Regulation of glutamine synthetase activity in the unicellular cyanobacterium Synechocystis sp. strain PCC 6803 by the nitrogen source: effect of ammonium

Synergistic regulation of hydrogen sulfide and nitric oxide on biochemical components, exopolysaccharides, and nitrogen metabolism in nickel stressed rice field cyanobacteria

The present study examined the regulatory mechanism of hydrogen sulfide (H2S) and nitric oxide (NO) in nickel (Ni) stressed cyanobacteria viz., Nostoc muscorum and Anabaena sp. by analyzing growth, photosynthetic pigments, biochemical components (protein and carbohydrate), exopolysaccharides (EPS), inorganic nitrogen content, and activity of enzymes comprised in nitrogen metabolism and Ni accumulation. The 1 µM Ni substantially diminished growth by 18% and 22% in N. muscorum and Anabaena sp. respectively, along with declining the pigment contents (Chl a/Car ratio and phycobiliproteins), and biochemical components. It also exerted negative impacts on inorganic uptake of nitrate and nitrite contents; nitrate reductase and nitrite reductase; and ammonium assimilating enzymes (glutamine synthetase, glutamate synthase, and glutamate dehydrogenase exhibited a reverse trend) activities. Nonetheless, the adverse impact of Ni can be mitigated through the exogenous supplementation of NaHS [sodium hydrosulfide (8 µM); H2S donor] and SNP [sodium nitroprusside (10 µM); NO donor] which showed substantial improvement on growth, pigments, nitrogen metabolism, and EPS layer and noticeably occurred as a consequence of a substantial reduction in Ni accumulation content which minimized the toxicity effects. The accumulation of Ni on both the cyanobacterial cell surface (EPS layer) are confirmed by the SEM-EDX analysis. Further, the addition of NO scavenger (PTIO; 20 µM) and inhibitor of NO (L-NAME; 100 µM); and H2S scavenger (HT; 20 µM) and H2S inhibitor (PAG; 50 µM) reversed the positive responses of H2S and NO and damages were more prominent under Ni stress thereby, suggesting the downstream signaling of H2S on NO-mediated alleviation. Thus, this study concludes the crosstalk mechanism of H2S and NO in the mitigation of Ni-induced toxicity in rice field cyanobacteria.

Improved lipid production and component of mycosporine-like amino acids by co-overexpression of amt1 and aroB genes in Synechocystis sp. PCC6803

Implementing homologous overexpression of the amt1 (A) and aroB (B) genes involved in ammonium transporter and the synthesis of mycosporine-like amino acids (MAAs) and aromatic amino acids, respectively, we created three engineered Synechocystis sp. PCC6803 strains, including Ox-A, Ox-B, and Ox-AB, to study the utilization of carbon and nitrogen in cyanobacteria for the production of valuable products. With respect to amt1 overexpression, the Ox-A and Ox-AB strains had a greater growth rate under (NH4)2SO4 supplemented condition. Both the higher level of intracellular accumulation of lipids in Ox-A and Ox-AB as well as the increased secretion of free fatty acids from the Ox-A strain were impacted by the late-log phase of cell growth. It is noteworthy that among all strains, the Ox-B strain undoubtedly spotted a substantial accumulation of glycogen as a consequence of aroB overexpression. Additionally, the ammonium condition drove the potent antioxidant activity in Ox strains with a late-log phase, particularly in the Ox-B and Ox-AB strains. This was probably related to the altered MAA component inside the cells. The higher proportion of P4-fraction was induced by the ammonium condition in both Ox-B and Ox-AB, while the noted increase of the P1 component was found in the Ox-A strain.

The Signal Transduction Protein PII Controls the Levels of the Cyanobacterial Protein PipX

Cyanobacteria, microorganisms performing oxygenic photosynthesis, must adapt their metabolic processes to environmental challenges such as day and night changes. PipX, a unique regulatory protein from cyanobacteria, provides a mechanistic link between the signalling protein PII, a widely conserved (in bacteria and plants) transducer of carbon/nitrogen/energy richness, and the transcriptional regulator NtcA, which controls a large regulon involved in nitrogen assimilation. PipX is also involved in translational regulation through interaction with the ribosome-assembly GTPase EngA. However, increases in the PipX/PII ratio are toxic, presumably due to the abnormally increased binding of PipX to other partner(s). Here, we present mutational and structural analyses of reported PipX-PII and PipX-NtcA complexes, leading to the identification of single amino acid changes that decrease or abolish PipX toxicity. Notably, 4 out of 11 mutations decreasing toxicity did not decrease PipX levels, suggesting that the targeted residues (F12, D23, L36, and R54) provide toxicity determinants. In addition, one of those four mutations (D23A) argued against the over-activation of NtcA as the cause of PipX toxicity. Most mutations at residues contacting PII decreased PipX levels, indicating that PipX stability would depend on its ability to bind to PII, a conclusion supported by the light-induced decrease of PipX levels in Synechococcus elongatus PCC7942 (hereafter S. elongatus).

Glycine differentially improved the growth and biochemical composition of Synechocystis sp. PAK13 and Chlorella variabilis DT025

The potential of microalgae to produce valuable compounds has garnered considerable attention. However, there are various challenges that hinder their large-scale industrial utilization, such as high production costs and the complexities associated with achieving optimal growth conditions. Therefore, we investigated the effects of glycine at different concentrations on the growth and bioactive compounds production of Synechocystis sp. PAK13 and Chlorella variabilis cultivated under nitrogen availability. Glycine supplementation resulted in increased biomass and bioactive primary metabolites accumulation in both species. Sugar production, particularly glucose content, significantly improved in Synechocystis at 3.33 mM glycine (1.4 mg/g). This led to enhanced organic acid, particularly malic acid, and amino acids production. Glycine stress also influenced the concentration of indole-3-acetic acid, which was significantly higher in both species compared to the control. Furthermore, fatty acids content increased by 2.5-fold in Synechocystis and by 1.36-fold in Chlorella. Overall, the exogenous application of glycine is a cheap, safe, and effective approach to enhancing sustainable microalgal biomass and bioproducts production.

A mechanistic study of the influence of nitrogen and energy availability on the NH4+ sensitivity of nitrogen assimilation in Synechococcus

In most algae, NO3- assimilation is tightly controlled and is often inhibited by the presence of NH4+. In the marine, non-colonial, non-diazotrophic cyanobacterium Synechococcus UTEX 2380, NO3- assimilation is sensitive to NH4+ only when N does not limit growth. We sequenced the genome of Synechococcus UTEX 2380, studied the genetic organization of the nitrate assimilation related (NAR) genes, and investigated expression and kinetics of the main NAR enzymes, under N or light limitation. We found that Synechococcus UTEX 2380 is a β-cyanobacterium with a full complement of N uptake and assimilation genes and NAR regulatory elements. The nitrate reductase of our strain showed biphasic kinetics, previously observed only in freshwater or soil diazotrophic Synechococcus strains. Nitrite reductase and glutamine synthetase showed little response to our growth treatments, and their activity was usually much higher than that of nitrate reductase. NH4+ insensitivity of NAR genes may be associated with the stimulation of the binding of the regulator NtcA to NAR gene promoters by the high 2-oxoglutarate concentrations produced under N limitation. NH4+ sensitivity in energy-limited cells fits with the fact that, under these conditions, the use of NH4+ rather than NO3- decreases N-assimilation cost, whereas it would exacerbate N shortage under N limitation.

