Nitrate signalling on the nitrate reductase gene promoter depends directly on the activity of the nitrate transport systems in Chlamydomonas

Nutrient removal and biomass production of marine microalgae cultured in recirculating aquaculture systems (RAS) water with low phosphate concentration

This study was conducted to investigate the feasibility of microalgal biomass production and nutrient removal from recirculating aquaculture systems (RAS) water (RASW) with low phosphate concentration. For this purpose, Nannochloropsis oculata, Pavlova gyrans, Tetraselmis suecica, Phaeodactylum tricornutum, and their consortium were cultivated in RASW and RASW supplemented with vitamins (+V). Among them, N. oculata showed the maximum biomass production of 0.4 g/L in RASW. Vitamins supplementation significantly increased the growth of T. suecica from 0.16 g/L in RASW to 0.33 g/L in RASW + V. Additionally, T. suecica showed the highest nitrate (NO3-N) removal efficiency of 80.88 ± 2.08 % in RASW and 83.82 ± 2.08 % in RASW + V. Accordingly, T. suecica was selected for scaling up study of microalgal cultivation in RASW and RASW supplemented with nitrate (RASW + N) in 4-L airlift photobioreactors. Nitrate supplementation enhanced the growth of T. suecica up to 2.2-fold (day 15). The fatty acid nutritional indices in T. suecica cultivated in RASW and RASW + N showed optimal polyunsaturated fatty acids (PUFAs)/saturated fatty acid (SFAs), omega-6 fatty acid (n-6)/omega-3 fatty acid (n-3), indices of atherogenicity (IA), and thrombogenicity (IT)). Overall, the findings of this study revealed that despite low phosphate concentration, marine microalgae can grow in RASW and relatively reduce the concentration of nitrate. Furthermore, the microalgal biomass cultivated in RASW consisting of pigments and optimal fatty acid nutritional profile can be used as fish feed, thus contributing to a circular bioeconomy.

Emerging trends in nitrogen and phosphorus signalling in photosynthetic eukaryotes

Phosphorus (P) and nitrogen (N) are the major nutrients that constrain plant and algal growth in nature. Recent advances in understanding nutrient signalling mechanisms of these organisms have revealed molecular attributes to optimise N and P acquisition. This has illuminated the importance of interplay between N and P regulatory networks, highlighting a need to study synergistic interactions rather than single-nutrient effects. Emerging insights of nutrient signalling in polyphyletic model plants and algae hint that, although core P-starvation signalling components are conserved, distinct mechanisms for P (and N) sensing have arisen. Here, the N and P signalling mechanisms of diverse photosynthetic eukaryotes are examined, drawing parallels and differences between taxa. Future directions to understand their molecular basis, evolution, and ecology are proposed.

Reticulate evolution in eukaryotes: Origin and evolution of the nitrate assimilation pathway

Genes and genomes can evolve through interchanging genetic material, this leading to reticular evolutionary patterns. However, the importance of reticulate evolution in eukaryotes, and in particular of horizontal gene transfer (HGT), remains controversial. Given that metabolic pathways with taxonomically-patchy distributions can be indicative of HGT events, the eukaryotic nitrate assimilation pathway is an ideal object of investigation, as previous results revealed a patchy distribution and suggested that the nitrate assimilation cluster of dikaryotic fungi (Opisthokonta) could have been originated and transferred from a lineage leading to Oomycota (Stramenopiles). We studied the origin and evolution of this pathway through both multi-scale bioinformatic and experimental approaches. Our taxon-rich genomic screening shows that nitrate assimilation is present in more lineages than previously reported, although being restricted to autotrophs and osmotrophs. The phylogenies indicate a pervasive role of HGT, with three bacterial transfers contributing to the pathway origin, and at least seven well-supported transfers between eukaryotes. In particular, we propose a distinct and more complex HGT path between Opisthokonta and Stramenopiles than the one previously suggested, involving at least two transfers of a nitrate assimilation gene cluster. We also found that gene fusion played an essential role in this evolutionary history, underlying the origin of the canonical eukaryotic nitrate reductase, and of a chimeric nitrate reductase in Ichthyosporea (Opisthokonta). We show that the ichthyosporean pathway, including this novel nitrate reductase, is physiologically active and transcriptionally co-regulated, responding to different nitrogen sources; similarly to distant eukaryotes with independent HGT-acquisitions of the pathway. This indicates that this pattern of transcriptional control evolved convergently in eukaryotes, favoring the proper integration of the pathway in the metabolic landscape. Our results highlight the importance of reticulate evolution in eukaryotes, by showing the crucial contribution of HGT and gene fusion in the evolutionary history of the nitrate assimilation pathway.

