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Journal of Bacteriology, February 2006, p. 934-940, Vol. 188, No. 3
0021-9193/06/$08.00+0 doi:10.1128/JB.188.3.934-940.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
Departments of Chemistry,1 Biological Sciences, Wellesley College, Wellesley, Massachusetts 024812
Received 28 June 2005/ Accepted 2 November 2005
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Utilization of different nitrogen sources first requires their passage through the permeability barrier of the cytoplasmic membrane into the cyanobacterial cell. At low nitrate concentrations, the endergonic uptake of nitrate in freshwater cyanobacteria takes place through ABC-type transporters that exhibit high affinity for nitrate (27). Passive diffusion of nitrate takes place in Synecchococcus sp. strain PCC 7942 at nitrate concentrations above 1 mM (26). Ammonium at low concentrations (<0.25 mM) is taken up by a permease that catalyzes a membrane potential-dependent active transport, but this system is repressed in higher concentrations of ammonium where passive diffusion of unprotonated ammonia may be the mechanism for net uptake of ammonium (24). After diffusion, intracellular ammonium is trapped by glutamine synthetase. All nitrogen sources that are assimilated are converted to intracellular ammonium. Intracellular nitrate, for example, is reduced to nitrite by nitrate reductase; the nitrite is then reduced to ammonium by nitrite reductase. The ammonium then enters the glutamine synthetase/glutamate synthase cycle to be incorporated into 2-oxoglutarate (21, 24, 25, 35).
Many forms of transcriptional and posttranslational control have been shown to be involved in nitrogen assimilation when cells are grown under different physiological conditions (reviewed in references 11 and 12). A global nitrogen-regulating gene, ntcA, has been shown to synthesize a transcriptional regulator whose activity is influenced by 2-oxoglutarate. This gene is activated by the ATP binding, signal transduction protein PII (glnB gene product [13]) especially when the C-to-N ratio in the cell is high (21, 28), as is true in cases of nitrogen limitation. PII in its phosphorylated form also is required for the activation of transcription of NtcA-dependent genes, such as nitrate reductase, under conditions of nitrogen limitation (1). However, when cells are placed in conditions where there are low 2-oxoglutarate levels (high N-to-C levels), the nonphosphorylated form of PII appears to cause inhibition of the nitrate/nitrite permease (18). In nitrogen-starved Synechocystis sp. strain PCC 6803, the expression of three ammonium permeases was higher than when cells were incubated in either ammonium or nitrate (24). Similarly, glutamine synthetase in Synechocystis sp. strain PCC 6803 is inactivated in the presence of ammonium by two small protein factors (IF7 and IF17); these factors are regulated by NtcA (14).
Two molecules, both with high nitrogen content, appear to be nitrogen storage compounds in cyanobacteria: phycocyanin and cyanophycin. Phycocyanin is the principal accessory pigment in most cyanobacteria, whereas cyanophycin is thought to function primarily as a nitrogen reserve. Cyanophycin, a non-ribosomally synthesized peptide, composed of arginine and aspartic acid, accumulates in cyanobacteria when they are grown under all unbalanced nutrient conditions except nitrogen starvation (33, 3). Cyanobacteria that synthesize cyanophycin tend to use it as a nitrogen source during nitrogen starvation before using phycocyanin and other sources of cellular nitrogen such as proteins (5).
There is evidence that cyanophycin acts as transient store for newly fixed nitrogen in the heterocysts of diazotrophic cyanobacteria (19), and several studies have suggested that cyanophycin is a dynamic reservoir in most cyanobacteria (8, 22, 20). When cyanobacteria are starved for nitrogen, cyanophycin is broken down; when nitrogen becomes available, cyanophycin is again synthesized. Upon reintroduction of nitrogen, cells rebuild their nitrogen stores and begin to grow. It appears that cyanophycin may play an even more important role as a nitrogen reserve in diazotrophic unicellular strains (20) than in nondiazotrophic unicellular strains such as Synechocystis sp. strain PCC 6803, where phycobilisomes appear to be the main nitrogen reserve. Picossi et al. (29) showed that expression of the genes for cyanophycin metabolism (cphA for cyanophycin synthesis and cphB for cyanophycinase) increases in the absence of ammonium in Anabaena sp. strain PCC 7120. The inability to degrade cyanophycin is detrimental to the diazotrophic growth of this strain.