Nitrogen Availability Affects the Metabolic Profile in Cyanobacteria

Nitrogen is essential for the biosynthesis of various molecules in cells, such as amino acids and nucleotides, as well as several types of lipids and sugars. Cyanobacteria can assimilate several forms of nitrogen, including nitrate, ammonium, and urea, and the physiological and genetic responses to these nitrogen sources have been studied previously. However, the metabolic changes in cyanobacteria caused by different nitrogen sources have not yet been characterized. This study aimed to elucidate the influence of nitrate and ammonium on the metabolic profiles of the cyanobacterium Synechocystis sp. strain PCC 6803. When supplemented with NaNO₃ or NH₄Cl as the nitrogen source, Synechocystis sp. PCC 6803 grew faster in NH₄Cl medium than in NaNO₃ medium. Metabolome analysis indicated that some metabolites in the CBB cycle, glycolysis, and TCA cycle, and amino acids were more abundant when grown in NH₄Cl medium than NaNO₃ medium. ¹⁵N turnover rate analysis revealed that the nitrogen assimilation rate in NH₄Cl medium was higher than in NaNO₃ medium. These results indicate that the mechanism of nitrogen assimilation in the GS-GOGAT cycle differs between NaNO₃ and NH₄Cl. We conclude that the amounts and biosynthetic rate of cyanobacterial metabolites varies depending on the type of nitrogen.

Interplay of hydrogen peroxide and nitric oxide: systemic regulation of photosynthetic performance and nitrogen metabolism in cadmium challenged cyanobacteria

In the present study, the potential role of hydrogen peroxide (H₂O₂) and nitric oxide (NO) has been well recorded in the induction of cadmium (Cd) stress tolerance in cyanobacteria. In this regard, H₂O₂ and SNP (sodium nitroprusside, NO donor), were applied to Nostoc muscorum and Anabaena sp. exposed to Cd (6 µM) stress, to analyze different physiological and biochemical parameters. Results revealed that treatment of Cd reduced the growth, pigment contents, photosynthetic oxygen yield and performance of PS II photochemistry (decreased chlorophyll a fluorescence parameters, i.e., ФP_o, Ψ_o, ФE_o, PI_ABS along with F_v/F_o and increased the energy flux parameters, i.e., ABS/RC, TR_o/RC, ET_o/RC, DI_o/RC along with F_o/F_v. Similarly, uptake of nitrate (NO₃ ^-) and nitrite (NO₂ ^-), as well as the activities of nitrate and ammonia assimilating enzymes along with carbohydrate content, were severely affected by Cd toxicity and notwithstanding this, glutamate dehydrogenase (GDH) activity exhibited reverse trend. Exogenous application of a very low dose (1 µM) of H₂O₂ (only for 3 h) and NO (SNP; 10 µM) notably counteracted Cd-induced toxicity. Nevertheless, the positive impact of H₂O₂ got reversed under the treatment of PTIO (NO scavenger) and _LNAME (inhibitor of nitric oxide synthase; NOS) while NO could work efficiently even in the presence of NAC (H₂O₂ scavenger) and DPI (inhibitor of NADPH oxidase); hence indicated towards the H₂O₂ mediated NO signaling in averting Cd induced toxicity in test cyanobacteria. In conclusion, current finding demonstrated a positive cross-talk between H₂O₂ and NO for providing tolerance to cyanobacteria against Cd stress.

Calcium mediated nitric oxide responses: Acquisition of nickel stress tolerance in cyanobacterium Nostoc muscorum ATCC 27893

Calcium (Ca2+) and nitric oxide (NO) are potentially active and multitasking signaling molecules which are known to regulate abiotic stresses in plants, but their interactive role in the acquisition of metal stress tolerance in cyanobacteria remains elusive. In current study the signaling role of Ca2+ (800 μM) and NO (10 μM SNP) on key physiological and biochemical attributes of the agriculturally and economically important cyanobacterium Nostoc muscorum ATCC 27893 subjected to Ni stress (2 μM) was examined. Results revealed that Ni at elevated level caused severe damages to the test organism but exogenous supplementation of Ca2+ and NO efficiently mitigated its toxic effects and up-regulated the growth, pigment contents, rate of photosynthesis (whole cell oxygen evolution and Chl a fluorescence indices: Kinetic traits: ΦP0, Ψ0, ΦE0 and PIABS, along with Fv/F0), nitrogen metabolism (NO3‾ and NO2‾ uptake, nitrate:NR and NiR; and ammonia:GS and GOGAT; assimilating enzymes), and boosted the enzymatic (SOD, POD, CAT and GST) along with non-enzymatic (proline, cysteine and NP-SH) antioxidants. Whereas the increased values of energy flux traits: (ABS/RC, TR0/RC, DI0/RC and ET0/RC) along with F0/Fv, rate of respiration, oxidative stress biomarkers (SOR, H2O2 and MDA), and activity of GDH enzyme exhibited lowering trends with application of Ca2+ and NO. Further, addition of EGTA (Ca2+ scavenger) and PTIO (NO scavenger) reversed the positive impacts of Ca2+ and NO and worsened the toxicity of Ni on test cyanobacterium, but the damages were more pronounced under PTIO application that demonstrated Ca2+ mediated signaling role of NO in Ni toxicity alleviation.

Calm on the surface, dynamic on the inside. Molecular homeostasis of Anabaena sp. PCC 7120 nitrogen metabolism

Nitrogen sources are all converted into ammonium/ia as a first step of assimilation. It is reasonable to expect that molecular components involved in the transport of ammonium/ia across biological membranes connect with the regulation of both nitrogen and central metabolism. We applied both genetic (i.e., Δamt mutation) and environmental treatments to a target biological system, the cyanobacterium Anabaena sp PCC 7120. The aim was to both perturb nitrogen metabolism and induce multiple inner nitrogen states, respectively, followed by targeted quantification of key proteins, metabolites and enzyme activities. The absence of AMT transporters triggered a substantial whole-system response, affecting enzyme activities and quantity of proteins and metabolites, spanning nitrogen and carbon metabolisms. Moreover, the Δamt strain displayed a molecular fingerprint indicating nitrogen deficiency even under nitrogen replete conditions. Contrasting with such dynamic adaptations was the striking near-complete lack of an externally measurable altered phenotype. We conclude that this species evolved a highly robust and adaptable molecular network to maintain homeostasis, resulting in substantial internal but minimal external perturbations. This analysis provides evidence for a potential role of AMT transporters in the regulatory/signalling network of nitrogen metabolism and the existence of a novel fourth regulatory mechanism controlling glutamine synthetase activity.

Effect of Time Interval on Arsenic Toxicity to Paddy Field Cyanobacteria as Evident by Nitrogen Metabolism, Biochemical Constituent, and Exopolysaccharide Content

Arsenic poisoning in aquatic ecosystem is a global concern that obstructs the productivity of agricultural lands (paddy fields) by targeting the growth of cyanobacteria. The cyanobacteria also tolerate and accumulate elevated concentration of arsenic (As) inside the cell and excrete out from cells in less toxic forms after the successive time interval. Thus to validate this, the study was carried out at two different time intervals, i.e., 48 h and 96 h. Two redox forms of As arsenate (As^V) and arsenite (As^III) at different concentrations (50, 100, and 150 mM As^V; 50, 100, and 150 μM As^III) caused substantial reduction in growth, pigments (Chl a/Car and phycobiliproteins: phycocyanin, allophycocyanin, and phycoerythrin), inorganic nitrogen ( nitrate (NO₃^-) and nitrite (NO₂^-)) uptake, activity of enzymes (NR, NiR, GS, and GOGAT) of nitrogen metabolism, biochemical constituents (protein, carbohydrate, and exopolysaccharide (EPS) contents of Nostoc muscorum, and Anabaena sp. PCC7120. The tested doses of As^V and As^III after 48 h of exposure exhibited adverse impact on these parameters, but after 96 h with lower doses of As^V (50 mM and 100 mM) and As^III (50 μM and 100 μM), significant recovery was recorded. Contrary to this, at higher dose of As^V (150 mM) and As^III (150 μM), the adverse impact was further aggravated with increasing time exposure. Contrary to the activity of NR, NiR, GS, and GOGAT, GDH activity (alternative NH₃⁺ assimilating enzyme) was found to increase, and after 96 h, the activity showed declining trend but still higher than the control. The biochemical constituent EPS (first protective barrier) under scanning electron microscope showed more accumulation of dry adsorbent in the case of As^III stress hence displayed more toxic nature of As^III than As^V. The study concludes that with increasing time exposure, the recovery in growth and related parameters mainly at lower doses of As^V and As^III points toward adaptability of cyanobacteria which was more pronounced in Nostoc muscorum.