One of the most relevant findings in evolution was that lineages, either genes or genomes, can evolve through interchanging genetic material. For example, exon shuffling can lead to genes with complete novel functions, and genomes can acquire novel functionalities by means of horizontal gene transfer (HGT). Whereas HGT is known to be an important driver of metabolic remodelling and ecological adaptations in Bacteria, its importance and prevalence in eukaryotes remains controversial. We show that HGT played a major role in the origin and evolution of the eukaryotic nitrate assimilation pathway, with several bacteria-to-eukaryote and eukaryote-to-eukaryote transfers promoting the acquisition of this ecologically-relevant pathway to autotrophs and to distinct groups of osmotrophs. Moreover, we also show that gene fusion was important in this evolutionary history, underlying the origin of the canonical eukaryotic nitrate reductase, but also of a non-canonical nitrate reductase that we describe in Ichthyosporea, a poorly-characterized eukaryotic group that includes many parasitic species. In conclusion, our results highlight the importance of reticulate evolution in eukaryotes, by showing the contribution of HGT and gene fusion in the evolutionary history of the nitrate assimilation pathway.

Development of a silicon limitation inducible expression system for recombinant protein production in the centric diatoms Thalassiosira pseudonana and Cyclotella cryptica

Background

An inducible promoter for recombinant protein expression provides substantial benefits because under induction conditions cellular energy and metabolic capability can be directed into protein synthesis. The most widely used inducible promoter for diatoms is for nitrate reductase, however, nitrogen metabolism is tied into diverse aspects of cellular function, and the induction response is not necessarily robust. Silicon limitation offers a means to eliminate energy and metabolic flux into cell division processes, with little other detrimental effect on cellular function, and a protein expression system that works under those conditions could be advantageous.

Results

In this study, we evaluate a number of promoters for recombinant protein expression induced by silicon limitation and repressed by the presence of silicon in the diatoms Thalassiosira pseudonana and Cyclotella cryptica. In addition to silicon limitation, we describe additional strategies to elevate recombinant protein expression level, including inclusion of the 5′ fragment of the coding region of the native gene and reducing carbon flow into ancillary processes of pigment synthesis and formation of photosynthetic storage products. We achieved yields of eGFP to 1.8% of total soluble protein in C. cryptica, which is about 3.6-fold higher than that obtained with chloroplast expression and ninefold higher than nuclear expression in another well-established algal system.

Conclusions

Our studies demonstrate that the combination of inducible promoter and other strategies can result in robust expression of recombinant protein in a nuclear-based expression system in diatoms under silicon limited conditions, separating the protein expression regime from growth processes and improving overall recombinant protein yields.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-017-0760-3) contains supplementary material, which is available to authorized users.

How Chlamydomonas handles nitrate and the nitric oxide cycle

The green alga Chlamydomonas is a valuable model system capable of assimilating different forms of nitrogen (N). Nitrate (NO3-) has a relevant role in plant-like organisms, first as a nitrogen source for growth and second as a signalling molecule. Several modules are necessary for Chlamydomonas to handle nitrate, including transporters, nitrate reductase (NR), nitrite reductase (NiR), GS/GOGAT enzymes for ammonium assimilation, and regulatory protein(s). Transporters provide a first step for influx/efflux, homeostasis, and sensing of nitrate; and NIT2 is the key transcription factor (RWP-RK) for mediating the nitrate-dependent activation of a number of genes. Here, we review how NR participates in the cycle NO3- →NO2- →NO →NO3-. NR uses the partner protein amidoxime-reducing component/nitric oxide-forming nitrite reductase (ARC/NOFNiR) for the conversion of nitrite (NO2-) into nitric oxide (NO). It also uses the truncated haemoglobin THB1 in the conversion of nitric oxide to nitrate. Nitric oxide is a negative signal for nitrate assimilation; it inhibits the activity and expression of high-affinity nitrate/nitrite transporters and NR. During this cycle, the positive signal of nitrate is transformed into the negative signal of nitric oxide, which can then be converted back into nitrate. Thus, NR is back in the spotlight as a strategic regulator of the nitric oxide cycle and the nitrate assimilation pathway.