Cyanophycin is synthesized in Synechocytis sp. strain PCC 6308 immediately after nitrogen is replenished (4), whereas phycocyanin is not synthesized until about 6 h later. The synthesis of cyanophycin peaks at up to 12% of the dry weight of the cells by 10 to 12 h and then decreases to the low levels found in typical exponential growth. After growth of the same strain in medium containing ammonium, and then starvation and replenishing with ammonium, Mackerras et al. (22) also found that cyanophycin was synthesized immediately and then degraded within 24 h. A salt-sensitive, glycoprotease-negative mutant (gcp mutant) of Synechocystis sp. strain PCC 6803 accumulated cyanophycin to a level 40 times that of the wild-type strain since it was unable to remobilize cyanophycin (37). In this mutant, phycobilisomes were degraded as a source of nitrogen.
Recently, we have shown that cells grown in low light with or without the protein synthesis inhibitor chloramphenicol (CM), as well as cells grown in normal light with CM, synthesize cyanophycin from nitrogen obtained both from degradation of cellular proteins and directly from the medium (6). Nitrogen from the medium was incorporated at a faster rate and to a greater extent than nitrogen from protein degradation.
Since cyanophycin is a nitrogen storage molecule that may be a dynamic reserve, the experiments described here were designed to determine how the source of nitrogen affects whether cyanophycin is synthesized from nitrogen derived from proteolysis of cellular protein or from nitrogen in the cells' growth medium. Experiments were carried out here to examine the effects of nitrogen limitation on nitrogen incorporation into cyanophycin with or without inhibition of protein synthesis in cells growing on either nitrate or ammonium. Cells were grown in 14N medium and then either washed or allowed to deplete their nitrogen before being transferred into 15N repletion medium. The use of 14N in the growth medium and 15N in the repletion medium allows the determination of the source of nitrogen in cyanophycin using proton nuclear magnetic resonance (NMR) spectroscopy (34). In all cases, the nitrogen in cyanophycin came from both the breakdown of cellular protein and nitrogen in the medium but at different rates and to different extents depending on the nitrogen source and stress condition.
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Cyanophycin was extracted from cells harvested immediately and at increasing times up to 24 h after transfer from starvation conditions or washing to 15N growth medium, either with or without CM, and dissolved in 0.1 M HCl as described by Allen et al. (6). 1H NMR spectra of all cyanophycin samples were run on a Bruker Avance spectrometer (Bruker Instruments, Billerica, MA) at 400.152 MHz (34, 6). Spectra were calibrated to a 0.010 M solution of TSP (3-trimethylsilyl-2,2,3,3-tetradeutero sodium propionate; Cambridge Isotopes) in D2O (Aldrich Chemical Co., Milwaukee, WI) and analyzed as described in Allen et al. (6), using the 1D WIN-NMR PC program (Bruker Instruments, Billerica, MA). In some cases only the NH peaks at 6.8 ppm (
,
'-14N, or 15N) and 7.4 ppm (
-14N or 15N) were integrated because the small chemical shift difference between the
-NH peaks for Asp and Arg (8.4 to 8.5 ppm) made the multiplets difficult to resolve and integrate accurately. Ratios of integration of peaks due to protons bonded to each 14N and 15N were divided by the sum of the integrations of the peaks for protons bonded to both nitrogen isotopes to calculate the percentages of each isotopic form of cyanophycin present at each time point. Total cyanophycin was determined by integrating the arginine
-CH proton peak at 3.25 ppm (9). These integrations were standardized to the TSP integration and then corrected for the volume of the sample. Amounts of cyanophycin containing 14N and 15N at each time point were thus the product of the total cyanophycin and the fraction of each isotopic species.
Non-nitrogen-starved cells have different amounts of cyanophycin present when they are washed and placed into new nitrogen-containing medium, depending on their growth stage. Exponentially growing cells have small, but sometimes measurable amounts of cyanophycin when transferred. The amount of cyanophycin present in these cells (determined from the arginine
-CH peak at 3.25 ppm) at the time of transfer was subtracted from the amount of cyanophycin at each point in time course experiments in order to calculate rates and times of incorporation of 14N and 15N comparable to the starved cell experiments. Without this correction, rates of 15N incorporation would have appeared lower and the time at which 15N=14N would have appeared later. Nitrogen-starved cells had no cyanophycin at the time of medium switch.
The concentration of chlorophyll a in the cultures was measured by adding 1 ml of methanol to 50 µl of culture, microfuging the mixture for 3 min, and measuring the absorbance of the supernatant at 665 nm. Pigments were also observed by recording whole-cell visible spectra between 400 and 750 nm using an opal glass technique (32). Nitrate reductase assays were performed at various times on cells grown with either nitrate or ammonium, with or without the addition of CM, as described by Herrero et al. (16). Cells were permeabilized by using toluene and incubated for 5 min at 30°C with substrate, methyl viologen, and sodium dithionite. The reaction was stopped and the colored nitrite complex developed by addition of sulfanilamide in HCl and N-(1-naphthyl)-ethylenediamine.