The essential role of sodium bioenergetics and ATP homeostasis in the developmental transitions of a cyanobacterium

The ability to resume growth after a dormant period is an important strategy for the survival and spreading of bacterial populations. Energy homeostasis is critical in the transition into and out of a quiescent state. Synechocystis sp. PCC 6803, a non-diazotrophic cyanobacterium, enters metabolic dormancy as a response to nitrogen starvation. We used Synechocystis as a model to investigate the regulation of ATP homeostasis during dormancy, and we unraveled a critical role for sodium bioenergetics in dormant cells. During nitrogen starvation, cells reduce their ATP levels and engage sodium bioenergetics to maintain the minimum ATP content required for viability. When nitrogen becomes available, energy requirements rise, and cells immediately increase ATP levels, employing sodium bioenergetics and glycogen catabolism. These processes allow them to restore the photosynthetic machinery and resume photoautotrophic growth. Our work reveals a precise regulation of the energy metabolism essential for bacterial survival during periods of nutrient deprivation.

CfrA, a Novel Carbon Flow Regulator, Adapts Carbon Metabolism to Nitrogen Deficiency in Cyanobacteria

Cyanobacteria unable to fix atmospheric nitrogen have evolved sophisticated adaptations to survive to long periods of nitrogen starvation. These genetic programs are still largely unknown-as evidenced by the many proteins whose expression is regulated in response to nitrogen availability, but which belong to unknown or hypothetical categories. In Synechocystis sp. PCC 6803, the global nitrogen regulator NtcA activates the expression of the sll0944 gene upon nitrogen deprivation. This gene encodes a protein that is highly conserved in cyanobacteria, but of unknown function. Based on the results described herein, we named the product of sll0944 carbon flow regulator A (CfrA). We analyzed the phenotypes of strains containing different levels of CfrA, including a knock-out strain (ΔcfrA), and two strains overexpressing CfrA from either the constitutive P _trc promoter (Ptrc-cfrA) or the arsenite-inducible promoter P _arsB (Pars-cfrA). Our results show that the amount of CfrA determines the accumulation of glycogen, and affects the synthesis of protein and photosynthetic pigments as well as amino acid pools. Strains with high levels of CfrA present high levels of glycogen and a decrease in photosynthetic pigments and protein content when nitrogen is available. Possible interactions between CfrA and the pyruvate dehydrogenase complex or PII protein have been revealed. The phenotype associated with CfrA overexpression is also observed in PII-deficient strains; however, it is lethal in this genetic background. Taken together, our results indicate a role for CfrA in the adaptation of carbon flux during acclimation to nitrogen deficiency.

β-Ν-Methylamino-L-alanine interferes with nitrogen assimilation in the cyanobacterium, non-BMAA producer, Synechococcus sp. TAU-MAC 0499

The production of β-Ν-methylamino-L-alanine (BMAA) in cyanobacteria is triggered by nitrogen-starvation conditions and its biological role, albeit unknown, is associated with nitrogen assimilation. In the present study, the effect of BMAA (773 μg L^-1) on nitrogen metabolism and physiology of the non-diazotrophic cyanobacterium and non-BMAA producer, Synechococcus sp. TAU-MAC 0499, was investigated. In order to study the combined effect of nitrogen availability and BMAA, nitrogen-starvation conditions were induced by transferring cells in nitrogen-free medium and subsequently exposing the cultures to BMAA. After short-term treatment (180 min) and in the presence of nitrogen, BMAA inhibited glutamine synthetase, which resulted in low concentration of glutamine. In the absence of nitrogen, although there was no effect on glutamine synthetase, a possible perturbation in nitrogen assimilation is reflected on the significant decrease in glutamate levels. During the long-term exposure (24-96 h), growth, photosynthetic pigments and total protein were not affected by BMAA exposure, except for an increase in protein and phycocyanin levels at 48 h in nitrogen replete conditions. Results suggest that BMAA interferes with nitrogen assimilation, in a different way, depending on the presence or absence of combined nitrogen, providing novel data on the potential biological role of BMAA.

Phytohormone up-regulates the biochemical constituent, exopolysaccharide and nitrogen metabolism in paddy-field cyanobacteria exposed to chromium stress

Background

Cyanobacteria are well known for their inherent ability to serve as atmospheric nitrogen fixers and as bio-fertilizers; however, increased contaminants in aquatic ecosystem significantly decline the growth and function of these microbes in paddy fields. Plant growth regulators play beneficial role in combating the negative effects induced by heavy metals in photoautotroph. Current study evaluates the potential role of indole acetic acid (IAA; 290 nm) and kinetin (KN; 10 nm) on growth, nitrogen metabolism and biochemical constituents of two paddy field cyanobacteria Nostoc muscorum ATCC 27893 and Anabaena sp. PCC 7120 exposed to two concentrations of chromium (Cr^VI; 100 μM and 150 μM).

Results

Both the tested doses of Cr^VI declined the growth, ratio of chlorophyll a to carotenoids (Chl a/Car), contents of phycobiliproteins; phycocyanin (PC), allophycocyanin (APC), and phycoerythrin (PE), protein and carbohydrate associated with decrease in the inorganic nitrogen (nitrate; NO₃^— and nitrite; NO₂^—) uptake rate that results in the decrease in nitrate and ammonia assimilating enzymes; nitrate reductase (NR), nitrite reductase (NiR), glutamine synthetase (GS), glutamate synthase (GOGAT) except glutamate dehydrogenase (GDH). However, exogenous supplementation of IAA and KN exhibited alleviating effects on growth, nitrogen metabolism and exopolysaccharide (EPS) (first protective barrier against metal toxicity) contents in both the cyanobacteria, which probably occurred as a result of a substantial decrease in the Cr uptake that lowers the damaging effects.

Conclusion

Overall result of the present study signifies affirmative role of the phytohormone in minimizing the toxic effects induced by chromium by stimulating the growth of cyanobacteria thereby enhancing its ability as bio-fertilizer that improved fertility and productivity of soil even in metal contaminated condition.

Increased ethylene production by overexpressing phosphoenolpyruvate carboxylase in the cyanobacterium Synechocystis PCC 6803

BACKGROUND

Cyanobacteria can be metabolically engineered to convert CO₂ to fuels and chemicals such as ethylene. A major challenge in such efforts is to optimize carbon fixation and partition towards target molecules.

RESULTS

The efe gene encoding an ethylene-forming enzyme was introduced into a strain of the cyanobacterium Synechocystis PCC 6803 with increased phosphoenolpyruvate carboxylase (PEPc) levels. The resulting engineered strain (CD-P) showed significantly increased ethylene production (10.5 ± 3.1 µg mL^-1 OD^-1 day^-1) compared to the control strain (6.4 ± 1.4 µg mL^-1 OD^-1 day^-1). Interestingly, extra copies of the native pepc or the heterologous expression of PEPc from the cyanobacterium Synechococcus PCC 7002 (Synechococcus) in the CD-P, increased ethylene production (19.2 ± 1.3 and 18.3 ± 3.3 µg mL^-1 OD^-1 day^-1, respectively) when the cells were treated with the acetyl-CoA carboxylase inhibitor, cycloxydim. A heterologous expression of phosphoenolpyruvate synthase (PPSA) from Synechococcus in the CD-P also increased ethylene production (16.77 ± 4.48 µg mL^-1 OD^-1 day^-1) showing differences in the regulation of the native and the PPSA from Synechococcus in Synechocystis.

CONCLUSIONS

This work demonstrates that genetic rewiring of cyanobacterial central carbon metabolism can enhance carbon supply to the TCA cycle and thereby further increase ethylene production.