Post-translational regulation of nitrogen transporters in plants and microorganisms

For microorganisms and plants, nitrate and ammonium are the main nitrogen sources and they are also important signaling molecules controlling several aspects of metabolism and development. Over the past decade, numerous studies revealed that nitrogen transporters are strongly regulated at the transcriptional level. However, more and more reports are now showing that nitrate and ammonium transporters are also subjected to post-translational regulations in response to nitrogen availability. Phosphorylation is so far the most well studied post-translational modification for these transporters and it affects both the regulation of nitrogen uptake and nitrogen sensing. For example, in Arabidopsis thaliana, phosphorylation was shown to activate the sensing function of the root nitrate transporter NRT1.1 and to switch the transport affinity. Also, for ammonium transporters, a phosphorylation-dependent activation/inactivation mechanism was elucidated in recent years in both plants and microorganisms. However, despite the fact that these regulatory mechanisms are starting to be thoroughly described, the signaling pathways involved and their action on nitrogen transporters remain largely unknown. In this review, we highlight the inorganic nitrogen transporters regulated at the post-translational level and we compare the known mechanisms in plants and microorganisms. We then discuss how these mechanisms could contribute to the regulation of nitrogen uptake and/or nitrogen sensing.

Understanding nitrate assimilation and its regulation in microalgae

Nitrate assimilation is a key process for nitrogen (N) acquisition in green microalgae. Among Chlorophyte algae, Chlamydomonas reinhardtii has resulted to be a good model system to unravel important facts of this process, and has provided important insights for agriculturally relevant plants. In this work, the recent findings on nitrate transport, nitrate reduction and the regulation of nitrate assimilation are presented in this and several other algae. Latest data have shown nitric oxide (NO) as an important signal molecule in the transcriptional and posttranslational regulation of nitrate reductase and inorganic N transport. Participation of regulatory genes and proteins in positive and negative signaling of the pathway and the mechanisms involved in the regulation of nitrate assimilation, as well as those involved in Molybdenum cofactor synthesis required to nitrate assimilation, are critically reviewed.

The inducible nitA promoter provides a powerful molecular switch for transgene expression in Volvox carteri

BACKGROUND

The multicellular green alga Volvox carteri represents an attractive model system to study various aspects of multicellularity like cellular differentiation, morphogenesis, epithelial folding and ECM biogenesis. However, functional and molecular analyses of such processes require a wide array of molecular tools for genetic engineering. So far there are only a limited number of molecular tools available in Volvox.

RESULTS

Here, we show that the promoter of the V. carteri nitrate reductase gene (nitA) is a powerful molecular switch for induction of transgene expression. Strong expression is triggered by simply changing the nitrogen source from ammonium to nitrate. We also show that the luciferase (g-luc) gene from the marine copepod Gaussia princeps, which previously was engineered to match the codon usage of the unicellular alga Chlamydomonas reinhardtii, is a suitable reporter gene in V. carteri. Emitted light of the chemiluminescent reaction can be easily detected and quantified with a luminometer. Long-term stability of inducible expression of the chimeric nitA/g-luc transgenes after stable nuclear transformation was demonstrated by transcription analysis and bioluminescence assays.

CONCLUSION

Two novel molecular tools for genetic engineering of Volvox are now available: the nitrate-inducible nitA promoter of V. carteri and the codon-adapted luciferase reporter gene of G. princeps. These novel tools will be useful for future molecular research in V. carteri.

Chlamydomonas NZF1, a tandem-repeated zinc finger factor involved in nitrate signalling by controlling the regulatory gene NIT2

The Chlamydomonas reinhardtii NIT2 gene plays a central role in nitrate assimilation, thus, nit2 mutants are not able to sense or to use nitrate for growth. NIT2 protein is an RWP-RK-type transcriptional factor related to nodule inception (Nin, NLP) proteins from plants. NIT2 expression is down-regulated in ammonium and up-regulated under nitrogen deprivation. However, intracellular nitrate is required to activate NIT2 for subsequent expression of NIA1 and other nitrate assimilation genes. In this work, mutants defective in nitrate sensing have been studied. The identification of genomic regions affected allows proposing putative loci/genes for nitrate signalling in the alga. Among them, a CrNZF1 (Nitrate Zinc Finger 1) that encodes a tandem zinc finger protein CCCH-type. In the nzf1 mutant, the expression of the regulatory gene NIT2 is decreased and also that of nitrate assimilation genes. In this mutant, polyadenylated forms of NIT2 with different lengths could be detected, whereas in the wild type there appeared preferentially the longest forms. CrNZF1 is proposed to regulate NIT2 polyadenylation and thus nitrate signalling and nitrate-dependent growth in the alga.

