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

Cyanophycin and its biosynthesis: not hot but very cool

Covering: 1878 to early 2023Cyanophycin is a biopolymer consisting of a poly-aspartate backbone with arginines linked to each Asp sidechain through isopeptide bonds. Cyanophycin is made by cyanophycin synthetase 1 or 2 through ATP-dependent polymerization of Asp and Arg, or β-Asp-Arg, respectively. It is degraded into dipeptides by exo-cyanophycinases, and these dipeptides are hydrolyzed into free amino acids by general or dedicated isodipeptidase enzymes. When synthesized, chains of cyanophycin coalesce into large, inert, membrane-less granules. Although discovered in cyanobacteria, cyanophycin is made by species throughout the bacterial kingdom, and cyanophycin metabolism provides advantages for toxic bloom forming algae and some human pathogens. Some bacteria have developed dedicated schemes for cyanophycin accumulation and use, which include fine temporal and spatial regulation. Cyanophycin has also been heterologously produced in a variety of host organisms to a remarkable level, over 50% of the host's dry mass, and has potential for a variety of green industrial applications. In this review, we summarize the progression of cyanophycin research, with an emphasis on recent structural studies of enzymes in the cyanophycin biosynthetic pathway. These include several unexpected revelations that show cyanophycin synthetase to be a very cool, multi-functional macromolecular machine.

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.

Nitrogen depletion in Arthrospira sp. PCC 8005, an ultrastructural point of view

In cyanobacteria, the nitrogen and carbon metabolisms are functionally bridged and consequently respond to the carbon-to-nitrogen ratio. Consequently, a nitrogen deficiency results in carbon excess. For the first time, the biological adaptation of Arthrospira sp. PCC 8005 to nitrogen starvation has been deeply characterized at the cellular structure scale. The results indicated that the carbon excess is rerouted into carbon storage granules, such as the polyhydroxyalkanoate and glycogen granules corroborating existing data. Additionally, this photosynthetic organism hugely secreted exopolysaccharides, which could constitute another biological carbon reservoir. It has been reported that few cells in trichomes of Arthrospira sp. PCC 8005 still display a high level of fluorescence after a long-term nitrogen starvation. The transmission electron microscopy showed that some cells still contained thylakoids and phycobilisomes after this long-term nitrogen starvation, which could explain the remaining fluorescence.

Carbon assimilation and accumulation of cyanophycin during the development of dormant cells (akinetes) in the cyanobacterium Aphanizomenon ovalisporum

Akinetes are spore-like non-motile cells that differentiate from vegetative cells of filamentous cyanobacteria from the order Nostocales. They play a key role in the survival and distribution of these species and contribute to their perennial blooms. Here, we demonstrate variations in cellular ultrastructure during akinete formation concomitant with accumulation of cyanophycin; a copolymer of aspartate and arginine that forms storage granules. Cyanophycin accumulation is initiated in vegetative cells few days post-exposure to akinete inducing conditions. This early accumulated cyanophycin pool in vegetative cells disappears as a nearby cell differentiates to an akinete and stores large pool of cyanophycin. During the akinete maturation, the cyanophycin pool is further increased and comprise up to 2% of the akinete volume. The cellular pattern of photosynthetic activity during akinete formation was studied by a nano-metric scale secondary ion mass spectrometry (NanoSIMS) analysis in (13)C-enriched cultures. Quantitative estimation of carbon assimilation in vegetative cells and akinetes (filament-attached and -free) indicates that vegetative cells maintain their basal activity while differentiating akinetes gradually reduce their activity. Mature-free akinetes practically lost their photosynthetic activity although small fraction of free akinetes were still photosynthetically active. Additional (13)C pulse-chase experiments indicated rapid carbon turnover during akinete formation and de novo synthesis of cyanophycin in vegetative cells 4 days post-induction of akinete differentiation.