Redox interference in nitrogen status via oxidative stress is mediated by 2-oxoglutarate in cyanobacteria

Reactive oxygen species (ROS) are generated naturally in photosynthetic organisms by respiration and photosynthesis. Therefore, detoxification of these compounds, avoiding oxidative stress, is essential for proper cell function. In cyanobacteria, some observations point to a crosstalk between ROS homeostasis, in particular hydrogen peroxide, and nitrogen metabolism by a mechanism independent of known redox regulators. Using glutamine synthetase (GS), a finely regulated enzyme essential for nitrogen assimilation, as a tool, we were able to monitor nitrogen metabolism in relation to oxidative stress. We show that hydrogen peroxide clearly alters the expression of different genes related to nitrogen metabolism, both in the wild-type strain of the cyanobacterium Synechocystis sp. PCC 6803 and in a mutant strain lacking the catalase-peroxidase encoded by the katG gene and therefore highly sensitive to oxidative stress. As cyanobacteria perceive nitrogen status by sensing intracellular 2-oxoglutarate (2-OG) concentrations, the hydrogen peroxide effect was analysed under different nitrogen conditions in the wild-type, the ∆katG strain and in a strain able to transport 2-OG. The results obtained demonstrate that hydrogen peroxide interferes with signalling of cellular carbon : nitrogen status by decreasing the intracellular concentrations of 2-OG and hence altering the function of the 2-OG-sensing global nitrogen regulator NtcA.

Metatranscriptomic Analyses of Diel Metabolic Functions During a Microcystis Bloom in Western Lake Erie (United States)

This study examined diel shifts in metabolic functions of Microcystis spp. during a 48-h Lagrangian survey of a toxin-producing cyanobacterial bloom in western Lake Erie in the aftermath of the 2014 Toledo Water Crisis. Transcripts mapped to the genomes of recently sequenced lower Great Lakes Microcystis isolates showed distinct patterns of gene expression between samples collected across day (10:00 h, 16:00 h) and night (22:00 h, 04:00 h). Daytime transcripts were enriched in functions related to Photosystem II (e.g., psbA), nitrogen and phosphate acquisition, cell division (ftsHZ), heat shock response (dnaK, groEL), and uptake of inorganic carbon (rbc, bicA). Genes transcribed during nighttime included those involved in phycobilisome protein synthesis and Photosystem I core subunits. Hierarchical clustering and principal component analysis (PCA) showed a tightly clustered group of nighttime expressed genes, whereas daytime transcripts were separated from each other over the 48-h duration. Lack of uniform clustering within the daytime transcripts suggested that the partitioning of gene expression in Microcystis is dependent on both circadian regulation and physicochemical changes within the environment.

The Distinctive Regulation of Cyanobacterial Glutamine Synthetase

Glutamine synthetase (GS) features prominently in bacterial nitrogen assimilation as it catalyzes the entry of bioavailable nitrogen in form of ammonium into cellular metabolism. The classic example, the comprehensively characterized GS of enterobacteria, is subject to exquisite regulation at multiple levels, among them gene expression regulation to control GS abundance, as well as feedback inhibition and covalent modifications to control enzyme activity. Intriguingly, the GS of the ecologically important clade of cyanobacteria features fundamentally different regulatory systems to those of most prokaryotes. These include the interaction with small proteins, the so-called inactivating factors (IFs) that inhibit GS linearly with their abundance. In addition to this protein interaction-based regulation of GS activity, cyanobacteria use alternative elements to control the synthesis of GS and IFs at the transcriptional level. Moreover, cyanobacteria evolved unique RNA-based regulatory mechanisms such as glutamine riboswitches to tightly tune IF abundance. In this review, we aim to outline the current knowledge on the distinctive features of the cyanobacterial GS encompassing the overall control of its activity, sensing the nitrogen status, transcriptional and post-transcriptional regulation, as well as strain-specific differences.

Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803

In cyanobacteria, nitrogen homeostasis is maintained by an intricate regulatory network around transcription factor NtcA. Although mechanisms controlling NtcA activity appear to be well understood, its regulon remains poorly defined. To determine the NtcA regulon during the early stages of nitrogen starvation for the model cyanobacterium Synechocystis sp. PCC 6803, we performed chromatin immunoprecipitation, followed by sequencing (ChIP-seq), in parallel with transcriptome analysis (RNA-seq). Through combining these methods, we determined 51 genes activated and 28 repressed directly by NtcA. In addition to genes associated with nitrogen and carbon metabolism, a considerable number of genes without current functional annotation were among direct targets providing a rich reservoir for further studies. The NtcA regulon also included eight non-coding RNAs, of which Ncr1071, Syr6 and NsiR7 were experimentally validated, and their putative targets were computationally predicted. Surprisingly, we found substantial NtcA binding associated with delayed expression changes indicating that NtcA can reside in a poised state controlled by other factors. Indeed, a role of PipX as modulating factor in nitrogen regulation was confirmed for selected NtcA-targets. We suggest that the indicated poised state of NtcA enables a more differentiated response to nitrogen limitation and can be advantageous in native habitats of Synechocystis.

Quantitative Proteomics Shows Extensive Remodeling Induced by Nitrogen Limitation in Prochlorococcusmarinus SS120

Prochlorococcus requires the capability to accommodate to environmental changes in order to proliferate in oligotrophic oceans, in particular regarding nitrogen availability. A precise knowledge of the composition and changes in the proteome can yield fundamental insights into such a response. Here we report a detailed proteome analysis of the important model cyanobacterium Prochlorococcus marinus SS120 after treatment with azaserine, an inhibitor of ferredoxin-dependent glutamate synthase (GOGAT), to simulate extreme nitrogen starvation. In total, 1,072 proteins, corresponding to 57% of the theoretical proteome, were identified-the maximum proteome coverage obtained for any Prochlorococcus strain thus far. Spectral intensity, calibrated quantification by the Hi3 method, was obtained for 1,007 proteins. Statistically significant changes (P value of <0.05) were observed for 408 proteins, with the majority of proteins (92.4%) downregulated after 8 h of treatment. There was a strong decrease in ribosomal proteins upon azaserine addition, while many transporters were increased. The regulatory proteins P_II and PipX were decreased, and the global nitrogen regulator NtcA was upregulated. Furthermore, our data for Prochlorococcus indicate that NtcA also participates in the regulation of photosynthesis. Prochlorococcus responds to the lack of nitrogen by slowing down translation, while inducing photosynthetic cyclic electron flow and biosynthesis of proteins involved in nitrogen uptake and assimilation. IMPORTANCEProchlorococcus is the most abundant photosynthetic organism on Earth, contributing significantly to global primary production and playing a prominent role in biogeochemical cycles. Here we study the effects of extreme nitrogen limitation, a feature of the oligotrophic oceans inhabited by this organism. Quantitative proteomics allowed an accurate quantification of the Prochlorococcus proteome, finding three main responses to nitrogen limitation: upregulation of nitrogen assimilation-related proteins, including transporters; downregulation of ribosome proteins; and induction of the photosystem II cyclic electron flow. This suggests that nitrogen limitation affects a range of metabolic processes far wider than initially believed, with the ultimate goal of saving nitrogen and maximizing the nitrogen uptake and assimilation capabilities of the cell.

Physiological and gene expression responses to nitrogen regimes and temperatures in Mastigocladus sp. strain CHP1, a predominant thermotolerant cyanobacterium of hot springs

Cyanobacteria are widely distributed primary producers with significant implications for the global biogeochemical cycles of carbon and nitrogen. Diazotrophic cyanobacteria of subsection V (Order Stigonematales) are particularly ubiquitous in photoautotrophic microbial mats of hot springs. The Stigonematal cyanobacterium strain CHP1 isolated from the Porcelana hot spring (Chile) was one of the major contributors of the new nitrogen through nitrogen fixation. Further morphological and genetic characterization verified that the strain CHP1 belongs to Stigonematales, and it formed a separate clade together with other thermophiles of the genera Fischerella and Mastigocladus. Strain CHP1 fixed maximum N₂ in the light, independent of the temperature range. At 50°C nifH gene transcripts showed high expression during the light period, whereas the nifH gene expression at 45°C was arrhythmic. The strain displayed a high affinity for nitrate and a low tolerance for high ammonium concentrations, whereas the narB and glnA genes showed higher expression in light and at the beginning of the dark phase. It is proposed that Mastigocladus sp. strain CHP1 would represent a good model for the study of subsection V thermophilic cyanobacteria, and for understanding the adaptations of these photoautotrophic organisms inhabiting microbial mats in hot springs globally.