Regulation by Light of Chemotaxis to Nitrite during the Sexual Life Cycle in Chlamydomonas reinhardtii

Nitrite plays an important role in the nitrogen metabolism of most cells, including Chlamydomonas reinhardtii. We have shown that vegetative cells of C. reinhardtii are attracted by nitrite. The Nia1nit2 mutant with defects in genes encoding the nitrate reductase and regulatory protein NIT2 respectively was found to exhibit normal chemotaxis to nitrite. The data suggest that chemotaxis events appear to be specific and independent of those involved in nitrate assimilation. Unlike vegetative cells and noncompetent pregametes, mature gametes did not show chemotaxis to nitrite. Just like gamete formation, the change in chemotaxis mode is controlled by the sequential action of two environmental cues, removal of nitrogen from the medium and light. Comparative analysis of wild-type and RNAi strains with reduced level of phototropin has indicated that switch-off of chemotaxis towards nitrite is dependent on phototropin. The studies revealed individual elements of the phototropin-dependent signal transduction pathway involved in the blue-light-controlled change in chemotaxis mode of C. reinhardtii during gamete formation: three protein kinases, one operating against signal flux and two that promote signal transduction. We have proposed a working model for the signaling pathway by which blue light controls chemotaxis towards attractants, which are nitrogen sources, during pregamete-to-gamete conversion of C. reinhardtii.

Combined intracellular nitrate and NIT2 effects on storage carbohydrate metabolism in Chlamydomonas

Microalgae are receiving increasing attention as alternative production systems for renewable energy such as biofuel. The photosynthetic alga Chlamydomonas reinhardtii is widely recognized as the model system to study all aspects of algal physiology, including the molecular mechanisms underlying the accumulation of starch and triacylglycerol (TAG), which are the precursors of biofuel. All of these pathways not only require a carbon (C) supply but also are strongly dependent on a source of nitrogen (N) to sustain optimal growth rate and biomass production. In order to gain a better understanding of the regulation of C and N metabolisms and the accumulation of storage carbohydrates, the effect of different N sources (NH4NO3 and ) on primary metabolism using various mutants impaired in either NIA1, NIT2 or both loci was performed by metabolic analyses. The data demonstrated that, using NH4NO3, nia1 strain displayed the most striking phenotype, including an inhibition of growth, accumulation of intracellular nitrate, and strong starch and TAG accumulation. The measurements of the different C and N intermediate levels (amino, organic, and fatty acids), together with the determination of acetate and remaining in the medium, clearly excluded the hypothesis of a slower and acetate assimilation in this mutant in the presence of NH4NO3. The results provide evidence of the implication of intracellular nitrate and NIT2 in the control of C partitioning into different storage carbohydrates under mixotrophic conditions in Chlamydomonas. The underlying mechanisms and implications for strategies to increase biomass yield and storage product composition in oleaginous algae are discussed.

In praise of erroneous hypotheses

In the sixties Cove and Pateman discovered that mutants of Aspergillus nidulans lacking nitrate reductase activity were constitutive for the expression of genes induced by nitrate and dependent on the transcription factor NirA. They proposed that the nitrate protein acted as a repressor, preventing the transcription factor activity of NirA. Nitrate-mediated regulation behaved similarly in other organisms. This "autogenous regulation hypothesis" has recently shown to be erroneous, in the very organism for which it was first proposed. Nevertheless this erroneous hypothesis have led to a thorough dissection of the process of regulation of nitrate assimilation and more importantly to a hypothesis bearing on the origin of metabolite-responsive transcription factors. In this article I discuss the heuristic value and evolutionary importance of autogenous regulation.

Pseudo-constitutivity of nitrate-responsive genes in nitrate reductase mutants

In fungi, transcriptional activation of genes involved in NO3- assimilation requires the presence of an inducer (nitrate or nitrite) and low intracellular concentrations of the pathway products ammonium or glutamine. In Aspergillus nidulans, the two transcription factors NirA and AreA act synergistically to mediate nitrate/nitrite induction and nitrogen metabolite derepression, respectively. In all studied fungi and in plants, mutants lacking nitrate reductase (NR) activity express nitrate-metabolizing enzymes constitutively without the addition of inducer molecules. Based on their work in A. nidulans, Cove and Pateman proposed an “autoregulation control” model for the synthesis of nitrate metabolizing enzymes in which the functional nitrate reductase molecule would act as co-repressor in the absence and as co-inducer in the presence of nitrate. However, NR mutants could simply show “pseudo-constitutivity” due to induction by nitrate which accumulates over time in NR-deficient strains. Here we examined this possibility using strains which lack flavohemoglobins (fhbs), and are thus unable to generate nitrate internally, in combination with nitrate transporter mutations (nrtA, nrtB) and a GFP-labeled NirA protein. Using different combinations of genotypes we demonstrate that nitrate transporters are functional also in NR null mutants and show that the constitutive phenotype of NR mutants is not due to nitrate accumulation from intracellular sources but depends on the activity of nitrate transporters. However, these transporters are not required for nitrate signaling because addition of external nitrate (10 mM) leads to standard induction of nitrate assimilatory genes in the nitrate transporter double mutants. We finally show that NR does not regulate NirA localization and activity, and thus the autoregulation model, in which NR would act as a co-repressor of NirA in the absence of nitrate, is unlikely to be correct. Results from this study instead suggest that transporter-mediated NO3- accumulation in NR deficient mutants, originating from traces of nitrate in the media, is responsible for the constitutive expression of NirA-regulated genes, and the associated phenotype is thus termed “pseudo-constitutive”.

