Artificial neural networks prediction and optimization based on four light regions for light utilization from Synechocystis sp. PCC 6803

Light is crucial in microalgae growth. However, dividing the microalgae growth region into light and dark regions has limitations. In this study, the light response of Synechocystis sp. PCC 6803 was investigated to define four light regions (FLRs): light compensation region, light limitation region, light saturation region, and photoinhibition region. The proportions of cells' residence time in the FLRs and the number of times cells (NTC) passed through the FLRs in photobioreactors were calculated by using MATLAB. Based on the FLRs and NTC passed through the FLRs, a growth model was established by using artificial neural network (ANN).The ANN model had a validation R2 value of 0.97, which was 76.36% higher than the model based on light-dark regions. The high accuracy of the ANN model was further verified through dynamic adjustment of light intensity experiments.This study confirmed the importance of the FLRs for studying microalgae growth dynamics.

Thylakoid attachment to the plasma membrane in Synechocystis sp. PCC 6803 requires the AncM protein

Thylakoids are the highly specialized internal membrane systems that harbor the photosynthetic electron transport machinery in cyanobacteria and in chloroplasts. In Synechocystis sp. PCC 6803, thylakoid membranes (TMs) are arranged in peripheral sheets that occasionally converge on the plasma membrane (PM) to form thylakoid convergence membranes (TCMs). TCMs connect several thylakoid sheets and form local contact sites called thylapses between the two membrane systems, at which the early steps of photosystem II (PSII) assembly occur. The protein CurT is one of the main drivers of TCM formation known so far. Here, we identify, by whole-genome sequencing of a curT- suppressor strain, the protein anchor of convergence membranes (AncM) as a factor required for the attachment of thylakoids to the PM at thylapses. An ancM- mutant is shown to have a photosynthetic phenotype characterized by reductions in oxygen-evolution rate, PSII accumulation, and PS assembly. Moreover, the ancM- strain exhibits an altered thylakoid ultrastructure with additional sheets and TCMs detached from the PM. By combining biochemical studies with fluorescence and correlative light-electron microscopy-based approaches, we show that AncM is an integral membrane protein located in biogenic TCMs that form thylapses. These data suggest an antagonistic function of AncM and CurT in shaping TM ultrastructure.

Redesigning the photosynthetic light reactions to enhance photosynthesis - the PhotoRedesign consortium

In this Perspective article, we describe the visions of the PhotoRedesign consortium funded by the European Research Council of how to enhance photosynthesis. The light reactions of photosynthesis in individual phototrophic species use only a fraction of the solar spectrum, and high light intensities can impair and even damage the process. In consequence, expanding the solar spectrum and enhancing the overall energy capacity of the process, while developing resilience to stresses imposed by high light intensities, could have a strong positive impact on food and energy production. So far, the complexity of the photosynthetic machinery has largely prevented improvements by conventional approaches. Therefore, there is an urgent need to develop concepts to redesign the light-harvesting and photochemical capacity of photosynthesis, as well as to establish new model systems and toolkits for the next generation of photosynthesis researchers. The overall objective of PhotoRedesign is to reconfigure the photosynthetic light reactions so they can harvest and safely convert energy from an expanded solar spectrum. To this end, a variety of synthetic biology approaches, including de novo design, will combine the attributes of photosystems from different photoautotrophic model organisms, namely the purple bacterium Rhodobacter sphaeroides, the cyanobacterium Synechocystis sp. PCC 6803 and the plant Arabidopsis thaliana. In parallel, adaptive laboratory evolution will be applied to improve the capacity of reimagined organisms to cope with enhanced input of solar energy, particularly in high and fluctuating light.

The NAD Kinase Slr0400 Functions as a Growth Repressor in Synechocystis sp. PCC 6803

NADP+, the phosphorylated form of nicotinamide adenine dinucleotide (NAD), plays an essential role in many cellular processes. NAD kinase (NADK), which is conserved in all living organisms, catalyzes the phosphorylation of NAD+ to NADP+. However, the physiological role of phosphorylation of NAD+ to NADP+ in the cyanobacterium Synechocystis remains unclear. In this study, we report that slr0400, an NADK-encoding gene in Synechocystis, functions as a growth repressor under light-activated heterotrophic growth conditions and light and dark cycle conditions in the presence of glucose. We show, via characterization of NAD(P)(H) content and enzyme activity, that NAD+ accumulation in slr0400-deficient mutant results in the unsuppressed activity of glycolysis and tricarboxylic acid (TCA) cycle enzymes. In determining whether Slr0400 functions as a typical NADK, we found that constitutive expression of slr0400 in an Arabidopsis nadk2-mutant background complements the pale-green phenotype. Moreover, to determine the physiological background behind the growth advantage of mutants lacking slr04000, we investigated the photobleaching phenotype of slr0400-deficient mutant under high-light conditions. Photosynthetic analysis found in the slr0400-deficient mutant resulted from malfunctions in the Photosystem II (PSII) photosynthetic machinery. Overall, our results suggest that NADP(H)/NAD(H) maintenance by slr0400 plays a significant role in modulating glycolysis and the TCA cycle to repress the growth rate and maintain the photosynthetic capacity.

