activity. In turn, after the 48th h an inhibition of the rate of growth and development of the alga takes place. In the range from 10⁻⁷ to 10⁻⁶ m the inhibition of growth and development of the alga was manifested by BRs. During the further toxic activity of BRs the cells of C. vulgaris undergo complete degradation. In turn, in concentrations lower than 10⁻¹² m, BRs do not exert any biologically significant influence upon C. vulgaris cells. On the basis of the study, the biological activity of BRs was arranged in the following order: BL > 24-epiBL > homoBL > CS > 24-epiCS > homoCS. Received July 21, 1997; accepted April 7, 1998     

Identification and characterization of a nitrate reductase gene from bean (Phaseolus vulgaris) containing four introns

A structural gene encoding nitrate reductase (NR) in bean ( Phaseolus vulgaris ) has been cloned and sequenced. The NR gene encodes a protein of 890 amino acids with a molecular mass of 100 kDa. Comparison to the other known NR gene from bean reveals 76% amino acid identity and comparison to NRs from other species shows amino acid identities ranging from 67 to 77%. At three positions the amino acid sequence displays differences from residues conserved in all other known NR proteins. The coding sequence is interrupted by four introns. Three of them are located at conserved positions in the region encoding the molybdenum cofactor-binding domain. The fourth intron is located in the hinge region between the heme and the FAD domain. This is the only example in which more than three introns have been found in a higher plant NR gene. The mRNA cap site was identified as an adenosine 79 nucleotides (nt) upstream of the ATG translation start codon. Northern analysis shows that the gene is nitrate inducible and highly expressed in trifoliolate leaves of 20-day-old bean plants and only weakly expressed in roots. The gene is also induced by light and sucrose in leaves of dark-adapted plants. The mRNA displays diurnal oscillation under the control of a circadian rhythm. Putative conserved GATA motifs in the promoter are discussed.     

Isolation and characterization of highly polymorphic microsatellite loci in the bladder campion,Silene vulgaris (Caryophyllaceae)

This study reports the isolation and characterization of seven highly polymorphic microsatellite loci in Silene vulgaris (Caryophyllaceae). The loci were isolated from two libraries constructed from genomic DNA enriched for CA and GA repeats. These markers yielded nine to 40 alleles per locus (mean 22.1) in a survey of 45 individuals from a single population located in the western Swiss Alps. Average observed heterozygosity ranged from 16.2 to 77.4%. These microsatellite loci should be valuable tools for studying fine‐scale genetic structure.     

Molecular characterization of sulfate-reducing bacteria in anaerobic hydrocarbon-degrading consortia and pure cultures using the dissimilatory sulfite reductase (dsrAB) genes

The characterization of sulfate-reducing bacteria (SRBs) is presented using the dissimilatory sulfite reductase (dsrAB) gene from various samples capable of mineralizing petroleum components. These samples include several novel, sulfidogenic pure cultures which degrade alkanes, toluene, and tribromophenol. Additionally, we have sulfidogenic consortia which re-mineralize benzene, naphthalene, 2-methylnaphthalene, and phenanthrene as a sole carbon source. In this study, 22 new dsrAB genes were cloned and sequenced. The dsrAB genes from our pollutant-degrading cultures or consortia were distributed among known SRBs and previously described dsrAB environmental clones, suggesting that many biodegradative SRBs are phylogenetically distinct and geographically wide spread. Specifically, the same dsrAB gene was discovered in independently established consortia capable of benzene, phenanthrene, and methylnaphthalene degradation, indicating that this particular SRB may be a key player in anaerobic degradation of hydrocarbons in the environment.     