Npr1 Ser/Thr protein kinase links nitrogen source quality and carbon availability with the yeast nitrate transporter (Ynt1) levels

Ynt1, the single high affinity nitrate and nitrite transporter of the yeast Hansenula polymorpha, is regulated by the quality of nitrogen sources. Preferred nitrogen sources cause Ynt1 dephosphorylation, ubiquitinylation, endocytosis, and vacuolar degradation. In contrast, under nitrogen limitation Ynt1 is phosphorylated and sorted to the plasma membrane. We show here the involvement of the Ser/Thr kinase HpNpr1 in Ynt1 phosphorylation and regulation of Ynt1 levels in response to nitrogen source quality and the availability of carbon. In Δnpr1, Ynt1 phosphorylation does not take place, although Ynt1 ubiquitin conjugates increase. As a result, in this strain Ynt1 is sorted to the vacuole, from both plasma membrane and the later biosynthetic pathway in nitrogen-free conditions and nitrate. In contrast, overexpression of NPR1 blocks down-regulation of Ynt1, increasing Ynt1 phosphorylation at Ser-244 and -246 and reducing ubiquitinylation. Furthermore, Npr1 is phosphorylated in response to the preferred nitrogen sources, and indeed it is dephosphorylated in nitrogen-free medium. Under conditions where Npr1 is phosphorylated, Ynt1 is not and vice versa. We show for the first time that carbon starvation leads to Npr1 phosphorylation, whereas Ynt1 is dephosphorylated and degraded in the vacuole. Rapamycin prevents this, indicating a possible role of the target of rapamycin signaling pathway in this process. We concluded that Npr1 plays a key role in adapting Ynt1 levels to the nitrogen quality and availability of a source of carbon.

Transcriptional regulation of CDP1 and CYG56 is required for proper NH4+ sensing in Chlamydomonas

The assimilation of inorganic nitrogen is an essential process for all plant-like organisms. In the presence of ammonium and nitrate as nitrogen sources, Chlamydomonas reinhardtii preferentially assimilates ammonium and represses the nitrate assimilation pathway through an unknown mechanism that in part involves the guanylate cyclase CYG56. It is demonstrated that cells not only respond quantitatively to the NH(4)(+) signal but are also able to sense a balance between both nitrogen sources. This quantitative response was altered in a collection of mutants that were partially insensitive to NH(4)(+). In one of these mutants, reduced function of a gene named CDP1 encoding a cysteine domain-containing protein was genetically linked to NH(4)(+) insensitivity. Alteration of CYG56 or CDP1 transcription was detected in several mutants, and combined down-regulation of both genes seemed to enhance the incapacity to sense NH(4)(+) properly. These results suggest that transcriptional regulation of CYG56 and CDP1 are central and independent steps of the NH(4)(+) signalling pathway.

A soluble guanylate cyclase mediates negative signaling by ammonium on expression of nitrate reductase in Chlamydomonas

Nitrate assimilation in plants and related organisms is a highly regulated and conserved pathway in which the enzyme nitrate reductase (NR) occupies a central position. Although some progress has been made in understanding the regulation of the protein, transcriptional regulation of the NR gene (NIA1) is poorly understood. This work describes a mechanism for the ammonium-mediated repression of NIA1. We report the characterization of a mutant defective in the repression of NIA1 and NR in response to ammonium and show that a gene (CYG56) coding for a nitric oxide (NO)-dependent guanylate cyclase (GC) was interrupted in this mutant. NO donors, cGMP analogs, a phosphodiesterase inhibitor isobutylmethylxanthine (IBMX), and a calcium ionophore (A23187) repress the expression of NIA1 in Chlamydomonas reinhardtii wild-type cells and also repress the expression of other ammonium-sensitive genes. In addition, the GC inhibitors LY83,583 (6-anilino-5,8-quinolinedione) and ODQ (1H-[1,2,4]oxadiazolo-[4,3-a]quinoxalin-1-one) release cells from ammonium repression. Intracellular NO and cGMP levels were increased in the presence of ammonium in wild-type cells. In the cyg56 mutant, NIA1 transcription was less sensitive to NO donors and A23187, but responded like the wild type to IBMX. Results presented here suggest that CYG56 participates in ammonium-mediated NIA1 repression through a pathway that involves NO, cGMP, and calcium and that similar mechanisms might be occurring in plants.