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FIG. 1. 1H NMR spectra of cyanophycin over time extracted from cells grown on 14NH4+, starved, and replenished with 15NH4+ and CM at 0 min. A broad water peak at 0 min demonstrates the effect of poor water suppression. Peaks to the left of the water peak are protons bonded to nitrogen, and those to the right of the water peak are protons bonded to carbon.
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FIG. 2. Evolution of percent 14N and percent 15N over time in cells grown on 14NH4+, starved, and replenished with 15NH4+ and CM. Solid symbols, 14N; open symbols, 15N [ , , '(Arg); , (Arg); , amide ( )(Asp, Arg)]. Ratios of integrations of peaks due to protons bonded to each 14N and 15N were divided by the sum of the integrations of the peaks for protons bonded to both nitrogen isotopes to calculate the percentages of each isotopic form of cyanophycin present at each time point.
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FIG. 3. Amount of incorporation of 14N and 15N (arbitrary units) into cyanophycin for cells grown on 14NH4+, starved, and replenished with 15NH4+ and CM plotted versus time. Amounts of cyanophycin containing 14N and 15N at each time point are the product of the total cyanophycin and the fraction of each isotopic species. , 15N; , 14N. The slopes of these lines are the rates of incorporation of 14N and 15N into cyanophycin.
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TABLE 1. Comparison of effect of CM on cyanophycin synthesis in nitrogen-starved cells grown and replenished with either nitrate or ammonium
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TABLE 2. Comparison of effects of nitrogen sources on cyanophycin synthesis in nitrogen-replete cells treated with CM
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Table 2 shows the response of nitrogen-replete cells to CM when the nitrogen source was the same or was switched. Nitrate-grown, nitrogen-replete cells utilized external nitrate or ammonium at approximately equal rates when treated with CM, but ammonium-grown nitrogen-replete cells utilized external ammonium slowly and external nitrate even more slowly when CM was present. For all of these nitrogen-replete cells treated with CM there was a lag before any new cyanophycin was synthesized, except in the case of cells grown initially in nitrate and replenished with nitrate.
Nitrate reductase activity was found to be significantly higher, by at least an order of magnitude, in cells growing in nitrate than in those growing in ammonium (t = 5.79, P = 3.99E-06). Figure 4 shows the activity of nitrate reductase expressed as µg of nitrite produced/µg of chlorophyll. Nitrate reductase activity was low in ammonium-grown cells but increased as ammonium was depleted from the medium during starvation. When starved cells were replenished with ammonium, enzyme activity decreased to its prestarvation level. When starved cells were replenished with nitrate, nitrate reductase activity increased dramatically until between 22 and 46 h after replenishing, after which activity began to decrease. When CM was added with nitrate at the time of replenishing nitrate-starved cells, nitrate reductase activity remained low for at least 5 h (data not shown), suggesting that the increase in nitrate reductase activity requires new protein synthesis.
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FIG. 4. Nitrate reductase activity during starvation of ammonium-grown cells in ammonium starvation medium followed by replenishment of these cells with ammonium or nitrate. Activity is expressed in terms of µg of nitrite/µg of chlorophyll. Nitrogen starvation began at time zero and cells were replenished with nitrogen at 96 h. Error bars represent range of data for three trials at each time point. ( , ammonium starvation. , replenished with ammonium; , replenished with nitrate.
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Using 1H NMR spectroscopy of cyanophycin from cells grown first in medium with a 14N nitrogen source, followed by transfer into 15N medium, allows the quantification of amounts of nitrogen in the macromolecule from both sources. In these experiments, Synechocystis sp. strain PCC 6308, which forms large amounts of cyanophycin (5), was grown in either 14N nitrate or in 14N ammonium to exponential phase. Cells were then either starved for nitrogen or not starved. If starved, cells would have little or no cyanophycin and cellular proteins would be degraded. Cells that were not starved would have small, but varying amounts of cyanophycin and more 14N cellular protein. In the presence of CM, new protein synthesis would be prevented. New cyanophycin synthesis would thus have to come largely from the medium nitrogen (15N) directly, or from previously synthesized protein (14N), without going through newly synthesized proteins in the cell.
The results from these experiments suggest that nitrogen for cyanophycin synthesis comes preferentially from the external medium unless this nitrogen cannot be used due to either none being present or to the absence of the enzymes necessary for its utilization. Furthermore, since cyanophycin appears to be synthesized more slowly when the nitrogen source is switched after starvation than when it remains the same (Table 1), either new enzyme synthesis or enzyme activation is necessary. Nitrate reductase activity was very low when ammonium was present in the medium (Fig. 4), a finding in agreement with data for other strains of cyanobacteria (16). Thus, when nitrate was added to ammonium-grown cells without prior nitrogen starvation, low levels of nitrate reductase would be present and little nitrate could reach cyanophycin.