Molecular structure, expression analysis and functional characterization of APRIL (TNFSF 13) in goat (Capra hircus)

A proliferation-inducing ligand (APRIL) is an important member of the tumor necrosis factor (TNF) superfamily. In the present study, a novel cDNA was isolated from the spleen of goat by RT-PCR and designated as goat APRIL (gAPRIL). The open reading frame (ORF) of this cDNA covered 753 bp, encoding a protein of 250 amino acids. Sequence comparison showed that gAPRIL contains a predicted transmembrane domain, a putative furin protease cleavage site, and two cysteine residues, which are the typical characteristics of TNF gene in mammals. The predicted three dimensional (3D) structure of soluble part of the gAPRIL (gsAPRIL) monomer analyzed by comparative protein modeling revealed that it is very similar to its counterparts. Real-time PCR analysis revealed that gAPRIL was constitutively expressed in various tissues. Recombinant gsAPRIL fused with NusA tag was efficiently produced in Escherichia coli BL21 (DE3) and then analyzed by the SDS-PAGE as well as western blot. Laser scanning confocal microscopy analysis showed gsAPRIL could bind to its receptors. In vitro, the MTT and flow cytometric methods revealed that purified gsAPRIL protein was not only able to promote survival/proliferation of goat splenocytes, but also able to stimulate survival/proliferation of mouse B cells. These results indicated that gAPRIL plays an important role in survival/proliferation of goat splenocytes and provided a basis for investigating its potential to be used as an immunoadjuvant for enhancing vaccine efficacy and as an immunotherapeutic in goats.     

Detection and characterization of acidic compartments (vacuoles) in Chlorella vulgaris 11h cells by 31P-in vivo NMR spectroscopy and cytochemical techniques

Acidic inorganic phosphate (Pi) pool (pH around 6) was detected besides the cytoplasmic pool in intact cells of Chlorella vulgaris 11h by ³¹P-in vivo nuclear magnetic resonance (NMR) spectroscopy. It was characterized as acidic compartments (vacuoles) in combination with the cytochemical technique; staining the cells with neutral red and chloroquine which are known as basic reagents specifically accumulated in acidic compartments. Under various conditions, the results obtained with the cytochemical methods were well correlated with those obtained from in vivo NMR spectra; the vacuoles were well developed in the cells at the stationary growth phase where the acidic Pi signal was detected. In contrast, cells at the logarithmic phase in which no acidic Pi signal was detected contained only smaller vesicles that accumulated these basic reagents. No acidic compartment was detected by both cytochemical technique and ³¹P-NMR spectroscopy when the cells were treated with NH₄OH. The vacuolar pH was lowered by the anaerobic treatment of the cells in the presence of glucose, while it was not affected by the external pH during the preincubation ranging from 3 to 10. Possible vacuolar functions in unicellular algae especially with respect to intracellular pH regulation are discussed.Non-standard abbreviations EDTA ethylenediaminetetraacetic acid - HEPES N-2-hydroxyethylpiperazine-N-2-ethanesulfonic acid - MDP methylene diphosphonic acid - NMR nuelear magnetic resonance - PCA perchloric acid - PCV packed cell volume - Pi inorganic phosphate - Pic sytoplasmic inorganic phosphate - Piv vacuolar inorganic phosphate - ppm parts per million - SP sugar phosphates - TCA trichloroacetic acid     

Isolation and characterization of polymorphic microsatellites isolated from the spotless starling (Sturnus unicolor) and cross‐species amplification in the European starling (Sturnus vulgaris)

Spotless and European starlings (Sturnus unicolor and Sturnus vulgaris) have attracted attention from researchers interested in sexual selection, evolution of parental care and reproductive strategies. Both species show high levels of intraspecific nest parasitism and extra‐pair paternity, but research in this area is hampered by a lack of molecular markers specific for these species. Here, we describe a set of primers for nine microsatellite loci in spotless starlings, eight of which are highly polymorphic (7.37 alleles in average). These microsatellites are also polymorphic in European starlings (6.75 alleles in average).     