Nuclear transformation of eukaryotic microalgae: historical overview, achievements and problems

Transformation of microalgae is a first step in their use for biotechnological applications involving foreign protein production or molecular modifications of specific cell metabolic pathways. Since the first reliable achievements of nuclear transformation in Chlamydomonas, other eukaryotic microalgae have become transformed with molecular markers that allow a direct selection. Different methods--glass beads, electroporation, particle bombardment, or Agrobacterium--and constructions have been set up in several organisms and successfully used. However, some problems associated with efficiency, integration, or stability of the transgenes still persist and are analysed herein. Though the number of microalgae species successfully transformed is not very high, prospects for transformation of many more are good enough on the basis of what has been achieved so far.

Phosphorylation of the yeast nitrate transporter Ynt1 is essential for delivery to the plasma membrane during nitrogen limitation

Ynt1 is the sole high affinity nitrate transporter of the yeast Hansenula polymorpha. It is highly regulated by the nitrogen source, by being down-regulated in response to glutamine by repression of the YNT1 gene and Ynt1 ubiquitinylation, endocytosis, and vacuolar degradation. On the contrary, we show that nitrogen limitation stabilizes Ynt1 levels at the plasma membrane, requiring phosphorylation of the transporter. We determined that Ser-246 in the central intracellular loop plays a key role in the phosphorylation of Ynt1 and that the nitrogen permease reactivator 1 kinase (Npr1) is necessary for Ynt1 phosphorylation. Abolition of phosphorylation led Ynt1 to the vacuole by a pep12-dependent end4-independent pathway, which is also dependent on ubiquitinylation, whereas Ynt1 protein lacking ubiquitinylation sites does not follow this pathway. We found that, under nitrogen limitation, Ynt1 phosphorylation is essential for rapid induction of nitrate assimilation genes. Our results suggest that, under nitrogen limitation, phosphorylation prevents Ynt1 delivery from the secretion route to the vacuole, which, aided by reduced ubiquitinylation, accumulates Ynt1 at the plasma membrane. This mechanism could be part of the response that allows nitrate-assimilatory organisms to cope with nitrogen depletion.

Nitrate reductases: structure, functions, and effect of stress factors

Structural and functional peculiarities of four types of nitrate reductases are considered: assimilatory nitrate reductase of eukaryotes, as well as cytoplasmic assimilatory, membrane-bound respiratory, and periplasmic dissimilatory bacterial nitrate reductases. Arguments are presented showing that eukaryotic organisms are capable of nitrate dissimilation. Data concerning new classes of extremophil nitrate reductases, whose active center does not contain molybdocofactor, are summarized.

Nitrite acts as a transcriptome signal at micromolar concentrations in Arabidopsis roots

Nitrate serves as a potent signal to control gene expression in plants and algae, but little is known about the signaling role of nitrite, the direct product of nitrate reduction. Analysis of several nitrate-induced genes showed that nitrite increases mRNA levels as rapidly as nitrate in nitrogen-starved Arabidopsis (Arabidopsis thaliana) roots. Both nitrite and nitrate induction are apparent at concentrations as low as 100 nm. The response at low nitrite concentrations was not due to contaminating nitrate, which was present at <1% of the nitrite concentration. High levels of ammonium (20 mm) in the growth medium suppressed induction of several genes by nitrate, but had varied effects on the nitrite response. Transcriptome analysis using 250 or 5 microm nitrate or nitrite showed that over one-half of the nitrate-induced genes, which included genes involved in nitrate and ammonium assimilation, energy production, and carbon and nitrogen metabolism responded equivalently to nitrite; however, the nitrite response was more robust and there were many genes that responded specifically to nitrite. Thus, nitrite can serve as a signal as well as if not better than nitrate.