Trade-Off between Growth and Carbohydrate Accumulation in Nutrient-Limited Arthrospira sp. PCC 8005 Studied by Integrating Transcriptomic and Proteomic Approaches

Cyanobacteria have a strong potential for biofuel production due to their ability to accumulate large amounts of carbohydrates. Nitrogen (N) stress can be used to increase the content of carbohydrates in the biomass, but it is expected to reduce biomass productivity. To study this trade-off between carbohydrate accumulation and biomass productivity, we characterized the biomass productivity, biomass composition as well as the transcriptome and proteome of the cyanobacterium Arthrospira sp. PCC 8005 cultured under N-limiting and N-replete conditions. N limitation resulted in a large increase in the carbohydrate content of the biomass (from 14 to 74%) and a decrease in the protein content (from 37 to 10%). Analyses of fatty acids indicated that no lipids were accumulated under N-limited conditions. Nevertheless, it did not affect the biomass productivity of the culture up to five days after N was depleted from the culture medium. Transcriptomic and proteomic analysis indicated that de novo protein synthesis was down-regulated in the N-limited culture. Proteins were degraded and partly converted into carbohydrates through gluconeogenesis. Cellular N derived from protein degradation was recycled through the TCA and GS-GOGAT cycles. In addition, photosynthetic energy production and carbon fixation were both down-regulated, while glycogen synthesis was up-regulated. Our results suggested that N limitation resulted in a redirection of photosynthetic energy from protein synthesis to glycogen synthesis. The fact that glycogen synthesis has a lower energy demand than protein synthesis might explain why Arthrospira is able to achieve a similar biomass productivity under N-limited as under N-replete conditions despite the fact that photosynthetic energy production was impaired by N limitation.

Combination of environmental stress and localization of L-asparaginase in Arthrospira platensis for production improvement

The diverse applications of l-asparaginase have led us to explore new sources of this enzyme. Arthrospira platensis has been scarcely reported as a new candidate for l-asparaginase production. In the present study, we localized l-asparaginase in A. platensis and enhanced its production. Enzyme localization was conducted by culturing cells in SOT medium and extracting the enzymes from different parts of the cell. The Taguchi method (factors studied: nitrogen, iron, sodium chloride, and temperature shock) using an L9 orthogonal array was designed for improving l-asparaginase production. The highest specific activity of l-asparaginase was found in subcellular, cytoplasmic extracts (0.166 ± 0.029 U/mg). Optimization data revealed that the highest production of l-asparaginase (0.275 ± 0.005 U) was attained by NaNO₃, NaCl, and FeSO₄·7H₂O at concentrations, 1.875 g/l, 0.25 M, and 0.0075 g/l, respectively, with 1-h temperature shock at 22 °C in the dark. Results revealed more than twofold higher production of l-asparaginase than that under the normal condition. In summary, l-asparaginase appeared dominantly in the cytoplasmic region and its production could be induced by employing combined stress conditions with a Taguchi experimental design. To our best knowledge, this is the first report on l-asparaginase production in cyanobacteria of the subclass Oscillatoriophycideae.

Proteomic and cellular views of Arthrospira sp. PCC 8005 adaptation to nitrogen depletion