Lack of nitrate reductase activity in nitrogen-replete cells grown in ammonium medium before being transferred to nitrate and CM was hypothesized as the factor responsible for the very late and limited incorporation of medium nitrogen into cyanophycin (Table 2). Figure 4 shows that nitrate reductase activity was very low when ammonium was present in the medium. Since synthesis of new nitrate reductase should be inhibited in the presence of CM, nitrate would not be converted into useable nitrogen for the cell. Figure 4 also shows that when ammonium-grown cells were starved for nitrogen, the amount of nitrate reductase activity increased; starved cells transferred to nitrate with or without CM should therefore have the ability to utilize nitrate more quickly than nitrogen-replete cells, a finding consistent with our observations. (Compare Tables 1 and 2.) However, 15N was first observed in cyanophycin in ammonium/starve/nitrate experiments at the latest time (6 h) of any of the nitrogen starvation (without CM) experiments (Table 1). Since, as shown in Fig. 4, the activity of nitrate reductase increased almost 10-fold during ammonium starvation (derepression), nitrate reductase could not have been limiting in this case.
In all cases in which CM was added with 15N to washed, but non-nitrogen-starved cells grown first in 14N (Table 2), 15N was incorporated into cyanophycin more slowly than in starved cells (Table 1), suggesting that new protein synthesis is necessary for the new nitrogen source to be incorporated and/or that more cyanophycin is made from nitrogen derived from cellular protein than from extracellular nitrogen in the nonstarved cells. On the other hand, for nitrogen-starved cells, whether or not CM was added with the source of replenishment nitrogen (Table 1), there was little effect on the time and rate at which extracellular nitrogen is incorporated into cyanophycin except in the case of ammonium/starve/nitrate cells. These cells incorporated medium nitrogen into cyanophycin earlier, and to a greater extent, in the presence of CM than without CM. Protein synthesis, therefore, does not appear to be necessary for either nitrate or ammonium incorporation into cyanophycin for nitrogen starved cells, even when switching nitrogen sources.
The regulation of cyanophycin formation could take place at many points when cells are nitrogen stressed or transferred to media with different nitrogen sources. Many proteins in addition to nitrate reductase are involved in nitrogen uptake and assimilation and in cyanophycin synthesis and degradation. The levels of these proteins appear to depend on whether or not nitrogen is limited and on whether nitrogen is present in the form of ammonium (23). In excess nitrogen, cyanophycin synthesis is promoted (3), and PII is in its nonphosphorylated form (12, 18). Nonphosphorylated PII was recently shown to stimulate N-acetyl glutamate kinase, which favors arginine synthesis and, hence, cyanophycin synthesis (15). Thus, cyanophycin synthesis may be enhanced by the presence of several enzymes present under conditions of excess nitrogen.
In the absence of ammonium, the cph genes are more highly expressed, and more cyanophycin accumulated in both filaments and heterocysts of Anabaena sp. strain PCC 7120 (29). If the cphA gene is also expressed at high levels during nitrogen starvation in Synechocystis sp. strain PCC 6308, the cyanophycin synthetase produced would be available to synthesize cyanophycin when nitrogen is replenished. A lower level of expression of the cph genes in the presence of ammonium in Synechocystis could explain the late appearance of cyanophycin in washed nitrogen replete cells (Table 2). However, all of the data for the addition of ammonium or ammonium plus CM to nitrogen-starved cells (Table 1) suggest rapid synthesis of cyanophycin from medium nitrogen less than 1 h after ammonium is added. These data also confirm that protein synthesis is not necessary for cyanophycin synthesis and that cyanophycin is synthesized more rapidly in the presence of a protein synthesis inhibitor when protein synthesis is not competing for nitrogen.
The experiments described here suggest that nitrogen is incorporated into cyanophycin from both the breakdown of cellular protein and directly from the medium. Nitrogen is incorporated into cyanophycin at different rates and to different extents, depending on the source of nitrogen (ammonium or nitrate) and whether or not the cells are first starved for nitrogen. These differences appear to be related to the activity of nitrate reductase in cells, but further work is necessary to determine whether and how other enzymes or transcription factors are involved. in Synechocystis sp. strain PCC 6308.
We gratefully acknowledge the scientific contributions of the following undergraduate students who participated in this work: Jiae Kim, Cristina Chae, Melissa Davis, Manisha Sijapati, and Salima Sheikh.
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