Nitrate signaling by the regulatory gene NIT2 in Chlamydomonas

Positive signaling by nitrate in its assimilation pathway has been studied in Chlamydomonas reinhardtii. Among >34,000 lines generated by plasmid insertion, 10 mutants were unable to activate nitrate reductase (NIA1) gene expression and had a Nit(-) (no growth in nitrate) phenotype. Each of these 10 lines was mutated in the nitrate assimilation-specific regulatory gene NIT2. The complete NIT2 cDNA sequence was obtained, and its deduced amino acid sequence revealed GAF, Gln-rich, Leu zipper, and RWP-RK domains typical of transcription factors and transcriptional coactivators associated with signaling pathways. The predicted Nit2 protein sequence is structurally related to the Nin (for nodule inception) proteins from plants but not to NirA/Nit4/Yna proteins from fungi and yeast. NIT2 expression is negatively regulated by ammonium and is optimal in N-free medium with no need for the presence of nitrate. However, intracellular nitrate is required to allow Nit2 to activate the NIA1 promoter activity. Nit2 protein was expressed in Escherichia coli and shown to bind to specific sequences at the NIA1 gene promoter. Our data indicate that NIT2 is a central regulatory gene required for nitrate signaling on the Chlamydomonas NIA1 gene promoter and that intracellular nitrate is needed for NIT2 function and to modulate NIA1 transcript levels.

Distinct roles of nitrate and nitrite in regulation of expression of the nitrate transport genes in the moss Physcomitrella patens

Five NRT2 genes and three Nar2 genes, encoding putative high-affinity nitrate transporters, and the respective cDNAs were identified and characterized in Physcomitrella patens. The deduced moss NRT2 and NAR2 proteins were more similar to the corresponding proteins of higher plants than to those of the green alga Chlamydomonas reinhardtii. Expression of all the genes was inhibited by ammonium added to the medium. The regulation by ammonium was abolished by an inhibitor of glutamine synthetase, but the effect of this inhibitor was counteracted by an inhibitor of glutamate synthase. Negative correlation was observed between the glutamine content of protonemata and the transcript levels of PpNRT2 and PpNar2. These results indicated that glutamine is the signal for repression of the genes. All the genes except PpNRT2;5 showed transient expression stimulated by nitrate but not by nitrite, peaking at 2-4 h after the medium was deprived of ammonium. When the glutamine synthetase inhibitor was used to inhibit assimilation of the ammonium generated intracellularly from nitrate or nitrite, the second phase of activation of genes became manifest at approximately 8 h after the medium was deprived of ammonium. Surprisingly, both nitrate and nitrite stimulated gene expression at this stage. PpNRT2;5 was distinct from the other genes in that its expression is sharply induced by nitrite, is strictly dependent on nitrite or nitrate, and is much less susceptible to the feedback regulation, retaining a constant level in nitrate-containing medium. These results indicated that P. patens has multiple mechanisms for sensing nitrate and nitrite.

The GATA factor AreA regulates localization and in vivo binding site occupancy of the nitrate activator NirA

The GATA factor AreA is a wide-domain regulator in Aspergillus nidulans with transcriptional activation and chromatin remodelling functions. AreA interacts with the nitrate-specific Zn(2)-C(6) cluster protein NirA and both proteins cooperate to synergistically activate nitrate-responsive genes. We have previously established that NirA in vivo DNA binding site occupancy is AreA dependent and in this report we provide a mechanistic explanation for our previous findings. We now show that AreA regulates NirA at two levels: (i) through the regulation of nitrate transporters, AreA affects indirectly the subcellular distribution of NirA which rapidly accumulates in the nucleus following induction; (ii) AreA directly stimulates NirA in vivo target DNA occupancy and does not act indirectly by chromatin remodelling. Simultaneous overexpression of NirA and the nitrate transporter CrnA bypasses the AreA requirement for NirA binding, permits utilization of nitrate and nitrite as sole N-sources in an areA null strain and leads to an AreA-independent nucleosome loss of positioning.

Functional genomics of the regulation of the nitrate assimilation pathway in Chlamydomonas

The existence of mutants at specific steps in a pathway is a valuable tool of functional genomics in an organism. Heterologous integration occurring during transformation with a selectable marker in Chlamydomonas (Chlamydomonas reinhardtii) has been used to generate an ordered mutant library. A strain, having a chimeric construct (pNia1::arylsulfatase gene) as a sensor of the Nia1 gene promoter activity, was transformed with a plasmid bearing the paramomycin resistance AphVIII gene to generate insertional mutants defective at regulatory steps of the nitrate assimilation pathway. Twenty-two thousand transformants were obtained and maintained in pools of 96 for further use. The mutant library was screened for the following phenotypes: insensitivity to the negative signal of ammonium, insensitivity to the positive signal of nitrate, overexpression in nitrate, and inability to use nitrate. Analyses of mutants showed that (1) the number or integrated copies of the gene marker is close to 1; (2) the probability of cloning the DNA region at the marker insertion site is high (76%); (3) insertions occur randomly; and (4) integrations at different positions and orientations of the same genomic region appeared in at least three cases. Some of the mutants analyzed were found to be affected at putative new genes related to regulatory functions, such as guanylate cyclase, protein kinase, peptidyl-prolyl isomerase, or DNA binding. The Chlamydomonas mutant library constructed would also be valuable to identify any other gene with a screenable phenotype.