Physiological Studies of Glutamine Synthetases I and III from Synechococcus sp. WH7803 Reveal Differential Regulation

The marine picocyanobacterium Synechococcus sp. WH7803 possesses two glutamine synthetases (GSs; EC 6.3.1.2), GSI encoded by glnA and GSIII encoded by glnN. This is the first work addressing the physiological regulation of both enzymes in a marine cyanobacterial strain. The increase of GS activity upon nitrogen starvation was similar to that found in other model cyanobacteria. However, an unusual response was found when cells were grown under darkness: the GS activity was unaffected, reflecting adaptation to the environment where they thrive. On the other hand, we found that GSIII did not respond to nitrogen availability, in sharp contrast with the results observed for this enzyme in other cyanobacteria thus far studied. These features suggest that GS activities in Synechococcus sp. WH7803 represent an intermediate step in the evolution of cyanobacteria, in a process of regulatory streamlining where GSI lost the regulation by light, while GSIII lost its responsiveness to nitrogen. This is in good agreement with the phylogeny of Synechococcus sp. WH7803 in the context of the marine cyanobacterial radiation.

Understanding Sugar Catabolism in Unicellular Cyanobacteria Toward the Application in Biofuel and Biomaterial Production

Synechocystis sp. PCC 6803 is a model species of the cyanobacteria that undergo oxygenic photosynthesis, and has garnered much attention for its potential biotechnological applications. The regulatory mechanism of sugar metabolism in this cyanobacterium has been intensively studied and recent omics approaches have revealed the changes in transcripts, proteins, and metabolites of sugar catabolism under different light and nutrient conditions. Several transcriptional regulators that control the gene expression of enzymes related to sugar catabolism have been identified in the past 10 years, including a sigma factor, transcription factors, and histidine kinases. The modification of these genes can lead to alterations in the primary metabolism as well as the levels of high-value products such as bioplastics and hydrogen. This review summarizes recent studies on sugar catabolism in Synechocystis sp. PCC 6803, emphasizing the importance of elucidating the molecular mechanisms of cyanobacterial metabolism for biotechnological applications.

S-sulfhydration: a cysteine posttranslational modification in plant systems

Hydrogen sulfide is a highly reactive molecule that is currently accepted as a signaling compound. This molecule is as important as carbon monoxide in mammals and hydrogen peroxide in plants, as well as nitric oxide in both eukaryotic systems. Although many studies have been conducted on the physiological effects of hydrogen sulfide, the underlying mechanisms are poorly understood. One of the proposed mechanisms involves the posttranslational modification of protein cysteine residues, a process called S-sulfhydration. In this work, a modified biotin switch method was used for the detection of Arabidopsis (Arabidopsis thaliana) proteins modified by S-sulfhydration under physiological conditions. The presence of an S-sulfhydration-modified cysteine residue on cytosolic ascorbate peroxidase was demonstrated using liquid chromatography-tandem mass spectrometry analysis, and a total of 106 S-sulfhydrated proteins were identified. Immunoblot and enzyme activity analyses of some of these proteins showed that the sulfide added through S-sulfhydration reversibly regulates the functions of plant proteins in a manner similar to that described in mammalian systems.

A core of three amino acids at the carboxyl-terminal region of glutamine synthetase defines its regulation in cyanobacteria

Glutamine synthetase (GS) type I is a key enzyme in nitrogen metabolism, and its activity is finely controlled by cellular carbon/nitrogen balance. In cyanobacteria, a reversible process that involves protein-protein interaction with two proteins, the inactivating factors IF7 and IF17, regulates GS. Previously, we showed that three arginine residues of IFs are critical for binding and inhibition of GS. In this work, taking advantage of the specificity of GS/IFs interaction in the model cyanobacteria Synechocystis sp. PCC 6803 and Anabaena sp. PCC 7120, we have constructed a different chimeric GSs from these two cyanobacteria. Analysis of these proteins, together with a site-directed mutagenesis approach, indicates that a core of three residues (E419, N456 and R459) is essential for the inactivation process. The three residues belong to the last 56 amino acids of the C-terminus of Synechocystis GS. A protein-protein docking modeling of Synechocystis GS in complex with IF7 supports the role of the identified core for GS/IF interaction.

Low and high doses of UV-B differentially modulate chlorpyrifos-induced alterations in nitrogen metabolism of cyanobacteria

The present study assessed the comparative responses on the specific growth rate, nitrogen metabolism and enzymes associated with nitrogen metabolism in two nitrogen fixing cyanobacteria-Nostoc muscorum and Phormidium foveolarum exposed to two UV-B doses (low; UV-BL: 0.5472kJm(-2) and high; UV-BH: 5.472kJm(-2)) and two doses of the insecticide chlorpyrifos (O,O-diethyl O-3,5,6-trichloro-2-pyridyl phosphorothioate; low i.e. CPL, 1µgml(-1) and high i.e. CPH, 2µgml(-1)) singly and in combination. The specific growth rate, NO3(-) and NO2(-) uptake, nitrate assimilating enzymes - nitrate reductase and nitrite reductase and ammonium assimilating enzymes - glutamine synthetase and glutamate synthase were severely affected when treated either with CPH or/and UV-BH while glutamate dehydrogenase exhibited a stimulatory response. CPL also reduced all the measured parameters (except GDH activity) after 24h, however, a stimulatory effect was observed after 72h due to an increase in nitrogen metabolism (and other antioxidant) enzymes during this period. UV-BL did not cause significant alteration in the studied parameters while in combination with CP doses, it either alleviated the inhibitory effects or further enhanced the CPL induced activities of these enzymes (except GDH). Overall results indicate the resistant nature of P. foveolarum against the inhibitory doses of UV-B and chlorpyrifos in comparison to N. muscorum.

Physiological regulation of isocitrate dehydrogenase and the role of 2-oxoglutarate in Prochlorococcus sp. strain PCC 9511

The enzyme isocitrate dehydrogenase (ICDH; EC 1.1.1.42) catalyzes the oxidative decarboxylation of isocitrate, to produce 2-oxoglutarate. The incompleteness of the tricarboxylic acids cycle in marine cyanobacteria confers a special importance to isocitrate dehydrogenase in the C/N balance, since 2-oxoglutarate can only be metabolized through the glutamine synthetase/glutamate synthase pathway. The physiological regulation of isocitrate dehydrogenase was studied in cultures of Prochlorococcus sp. strain PCC 9511, by measuring enzyme activity and concentration using the NADPH production assay and Western blotting, respectively. The enzyme activity showed little changes under nitrogen or phosphorus starvation, or upon addition of the inhibitors DCMU, DBMIB and MSX. Azaserine, an inhibitor of glutamate synthase, induced clear increases in the isocitrate dehydrogenase activity and icd gene expression after 24 h, and also in the 2-oxoglutarate concentration. Iron starvation had the most significant effect, inducing a complete loss of isocitrate dehydrogenase activity, possibly mediated by a process of oxidative inactivation, while its concentration was unaffected. Our results suggest that isocitrate dehydrogenase responds to changes in the intracellular concentration of 2-oxoglutarate and to the redox status of the cells in Prochlorococcus.