Cyanobacteria are photosynthetic prokaryotes that play a crucial role in the Earth's nitrogen and carbon cycles. Nitrogen availability is one of the most important factors in cyanobacterial growth. Interestingly, filamentous non-diazotrophic cyanobacteria, such as Arthrospira sp. PCC 8005, have developed survival strategies that enable them to adapt to nitrogen deprivation. Metabolic studies recently demonstrated a substantial synthesis and accumulation of glycogen derived from amino acids during nitrogen starvation. Nevertheless, the regulatory mechanism of this adaptation is poorly understood. To the best of our knowledge, this study is the first proteomic and cellular analysis of Arthrospira sp. PCC 8005 under nitrogen depletion. Label-free differential proteomic analysis indicated the global carbon and nitrogen reprogramming of the cells during nitrogen depletion as characterized by an upregulation of glycogen synthesis and the use of endogenous nitrogen sources. The degradation of proteins and cyanophycin provided endogenous nitrogen when exogenous nitrogen was limited. Moreover, formamides, cyanates and urea were also potential endogenous nitrogen sources. The transporters of some amino acids and alternative nitrogen sources such as ammonium permease 1 were induced under nitrogen depletion. Intriguingly, although Arthrospira is a non-diazotrophic cyanobacterium, we observed the upregulation of HetR and HglK proteins, which are involved in heterocyst differentiation. Moreover, after a long period without nitrate, only a few highly fluorescent cells in each trichome were observed, and they might be involved in the long-term survival mechanism of this non-diazotrophic cyanobacterium under nitrogen deprivation.

Rhythmic and sustained oscillations in metabolism and gene expression of Cyanothece sp. ATCC 51142 under constant light

Cyanobacteria, a group of photosynthetic prokaryotes, oscillate between day and night time metabolisms with concomitant oscillations in gene expression in response to light/dark cycles (LD). The oscillations in gene expression have been shown to sustain in constant light (LL) with a free running period of 24 h in a model cyanobacterium Synechococcus elongatus PCC 7942. However, equivalent oscillations in metabolism are not reported under LL in this non-nitrogen fixing cyanobacterium. Here we focus on Cyanothece sp. ATCC 51142, a unicellular, nitrogen-fixing cyanobacterium known to temporally separate the processes of oxygenic photosynthesis and oxygen-sensitive nitrogen fixation. In a recent report, metabolism of Cyanothece 51142 has been shown to oscillate between photosynthetic and respiratory phases under LL with free running periods that are temperature dependent but significantly shorter than the circadian period. Further, the oscillations shift to circadian pattern at moderate cell densities that are concomitant with slower growth rates. Here we take this understanding forward and demonstrate that the ultradian rhythm under LL sustains at much higher cell densities when grown under turbulent regimes that simulate flashing light effect. Our results suggest that the ultradian rhythm in metabolism may be needed to support higher carbon and nitrogen requirements of rapidly growing cells under LL. With a comprehensive Real time PCR based gene expression analysis we account for key regulatory interactions and demonstrate the interplay between clock genes and the genes of key metabolic pathways. Further, we observe that several genes that peak at dusk in Synechococcus peak at dawn in Cyanothece and vice versa. The circadian rhythm of this organism appears to be more robust with peaking of genes in anticipation of the ensuing photosynthetic and respiratory metabolic phases.

Carbon dioxide regulation of autotrophy and diazotrophy in the nitrogen-fixing cyanobacterium Nostoc muscorum

To understand how carbon and nitrogen metabolism are regulated in diazotrophically and non-diazotrophically grown cultures of the cyanobacterium Nostoc muscorum, we investigated the role of bicarbonate (HCO₃⁻) in regulating diazotrophy and autotrophy. Results showed that HCO₃⁻ concentration up to 12 mol m⁻³ enhanced growth, specific growth rate, photosynthetic pigments, photosynthetic O₂ evolution and nitrogenase activity under diazotrophic growth conditions. The co-existence of different nitrogen sources in the growth medium further accelerate the examined parameters in the order of NO₃⁻<NO₂⁻<NH₄⁺<proline. Further, we examined the Ca⁺⁺-dependent ATPase activity and cytochrome c oxidase activity in the presence of graded concentration of HCO₃⁻ under diazotrophically grown and non-diazotrophically grown cultures. The activity of these enzymes was higher in the cells grown under elevated HCO₃⁻ concentration. The Ca⁺⁺-dependent ATPase activity was higher than that of cytochrome c oxidase, when NAPH was supplied as the electron donor. This finding suggested that photosynthetic generation of ATP utilized NADPH as an electron donor and cytochrome c oxidase activity is independent of NADPH.