Diversity,abundance and expression of nitrite reductase (nirK)-like genes in marine thaumarchaea

Ammonia-oxidizing archaea (AOA) are widespread and abundant in aquatic and terrestrial habitats and appear to have a significant impact on the global nitrogen cycle. Like the ammonia-oxidizing bacteria, AOA encode a gene homologous to copper-containing nitrite reductases (nirK), which has been studied very little to date. In this study, the diversity, abundance and expression of thaumarchaeal nirK genes from coastal and marine environments were investigated using two mutually excluding primer pairs, which amplify the nirK variants designated as AnirKa and AnirKb. Only the AnirKa variant could be detected in sediment samples from San Francisco Bay and these sequences grouped with the nirK from Candidatus Nitrosopumilus maritimus and Candidatus Nitrosoarchaeum limnia. The two nirK variants had contrasting distributions in the water column in Monterey Bay and the California Current. AnirKa was more abundant in the epi- to mesopelagic Monterey Bay water column, whereas AnirKb was more abundant in the meso- to bathypelagic California Current water. The abundance and community composition of AnirKb, but not AnirKa, followed that of thaumarchaeal amoA, suggesting that either AnirKa is not exclusively associated with AOA or that commonly used amoA primers may be missing a significant fraction of AOA diversity in the epipelagic. Interestingly, thaumarchaeal nirK was expressed 10–100-fold more than amoA in Monterey Bay. Overall, this study provides valuable new insights into the distribution, diversity, abundance and expression of this alternative molecular marker for AOA in the ocean.     

Polyamine synthesis in plants: isolation and characterization of spermidine synthase from soybean (Glycine max) axes

Spermidine synthase (EC 2.5.1.16) was purified to homogeneity for the cytosol of soybean (Glycine max) axes using ammonium sulfate fractionation and chromatography on DEAE-Sephacel, Sephacryl S-300, ω-aminooctyl-Sepharose and ATPA-Sepharose. The molecular mass of the enzyme estimated by gel filtration and SDS–PAGE is 74 kDa. Cadaverin and 1,6-diaminohexane could not replace putrescine as the aminopropyl acceptor. Kinetic behaviors of the substrate are consistent with a ping pong mechanism. The kinetic mechanism is further supported by direct evidence confirming the presence of an aminopropylated enzyme and identification of product, 5′-deoxy-5′-methylthioadenosine, prior to adding putrescine. The K_m values for decarboxylated S-adenosylmethionine and putrescine are 0.43 μM and 32.45 μM, respectively. Optimum pH and temperature for the enzyme reaction are 8.5 and 37°C, respectively. The enzyme activity is inhibited by N-ethylmaleimide and DTNB, but stimulated by Co²⁺, Cu²⁺ and Ca²⁺ significantly, suggesting that these metal ions could be the cellular regulators in polyamine biosynthesis.     

Molecular identification and characterization of wine yeasts isolated from Tenerife (Canary Island, Spain)

AIMS: The present study was aimed at the identification, differentiation and characterization of indigenous yeasts isolated from Tenerife vineyards (viticulture region that has never been characterized before). Microbiota were studied from 14 samples taken during fermentations carried out in the 2002 vintage, from 11 wineries belonging to five wine regions on Tenerife Island. METHODS AND RESULTS: Yeasts' strains were identified and characterized through restriction analysis of the 5.8S-internal transcribed spacer region and the mitochondrial DNA. At the beginning of alcoholic fermentation, 26 yeast species were found, where 14 species were present in significant frequencies in only one sample. Likewise, the Saccharomyces cerevisiae strains isolated are very specific, as they were only present in one wine region. CONCLUSIONS: There were isolated specific yeasts from each region on Tenerife Island. The founded yeasts may be responsible for distinctive and interesting properties of the studied wines. SIGNIFICANCE AND IMPACT OF THE STUDY: This study forms part of an extensive taxonomic survey within the ecological framework of vineyards in Tenerife. This investigation is an essential step towards the preservation and exploitation of the hidden oenological potential of the untapped wealth of yeast biodiversity in the grape growing regions of this island. The results obtained demonstrate the value of using molecular genetic methods in taxonomic and ecological surveys. The results also shed some light on the ecology and oenological potential of S. cerevisiae strains isolated from this unique environment.