Decoupling of ammonium regulation and ntcA transcription in the diazotrophic marine cyanobacterium Trichodesmium sp. IMS101

Nitrogen (N) physiology in the marine cyanobacterium Trichodesmium IMS101 was studied along with transcript accumulation of the N-regulatory gene ntcA and of two of its target genes: napA (nitrate assimilation) and nifH (N(2) fixation). N(2) fixation was impaired in the presence of nitrite, nitrate and urea. Strain IMS101 was capable of growth on these combined N sources at <2 μM but growth rates declined at elevated concentrations. Assimilation of nitrate and urea was impaired in the presence of ammonium. Whereas ecologically relevant N concentrations (2-20 μM) suppressed growth and assimilation, much higher concentrations were required to affect transcript levels. Transcripts of nifH accumulated under nitrogen-fixing conditions; these transcript levels were maintained in the presence of nitrate (100 μM) and ammonium (20 μM). However, nifH transcript levels were below detection at ammonium concentrations >20 μM. napA mRNA was found at low levels in both N(2)-fixing and ammonium-utilizing filaments, and it accumulated in filaments grown with nitrate. The positive effect of nitrate on napA transcription was abolished by ammonium additions of >200 μM. This effect was restored upon addition of the glutamine synthetase inhibitor L-methionin-DL-sulfoximine. Surprisingly, ntcA transcript levels remained high in the presence of ammonium, even at elevated concentrations. These findings indicate that ammonium repression is decoupled from transcriptional activation of ntcA in Trichodesmium IMS101.

Mutational analysis of the inactivating factors, IF7 and IF17 from Synechocystis sp. PCC 6803: critical role of arginine amino acid residues for glutamine synthetase inactivation

The Synechocystis sp. PCC 6803 glutamine synthetase type I (GS) activity is controlled by a process that involves protein-protein interaction with two inactivating factors (IF7 and IF17). IF7 is a natively unfolded, 65-residue-long protein, homologous to the carboxy-terminal region of IF17. Both proteins have abundance of positively charged amino acid residues and a high isoelectric point. In this study, we analyse the IF amino acid residues involved in GS inactivation by a mutational approach, both in vitro and in vivo. The results clearly indicate that the GS-IF complex formation must be determined mainly by electrostatic interactions. We have identified three conserved arginine residues of IF7 and IF17 that are essential for the interaction of these proteins with GS. All these residues map in the homologous region of IFs. Furthermore, in vitro analysis of a truncated IF17 protein without the 82-residue-long amino-terminal part, together with the analysis of a Synechocystis strain expressing a chimeric protein, containing this amino-terminal part of IF17 fused to IF7, demonstrates that amino-terminal region of IF17 mostly confers a higher stability to this protein.

Posttranscriptional regulation of glutamine synthetase in the filamentous Cyanobacterium Anabaena sp. PCC 7120: differential expression between vegetative cells and heterocysts

Genes homologous to those implicated in glutamine synthetase (GS) regulation by protein-protein interaction in the cyanobacterium Synechocystis sp. strain PCC 6803 are conserved in several cyanobacterial sequenced genomes. We investigated this GS regulatory mechanism in Anabaena sp. strain PCC 7120. In this strain the system operates with only one GS inactivation factor (inactivation factor 7A [IF7A]), encoded by open reading frame (ORF) asl2329 (gifA). Following addition of ammonium, expression of gifA is derepressed, leading to the synthesis of IF7A, and consequently, GS is inactivated. Upon ammonium removal, the GS activity returns to the initial level and IF7A becomes undetectable. The global nitrogen control protein NtcA binds to the gifA promoter. Constitutive high expression levels of gifA were found in an Anabaena ntcA mutant (CSE2), indicating a repressor role for NtcA. In vitro studies demonstrate that Anabaena GS is not inactivated by Synechocystis IFs (IF7 and IF17), indicating the specificity of the system. We constructed an Anabaena strain expressing a second inactivating factor, containing the amino-terminal part of IF17 from Synechocystis fused to IF7A. GS inactivation in this strain is more effective than that in the wild type (WT) and resembles that observed in Synechocystis. Finally we found differential expression of the IF system between heterocysts and vegetative cells of Anabaena.

Physiological role and regulation of glutamate dehydrogenase in Prochlorococcus sp. strain MIT9313

Glutamate dehydrogenase is an enzyme catalysing a reaction for ammonium assimilation, alternative to those performed by glutamine synthetase and glutamate synthase. In the genus Prochlorococcus, genomic studies have shown the presence of the gdhA gene (encoding glutamate dehydrogenase) in only four of the sequenced strains, including MIT9313. We studied the physiological regulation of glutamate dehydrogenase in this strain, by measuring the expression of gdhA, the intracellular concentration of the enzyme and its activity. Our goal was to clarify the physiological role of glutamate dehydrogenase, in order to understand why it has been selectively conserved in certain strains. Studies performed in cultures under nitrogen starvation, or with inhibitors of the nitrogen assimilation, suggest that the main role of glutamate dehydrogenase is not the assimilation of ammonium. Glutamate dehydrogenase activity and gdhA expression increased along the growth of cultures. Besides, we found a significant upregulation in gene expression when cultures were grown on glutamate as nitrogen source. We suggest that the main physiological role of glutamate dehydrogenase in Prochlorococcus MIT9313 is the utilization of glutamate to produce ammonium and 2-oxoglutarate, and amino acid recycling, thus enabling to use amino acids as nitrogen source. Therefore we propose that glutamate dehydrogenase is present in the genome of strains for whom the utilization of amino acids is most important.

Expression of genes involved in nitrogen assimilation and the C/N balance sensing in Prochlorococcus sp. strain SS120

The expression of five genes involved in nitrogen assimilation in cyanobacteria, namely glnA, glsF, icd, ntcA, and glnB, encoding three key enzymes from that pathway (glutamine synthetase, glutamate synthase, isocitrate dehydrogenase) and two regulatory proteins (NtcA and PII), was studied in this work. Their changes under different conditions were analyzed by quantitative real-time RT-PCR. Nutrient limitation induced clear modifications on the expression of most studied genes: lack of nitrogen provoked an initial increase, followed by a marked decrease; in the cases of phosphorus and iron starvation, a general, stronger expression decrease was observed, particularly striking in the case of iron. Darkness and addition of the photosynthethic inhibitors DCMU and DBMIB also had a strong effect on gene expression. Methionine sulfoximine and azaserine, inhibitors of glutamine synthetase and glutamate synthase, respectively, provoked a sharp increase in icd expression. These results, together with previous studies, suggest that 2-oxoglutarate could be the molecule utilized by Prochlorococcus to sense the C/N balance. Besides, our results confirm the different regulation of nitrogen assimilation in Prochlorococcus with regard to other cyanobacteria.

Inactivation of spkD, encoding a Ser/Thr kinase, affects the pool of the TCA cycle metabolites in Synechocystis sp. strain PCC 6803

The inactivation of sll0776 (spkD), a gene encoding a protein Ser/Thr kinase in Synechocystis PCC 6803, led to a pleiotropic phenotype of the SpkD null mutant. This mutant is impaired in its growth ability under low concentration of inorganic carbon (C(i)), though its C(i)-uptake system is not affected. Addition of glucose, phosphoglyceraldehyde or pyruvate does not allow the mutant to grow under low-C(i) conditions. In contrast, this growth defect can be restored when the low-C(i) culture medium is supplemented with metabolites of the TCA cycle. Growth of the mutant is also inhibited when ammonium is provided as nitrogen source, whatever the carbon regime of the cells, due to the high demand for 2-oxoglutarate, which is the carbon skeleton for ammonium assimilation. When mutant cells are cultured under standard growth conditions, the intracellular concentration of 2-oxoglutarate is 20 % lower than is observed in the wild-type strain. However, this decrease of 2-oxoglutarate level only slightly affects the phosphorylation state of PII, a protein that regulates nitrogen and carbon metabolism according to the intracellular levels of 2-oxoglutarate. Properties of the SpkD mutant suggest that the Ser/Thr kinase SpkD could be involved in adjusting the pool of the TCA cycle metabolites according to C(i) supply in the culture medium.