Integrated OMICS guided engineering of biofuel butanol-tolerance in photosynthetic Synechocystis sp. PCC 6803

BACKGROUND

Photosynthetic cyanobacteria have been recently proposed as a 'microbial factory' to produce butanol due to their capability to utilize solar energy and CO2 as the sole energy and carbon sources, respectively. However, to improve the productivity, one key issue needed to be addressed is the low tolerance of the photosynthetic hosts to butanol.

RESULTS

In this study, we first applied a quantitative transcriptomics approach with a next-generation RNA sequencing technology to identify gene targets relevant to butanol tolerance in a model cyanobacterium Synechocystis sp. PCC 6803. The results showed that 278 genes were induced by the butanol exposure at all three sampling points through the growth time course. Genes encoding heat-shock proteins, oxidative stress related proteins, transporters and proteins involved in common stress responses, were induced by butanol exposure. We then applied GC-MS based metabolomics analysis to determine the metabolic changes associated with the butanol exposure. The results showed that 46 out of 73 chemically classified metabolites were differentially regulated by butanol treatment. Notably, 3-phosphoglycerate, glycine, serine and urea related to general stress responses were elevated in butanol-treated cells. To validate the potential targets, we constructed gene knockout mutants for three selected gene targets. The comparative phenotypic analysis confirmed that these genes were involved in the butanol tolerance.

CONCLUSION

The integrated OMICS analysis provided a comprehensive view of the complicated molecular mechanisms employed by Synechocystis sp. PCC 6803 against butanol stress, and allowed identification of a series of potential gene candidates for tolerance engineering in cyanobacterium Synechocystis sp. PCC 6803.

Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust

Biological soil crusts (BSCs) cover extensive portions of the earth's deserts. In order to survive desiccation cycles and utilize short periods of activity during infrequent precipitation, crust microorganisms must rely on the unique capabilities of vegetative cells to enter a dormant state and be poised for rapid resuscitation upon wetting. To elucidate the key events involved in the exit from dormancy, we performed a wetting experiment of a BSC and followed the response of the dominant cyanobacterium, Microcoleus vaginatus, in situ using a whole-genome transcriptional time course that included two diel cycles. Immediate, but transient, induction of DNA repair and regulatory genes signaled the hydration event. Recovery of photosynthesis occurred within 1 h, accompanied by upregulation of anabolic pathways. Onset of desiccation was characterized by the induction of genes for oxidative and photo-oxidative stress responses, osmotic stress response and the synthesis of C and N storage polymers. Early expression of genes for the production of exopolysaccharides, additional storage molecules and genes for membrane unsaturation occurred before drying and hints at preparedness for desiccation. We also observed signatures of preparation for future precipitation, notably the expression of genes for anaplerotic reactions in drying crusts, and the stable maintenance of mRNA through dormancy. These data shed light on possible synchronization between this cyanobacterium and its environment, and provides key mechanistic insights into its metabolism in situ that may be used to predict its response to climate, and or, land-use driven perturbations.

Dynamic proteome analysis of Cyanothece sp. ATCC 51142 under constant light

Understanding the dynamic nature of protein abundances provides insights into protein turnover not readily apparent from conventional, static mass spectrometry measurements. This level of data is particularly informative when surveying protein abundances in biological systems subjected to large perturbations or alterations in environment such as cyanobacteria. Our current analysis expands upon conventional proteomic approaches in cyanobacteria by measuring dynamic changes of the proteome using a (13)C(15)N-l-leucine metabolic labeling in Cyanothece ATCC51142. Metabolically labeled Cyanothece ATCC51142 cells grown under nitrogen-sufficient conditions in continuous light were monitored longitudinally for isotope incorporation over a 48 h period, revealing 414 proteins with dynamic changes in abundances. In particular, proteins involved in carbon fixation, pentose phosphate pathway, cellular protection, redox regulation, protein folding, assembly, and degradation showed higher levels of isotope incorporation, suggesting that these biochemical pathways are important for growth under continuous light. Calculation of relative isotope abundances (RIA) values allowed the measurement of actual active protein synthesis over time for different biochemical pathways under high light exposure. Overall results demonstrated the utility of "non-steady state" pulsed metabolic labeling for systems-wide dynamic quantification of the proteome in Cyanothece ATCC51142 that can also be applied to other cyanobacteria.