Ammonium transporter genes in Chlamydomonas: the nitrate-specific regulatory gene Nit2 is involved in Amt1;1 expression

Ammonium transport is a key process in nitrogen metabolism. In the green alga Chlamydomonas, we have characterized molecularly the largest family of ammonium transporters (AMT1) so far described consisting of eight members. CrAmt1 genes have an interesting transcript structure with some very small exons. Differential expression patterns were found for each CrAmt1 gene in response to the nitrogen source by using Real Time PCR. These expression patterns were similar under high and low CO2 atmosphere. CrAmt1;1 expression was characterized in detail. It was repressed in both ammonium and nitrate medium, and strongly expressed in nitrogen-free media. Treatment with a Glutamine synthetase inhibitor released partially repression in ammonium and nitrate suggesting that ammonium and its derivatives participate in the observed repressing effects. By studying CrAmt1;1 expression in mutants deficient at different steps of the nitrate assimilation pathway, it has been shown that nitrate has a double negative effect on this gene expression; one related to its reduction to ammonium, and a second one by itself. This second effect of nitrate was dependent on the functionality of the regulatory gene Nit2, specific for nitrate assimilation. Thus, NIT2 would have a dual role on gene expression: the well-known positive one on nitrate assimilation and a novel negative one on Amt1;1 regulation.

The role of nitrate reductase in the regulation of the nitrate assimilation pathway in the yeast Hansenula polymorpha

The role of nitrate reductase (NR) in the regulation of the nitrate assimilation pathway was evaluated in the yeast Hansenula polymorpha. Posttranscriptional regulation of NR in response to reduced nitrogen sources and the effect of a heterologous NR on the transcriptional regulation of nitrate-assimilatory gene expression was examined. The strain bearing YNR1 (nitrate reductase gene) under the control of the methanol-induced MOX (methanol oxidase) promoter showed that NR is active in the presence of reduced nitrogen sources. In cells incubated with glutamine plus nitrate, rapamycin abolished nitrogen catabolite repression, NR activity being very similar to that in cells induced by nitrate alone. This reveals the involvement of the Tor-signalling pathway in the transcriptional regulation of H. polymorpha nitrate assimilation genes. To assess the role of NR in nitrate-assimilatory gene expression, different strains lacking YNR1, or both YNR1 and YNT1 (high-affinity nitrate transporter) genes, or expressing the tobacco NR under the YNR1 promoter, were used. Tobacco NR abolished the constitutive nitrate-assimilatory gene induction shown by an NR gene disruptant strain. Moreover, in strains lacking the high-affinity nitrate transporter and NR this deregulation disappeared. These facts discard the role of NR protein in the transcriptional induction of the nitrate-assimilatory genes and point out the involvement of the high-affinity nitrate transporter as a part of the nitrate-signalling pathway.

Regulation of the alternative oxidase Aox1 gene in Chlamydomonas reinhardtii. Role of the nitrogen source on the expression of a reporter gene under the control of the Aox1 promoter

In higher plants, various developmental and environmental conditions enhance expression of the alternative oxidase (AOX), whereas its induction in fungi is mainly dependent on cytochrome pathway restriction and triggering by reactive oxygen species. The AOX of the unicellular green alga Chlamydomonas reinhardtii is encoded by two different genes, the Aox1 gene being much more transcribed than Aox2. To analyze the transcriptional regulation of Aox1, we have fused its 1.4-kb promoter region to the promoterless arylsulfatase (Ars) reporter gene and measured ARS enzyme activities in transformants carrying the chimeric construct. We show that the Aox1 promoter is generally unresponsive to a number of known AOX inducers, including stress agents, respiratory inhibitors, and metabolites, possibly because the AOX activity is constitutively high in the alga. In contrast, the Aox1 expression is strongly dependent on the nitrogen source, being down-regulated by ammonium and stimulated by nitrate. Inactivation of nitrate reductase leads to a further increase of expression. The stimulation by nitrate also occurs at the AOX protein and respiratory levels. A deletion analysis of the Aox1 promoter region demonstrates that a short upstream segment (-253 to +59 with respect to the transcription start site) is sufficient to ensure gene expression and regulation, but that distal elements are required for full gene expression. The observed pattern of AOX regulation points to the possible interaction between chloroplast and mitochondria in relation to a potential increase of photogenerated ATP when nitrate is used as a nitrogen source.