The ammonium-inactivated cyanobacterial glutamine synthetase I is reactivated in vivo by a mechanism involving proteolytic removal of its inactivating factors

The Synechocystis sp. PCC 6803 glutamine synthetase type I (GS) activity is controlled by a process that involves protein-protein interaction with two inactivating factors (IF7 and IF17). Following addition of ammonium, the genes encoding these proteins, gifA and gifB, respectively, are derepressed, leading to the synthesis of IF7 and IF17 and consequently GS is inactivated. Upon ammonium removal, the GS activity rapidly returns to the initial level within 20 min. In this study, we analyse the mechanism underlying GS reactivation and find that this process involves IF7 and IF17 degradation. We show that the presence of ammonium as nitrogen source enhances IF17 but not IF7 stability independently of gif gene transcription. Studies with Synechocystis crude extracts under different conditions revealed that IF7 and IF17 display different stabilities in vitro. We found that IF7 is degraded in vitro by the activity of metalloproteases. Furthermore, the involvement of soluble processing metallopeptidases in IF7 degradation has also been demonstrated in vivo, by analysing Synechocystis mutant strains devoid of genes of the prp family. Finally, using a Synechocystis strain lacking GS type I, we establish the crucial role of the target protein GS for in vivo IF7 and IF17 stability.

Regulated expression of glutamyl-tRNA synthetase is directed by a mobile genetic element in the cyanobacterium Tolypothrix sp. PCC 7601

The genome of Tolypothrix sp. PCC 7601 carries two copies of a novel insertion sequence, ISTosp1. One of the two copies is located upstream of the gene encoding glutamyl-tRNA synthetase, an enzyme playing a key role in protein and pigment synthesis. The tnpA gene of the IS element and gltX were co-transcribed and their expression was transiently upregulated upon retrieval of the ammonium source irrespective of whether nitrate or no nitrogen source were available. The second copy is also transcribed and shows a similar regulatory pattern. Structural elements of the promoter (-10 and -35 sequences) directing the expression of the tnpA-gltX operon have been localized within the IS. Regulatory sequences involving the NtcA transcription factor in the control of tnpA-gltX expression were found both within and in sequences upstream of the insertion element. The expression of gltX in a closely related cyanobacterium, Nostoc sp. PCC 7120, which lacks the insertion upstream of gltX, decreased upon ammonium retrieval, a regulatory pattern that markedly differs from that observed in Tolypothrix sp. PCC 7601. ISTosp1 constitutes a good example of how cells can make use of a transposable element to evolve an original regulatory mechanism.

Effects of PII deficiency on expression of the genes involved in ammonium utilization in the cyanobacterium Synechocystis sp. Strain PCC 6803

The Synechocystis sp. strain PCC 6803 mutant deficient in PII protein (the glnB gene product) was found to express glutamine synthetase activity at levels several times higher than the wild-type strain. There was no significant difference in nitrate reductase activity levels between the two strains, and the nitrite reductase levels were somewhat lower in the mutant than in the wild-type strain. The higher glutamine synthetase activity in the mutant was ascribed to higher expression levels of the glutamine synthetase genes (glnA and glnN), which belong to the regulon controlled by NtcA, a Crp-family transcription regulator. Examination of the effects of PII deficiency on other NtcA-regulated genes revealed that the transcript levels of amt1 (encoding an ammonium permease) and gifB (encoding an inhibitor of glutamine synthetase) were increased, whereas that of gifA (a homolog of gifB, encoding another glutamine synthetase inhibitor) was decreased, with those of nirA, nrtC, icd, sigE (rpoD2-V), nblA and ntcA being unaffected. Unlike the Synechococcus elongatus strain PCC 7942, induction or repression of the NtcA-regulated genes proceeded normally in the PII-deficient mutant upon nitrogen depletion. The altered steady-state expression levels of glnA, glnN, amt1, gifA and gifB in the PII-deficient mutant suggested that Synechocystis sp. strain PCC 6803 has a mechanism for regulation of the subset of the NtcA-regulated genes related directly to ammonium assimilation.

Effect of nitrogen source on cyanophycin synthesis in Synechocystis sp. strain PCC 6308

Experiments were carried out to examine the effects of nitrogen source on nitrogen incorporation into cyanophycin during nitrogen limitation and repletion, both with or without inhibition of protein synthesis, in cyanobacteria grown on either nitrate or ammonium. The use of nitrate and ammonium, 14N labeled in the growth medium and 15N labeled in the repletion medium, allows the determination of the source of nitrogen in cyanophycin using proton nuclear magnetic resonance spectroscopy. The data suggest that nitrogen from both the breakdown of cellular protein (14N) and directly from the medium (15N) is incorporated into cyanophycin. Nitrogen is incorporated into cyanophycin at different rates and to different extents, depending on the source of nitrogen (ammonium or nitrate) and whether the cells are first starved for nitrogen. These differences appear to be related to the activity of nitrate reductase in cells and to the possible expression of cyanophycin synthetase during nitrogen starvation.

Ammonium assimilation in cyanobacteria

In cyanobacteria, after transport by specific permeases, ammonium is incorporated into carbon skeletons by the sequential action of glutamine synthetase (GS) and glutamate synthase (GOGAT). Two types of GS (GSI and GSIII) and two types of GOGAT (ferredoxin-GOGAT and NADH-GOGAT) have been characterized in cyanobacteria. The carbon skeleton substrate of the GS-GOGAT pathway is 2-oxoglutarate that is synthesized by the isocitrate dehydrogenase (IDH). In order to maintain the C-N balance and the amino acid pools homeostasis, ammonium assimilation is tightly regulated. The key regulatory point is the GS, which is controlled at transcriptional and posttranscriptional levels. The transcription factor NtcA plays a critical role regulating the expression of the GS and the IDH encoding genes. In the unicellular cyanobacterium Synechocystis sp. PCC 6803, NtcA controls also the expression of two small proteins (IF7 and IF17) that inhibit the activity of GS by direct protein-protein interaction. Cyanobacteria perceive nitrogen status by sensing the intracellular concentration of 2-oxoglutarate, a signaling metabolite that is able to modulate allosterically the function of NtcA, in vitro. In vivo, a functional dependence between NtcA and the signal transduction protein PII in controlling NtcA-dependent genes has been also shown.

Cellular differentiation and the NtcA transcription factor in filamentous cyanobacteria

Some filamentous cyanobacteria can undergo a variety of cellular differentiation processes that permit their better adaptation to certain environmental conditions. These processes include the differentiation of hormogonia, short filaments aimed at the dispersal of the organism in the environment, of akinetes, cells resistant to various stress conditions, and of heterocysts, cells specialized in the fixation of atmospheric nitrogen in oxic environments. NtcA is a transcriptional regulator that operates global nitrogen control in cyanobacteria by activating (and in some cases repressing) many genes involved in nitrogen assimilation. NtcA is required for the triggering of heterocyst differentiation and for subsequent steps of its development and function. This requirement is based on the role of NtcA as an activator of the expression of hetR and other multiple genes at specific steps of the differentiation process. The products of these genes effect development as well as the distinct metabolism of the mature heterocyst. The different features found in the NtcA-dependent promoters, together with the cellular level of active NtcA protein, should have a role in the determination of the hierarchy of gene activation during the process of heterocyst differentiation.

Nitrate/nitrite assimilation system of the marine picoplanktonic cyanobacterium Synechococcus sp. strain WH 8103: effect of nitrogen source and availability on gene expression

The genes encoding the structural components of the nitrate/nitrite assimilation system of the oceanic cyanobacterium Synechococcus sp. strain WH 8103 were cloned and characterized. The genes encoding nitrate reductase (narB) and nitrite reductase (nirA) are clustered on the chromosome but are organized in separate transcriptional units. Upstream of narB is a homologue of nrtP that encodes a nitrate/nitrite-bispecific permease rather than the components of an ABC-type nitrate transporter found in freshwater cyanobacteria. Unusually, neither nirA nor ntcA (encoding a positive transcription factor of genes subject to nitrogen control) were found to be tightly regulated by ammonium. Furthermore, transcription of glnA (encoding glutamine synthetase) is up-regulated in ammonium-grown cells, highlighting significant differences in nitrogen control in this cyanobacterium. Nitrogen depletion led to the transient up-regulation of ntcA, nirA, nrtP, narB, and glnA in what appears to be an NtcA-dependent manner. The NtcA-like promoters found upstream of nirA, nrtP, and narB all differ in sequence from the canonical NtcA promoter established for other cyanobacteria, and in the case of nirA, the NtcA-like promoter was functional only in cells deprived of combined nitrogen. The ecological implications of these findings are discussed in the context of the oligotrophic nature of oceanic surface waters in which Synechococcus spp. thrive.