RELEASE OF CARBOHYDRATES AND PROTEINS BY A SUBTROPICAL STRAIN OF RAPHIDIOPSIS BROOKII (CYANOBACTERIA) ABLE TO PRODUCE SAXITOXIN AT THREE NITRATE CONCENTRATIONS(1)

Raphidiopsis brookii P. J. Hill (cyanobacteria) was isolated from a small subtropical eutrophic pond (Biguá Pond) located in the grounds of Rio Grande University in the extreme south of Brazil, following a toxic bloom of this species. Growth, saxitoxin production, and release of carbohydrates and protein were monitored at three sodium nitrate concentrations (500, 1,000, and 1,500 μM), from inoculation up to the stationary growth phase. Growth was monitored by determining the biovolume, chl content, and trichome count. Growth was better described in terms of biovolume and chl measurements, because trichome fragmentation was observed to increase at the stationary growth phase. Carbohydrates and proteins were released in small amounts during most of the experiment, with a significant increase during the stationary phase. Extracellular polysaccharides were essentially composed of glucose, galactose, N-acetyl-glucosamine, mannose, xylose, rhamnose, arabinose, and fucose. The relative proportions of these units showed no significant variation during growth. Small quantities of extracellular free carbohydrates were also detected, and only fucose was released in significant amounts at the lowest nitrate concentration (500 μM). R. brookii produced both saxitoxin and dc-saxitoxin, the former at four times the rate of the latter. This was the first study demonstrating saxitoxin production and the release of both carbohydrate and protein by R. brookii.

Detection of an L-amino acid dehydrogenase activity in Synechocystis sp. PCC 6803

The protein Slr0782 from Synechocystis sp. PCC 6803, which has similarity to L-amino acid oxidase from Synechococcus elongatus PCC 6301 and PCC 7942, has been characterized in part. Immunoblot blot analysis showed that Slr0782 is mainly thylakoid membrane-associated. Moreover, expression of slr0782 mRNA and Slr0782 protein were analyzed and an activity assay was developed. Utilizing toluene-permeabilized cells, an L-arginine-stimulated O(2) uptake became detectable in Synechocystis sp. PCC 6803. Besides oxidizing the basic L-amino acids L-arginine, L-lysine, L-ornithine, and L-histidine, a number of other L-amino acids were also substrates, while D-amino acids were not. The best substrate was L-cysteine, and the second best was L-arginine. The L-arginine-stimulated O(2) uptake was inhibited by cations. The inhibition by o-phenanthroline and salicylhydroxamic acid suggested the presence of a transition metal besides FAD in the enzyme. Moreover, it is shown that inhibitors of the respiratory electron transport chain, such as KCN and 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone, also inhibited the L-arginine-stimulated O(2) uptake, suggesting that Slr0782 functions as an L-arginine dehydrogenase, mediating electron transfer from L-arginine into the respiratory electron transport chain utilizing O(2) as electron acceptor via cytochrome oxidase. The results imply that Slr0782 is an additional substrate dehydrogenase being able to interact with the electron transport chain of the thylakoid membrane.

Transcript profiling indicates that the absence of PsbO affects the coordination of C and N metabolism in Synechocystis sp. PCC 6803

Transcript profiling of nitrate-grown Synechocystis sp. PCC 6803 PsbO-free mutant cells in comparison to wild-type (WT) detected substantial deviations. Because we had previously observed phenotypical differences between Synechocystis sp. PCC 6803 WT and its corresponding PsbO-free mutant when cultivated with l-arginine as sole N source and a light intensity of 200 mumol photons m(-2) s(-1), we also performed transcript profiling for both strains grown either with nitrate or with l-arginine as sole N source. We observed a total number of 520 differentially regulated transcripts in Synechocystis WT because of a shift from nitrate- to l-arginine-containing BG11 medium, while we detected only 13 differentially regulated transcripts for the PsbO-free mutant. Thus, the PsbO-free Synechocystis mutant had already undergone a preconditioning process for growth with l-arginine in comparison to WT. While Synechocystis WT suffered from growth with l-arginine at a light intensity of 200 mumol photons m(-2) s(-1), the PsbO-free mutant developed only a minor stress phenotype. In summary, our results suggest that the absence of PsbO in Synechocystis affects the coordination of photosynthesis/respiration and l-arginine metabolism through complex probably redox-mediated regulatory pathways. In addition, we show that a comparison of the transcriptomes of nitrate-grown Synechococcus elongatus PCC 7942 WT cells and its corresponding PsbO-free mutant cells resulted in only a few differentially regulated transcripts between both strains. The absence of the manganese/calcium-stabilizing PsbO protein of PSII with an assigned regulatory function for photosynthetic water oxidation causes bigger changes in the transcriptome of the permissive photoheterotrophically growing Synechocystis sp. PCC 6803 than in the transcriptome of the obligate photoautotrophically growing S. elongatus PCC 7942.

Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803

BACKGROUND

So far very limited knowledge exists on L-arginine catabolism in cyanobacteria, although six major L-arginine-degrading pathways have been described for prokaryotes. Thus, we have performed a bioinformatic analysis of possible L-arginine-degrading pathways in cyanobacteria. Further, we chose Synechocystis sp. PCC 6803 for a more detailed bioinformatic analysis and for validation of the bioinformatic predictions on L-arginine catabolism with a transcript analysis.

RESULTS

We have evaluated 24 cyanobacterial genomes of freshwater or marine strains for the presence of putative L-arginine-degrading enzymes. We identified an L-arginine decarboxylase pathway in all 24 strains. In addition, cyanobacteria have one or two further pathways representing either an arginase pathway or L-arginine deiminase pathway or an L-arginine oxidase/dehydrogenase pathway. An L-arginine amidinotransferase pathway as a major L-arginine-degrading pathway is not likely but can not be entirely excluded. A rather unusual finding was that the cyanobacterial L-arginine deiminases are substantially larger than the enzymes in non-photosynthetic bacteria and that they are membrane-bound. A more detailed bioinformatic analysis of Synechocystis sp. PCC 6803 revealed that three different L-arginine-degrading pathways may in principle be functional in this cyanobacterium. These are (i) an L-arginine decarboxylase pathway, (ii) an L-arginine deiminase pathway, and (iii) an L-arginine oxidase/dehydrogenase pathway. A transcript analysis of cells grown either with nitrate or L-arginine as sole N-source and with an illumination of 50 mumol photons m-2 s-1 showed that the transcripts for the first enzyme(s) of all three pathways were present, but that the transcript levels for the L-arginine deiminase and the L-arginine oxidase/dehydrogenase were substantially higher than that of the three isoenzymes of L-arginine decarboxylase.

CONCLUSION

The evaluation of 24 cyanobacterial genomes revealed that five different L-arginine-degrading pathways are present in the investigated cyanobacterial species. In Synechocystis sp. PCC 6803 an L-arginine deiminase pathway and an L-arginine oxidase/dehydrogenase pathway represent the major pathways, while the L-arginine decarboxylase pathway most likely only functions in polyamine biosynthesis. The transcripts encoding the enzymes of the two major pathways were constitutively expressed with the exception of the transcript for the carbamate kinase, which was substantially up-regulated in cells grown with L-arginine.