Expression of the glutamyl-tRNA synthetase gene from the cyanobacterium Synechococcus sp PCC 7942 depends on nitrogen availability and the global regulator NtcA

We report here transcriptional analyses of a cyanobacterial gene encoding an aminoacyl-tRNA synthetase (aaRS), the gltX gene from Synechoccocus sp. PCC 7942, coding for the glutamyl-tRNA synthetase. We show that the transcript levels of gltX in Synechococcus depend on nitrogen availability and do not increase with the growth rate, which is at odds with observations from other bacteria. We also demonstrate the involvement of the cyanobacterial global regulator NtcA in transcriptional control of gltX according to nitrogen status. Our results support a regulatory model in which the gltX transcript level is finely tuned by a dynamic equilibrium between activation and repression relying upon the cellular concentration of NtcA.

Transcriptional activation of NtcA-dependent promoters of Synechococcus sp. PCC 7942 by 2-oxoglutarate in vitro

The transcription factor NtcA is a global regulator of nitrogen homeostasis in cyanobacteria. It thus positively regulates the expression of genes related to nitrogen assimilation such as glnA (which encodes glutamine synthetase) and ntcA itself in response to nitrogen shortage or depletion. The binding of NtcA to the glnA and ntcA promoters of Synechococcus sp. PCC 7942 in vitro now has been shown to be enhanced by 2-oxoglutarate. In vitro analysis of gene transcription also revealed that the interaction of NtcA with its promoter element was not sufficient for activation of transcription, and 2-oxoglutarate was required for transcriptional initiation by NtcA. Given that the intracellular concentration of 2-oxoglutarate is inversely related to nitrogen availability, it is proposed that this metabolite functions as a signaling molecule that transmits information on cellular nitrogen status to NtcA and thereby regulates the transcription of genes related to nitrogen assimilation in cyanobacteria.

2-Oxoglutarate increases the binding affinity of the NtcA (nitrogen control) transcription factor for the Synechococcus glnA promoter

The cyanobacterial NtcA global nitrogen regulator belongs to the catabolite activator protein (CAP) family and activates transcription of nitrogen assimilation genes in response to nitrogen step-down. The binding affinity of NtcA towards a DNA fragment carrying the promoter of the glnA gene from Synechococcus sp. PCC 7942, analyzed in vitro by band-shift assay, was increased five-fold by 2-oxoglutarate in the presence of Mg(2+) ions. The 2-oxoglutarate effect peaked at about 0.6 mM, a rather physiological concentration for this compound under nitrogen-limiting conditions, and could be partially reproduced by 3-oxoglutarate but not by oxaloacetate or glutamate. These results suggest 2-oxoglutarate as a signal of the C to N balance of the cells to regulate NtcA activity and provide a new example of regulation in the versatile CAP family of proteins.

Cyanobacteria perceive nitrogen status by sensing intracellular 2-oxoglutarate levels

The regulatory circuits that control nitrogen metabolism are relatively well known in several bacterial model groups. However, much less is understood about how the nitrogen status of the cell is perceived in vivo. In cyanobacteria, the transcription factor NtcA is required for regulation (activation or repression) of an extensive number of genes involved in nitrogen metabolism. In contrast, how NtcA activity is regulated is largely unknown. Assimilation of ammonium by most microorganisms occurs through the sequential action of two enzymes: glutamine synthetase (GS) and glutamate synthase. Interestingly, regulation of the expression of NtcA-dependent genes in the cyanobacterium Synechocystis sp. PCC 6803 is altered in mutants with modified levels of GS activity. Two types of mutants were analyzed: glnA null mutants that lack GS type I and gif mutants unable to inactivate GS in the presence of ammonium. Changes in the intracellular pools of 19 different amino acids and the keto acid 2-oxoglutarate were recorded in wild-type and mutant strains under different nitrogen conditions. Our data strongly indicate that the nitrogen status in cyanobacteria is perceived as changes in the intracellular 2-oxoglutarate pool.

In vivo regulation of glutamine synthetase activity in the marine chlorophyll b-containing cyanobacterium Prochlorococcus sp. strain PCC 9511 (oxyphotobacteria)

The physiological regulation of glutamine synthetase (GS; EC 6.3.1.2) in the axenic Prochlorococcus sp. strain PCC 9511 was studied. GS activity and antigen concentration were measured using the transferase and biosynthetic assays and the electroimmunoassay, respectively. GS activity decreased when cells were subjected to nitrogen starvation or cultured with oxidized nitrogen sources, which proved to be nonusable for Prochlorococcus growth. The GS activity in cultures subjected to long-term phosphorus starvation was lower than that in equivalent nitrogen-starved cultures. Azaserine, an inhibitor of glutamate synthase, provoked an increase in enzymatic activity, suggesting that glutamine is not involved in GS regulation. Darkness did not affect GS activity significantly, while the addition of diuron provoked GS inactivation. GS protein determination showed that azaserine induces an increase in the concentration of the enzyme. The unusual responses to darkness and nitrogen starvation could reflect adaptation mechanisms of Prochlorococcus for coping with a light- and nutrient-limited environment.

The GS-GOGAT pathway is not operative in the heterocysts. Cloning and expression of glsF gene from the cyanobacterium Anabaena sp. PCC 7120

The gene encoding the ferredoxin-dependent glutamate synthase (Fd-GOGAT), glsF, from the heterocyst-forming cyanobacterium Anabaena sp. PCC 7120, has been cloned and sequenced. Unlike other cyanobacteria, Anabaena 7120 contains only Fd-GOGAT, lacking NADH-GOGAT. The amount of glsF transcript and Fd-GOGAT activity were similar under all the nitrogen growth conditions tested. Enzyme activity, Western and Northern blot analyses indicated that Fd-GOGAT is absent in the heterocysts, while glutamine synthetase (GS) and NADP-isocitrate dehydrogenase (IDH) were present in these specialised cells. Our results clearly indicate that the GS-GOGAT pathway is not operative in the heterocysts, and hence glutamate must be imported from the adjacent vegetative cells, to sustain GS activity. Heterocysts probably export glutamine or another nitrogen rich compound like arginine to the vegetative cells.

NtcA represses transcription of gifA and gifB, genes that encode inhibitors of glutamine synthetase type I from Synechocystis sp. PCC 6803

Synechocystis sp. PCC 6803 glutamine synthetase type I (GS) activity is controlled by direct interaction with two inactivating factors (IF7 and IF17). IF7 and IF17 are homologous polypeptides encoded by the gifA and gifB genes respectively. We investigated the transcriptional regulation of these genes. Expression of both genes is maximum in the presence of ammonium, when GS is inactivated. Nitrogen starvation attenuates the ammonium-mediated induction of gifA and gifB as well as the ammonium-mediated inactivation of GS. Putative binding sites for the transcription factor NtcA were identified at -7.5 and -30.5 bp upstream of gifB and gifA transcription start points respectively. Synechocystis NtcA protein binding to both promoters was demonstrated by gel electrophoresis mobility shift assays. Constitutive high expression levels of both genes were found in a Synechocystis NtcA non-segregated mutant (SNC1), which showed a fourfold reduction in the ntcA expression. These experiments indicate a repressive role for NtcA on the transcription of gifA and gifB genes. Our results demonstrate that NtcA plays a central role in GS regulation in cyanobacteria, stimulating transcription of the glnA gene (GS structural gene) and suppressing transcription of the GS inactivating factor genes gifA and gifB.