Enhancing photosynthesis at high light levels by adaptive laboratory evolution

Photosynthesis is readily impaired by high light (HL) levels. Photosynthetic organisms have therefore evolved various mechanisms to cope with the problem. Here, we have dramatically enhanced the light tolerance of the cyanobacterium Synechocystis by adaptive laboratory evolution (ALE). By combining repeated mutagenesis and exposure to increasing light intensities, we generated strains that grow under extremely HL intensities. HL tolerance was associated with more than 100 mutations in proteins involved in various cellular functions, including gene expression, photosynthesis and metabolism. Co-evolved mutations were grouped into five haplotypes, and putative epistatic interactions were identified. Two representative mutations, introduced into non-adapted cells, each confer enhanced HL tolerance, but they affect photosynthesis and respiration in different ways. Mutations identified by ALE that allow photosynthetic microorganisms to cope with altered light conditions could be employed in assisted evolution approaches and could strengthen the robustness of photosynthesis in crop plants.

Reconstruction of the absorption spectrum of Synechocystis sp. PCC 6803 optical mutants from the in vivo signature of individual pigments

In this work, we reconstructed the absorption spectrum of different Synechocystis sp. PCC 6803 optical strains by summing the computed signature of all pigments present in this organism. To do so, modifications to in vitro pigment spectra were first required: namely wavelength shift, curve smoothing, and the package effect calculation derived from high pigment densities were applied. As a result, we outlined a plausible shape for the in vivo absorption spectrum of each chromophore. These are flatter and slightly broader in physiological conditions yet the mean weight-specific absorption coefficient remains identical to the in vitro conditions. Moreover, we give an estimate of all pigment concentrations without applying spectrophotometric correlations, which are often prone to error. The computed cell spectrum reproduces in an accurate manner the experimental spectrum for all the studied wavelengths in the wild-type, Olive, and PAL strain. The gathered pigment concentrations are in agreement with reported values in literature. Moreover, different illumination set-ups were evaluated to calculate the mean absorption cross-section of each chromophore. Finally, a qualitative estimate of light-limited cellular growth at each wavelength is given. This investigation describes a novel way to approach the cell absorption spectrum and shows all its inherent potential for photosynthesis research.

Model quantification of the light-induced thylakoid membrane processes in Synechocystis sp. PCC 6803 in vivo and after exposure to radioactive irradiation

Measurements of OJIP-SMT patterns of fluorescence induction (FI) in Synechocystis sp. PCC 6803 (Synechocystis) cells on a time scale up to several minutes were mathematically treated within the framework of thylakoid membrane (T-M) model (Belyaeva et al., Photosynth Res 140:1-19, 2019) that was renewed to account for the state transitions effects. Principles of describing electron transfer in reaction centers of photosystems II and I (PSII and PSI) and cytochrome b₆f complex remained unchanged, whereas parameters for dissipative reactions of non-radiative charge recombination were altered depending on the oxidation state of Q_B-site (neutral, reduced by one electron, empty, reduced by two electrons). According to our calculations, the initial content of plastoquinol (PQH₂) in the total quinone pool of Synechocystis cells adapted to darkness for 10 min ranged between 20 and 40%. The results imply that the PQ pool mediates photosynthetic and respiratory charge flows. The redistribution of PBS antenna units responsible for the increase of Chl fluorescence in cyanobacteria (qT_{2 → 1}) upon state 2 → 1 transition or the fluorescence lowering (qT_{1 → 2}) due to state 1 → 2 transition were described in the model by exponential functions. Parameters of dynamically changed effective cross section were found by means of simulations of OJIP-SMT patterns observed on Synechocystis cells upon strong (3000 μmol photons m^-2s^-1) and moderate (1000 μmol photons m^-2s^-1) actinic light intensities. The corresponding light constant values kL_ΣAnt = 1.2 ms^-1 and 0.4 ms^-1 define the excitation of total antenna pool dynamically redistributed between PSII and PSI reaction centers. Although the OCP-induced quenching of antenna excitation is not involved in the model, the main features of the induction signals have been satisfactorily explained. In the case of strong illumination, the effective cross section decreases by approximately 33% for irradiated Synechocystis cells as compared to untreated cells. Under moderate light, the irradiated Synechocystis cells showed in simulations the same cross section as the untreated cells. The thylakoid model renewed with state transitions description allowed simulation of fluorescence induction OJIP-SMT curves detected on time scale from microseconds to minutes.

iTRAQ-based proteomic analysis of the hepatopancreas from Litopenaeus vannamei after trans-vp28 gene Synechocystis sp. PCC6803 immunization

Litopenaeus vannamei (Pacific white shrimp) is one of the most commercially important varieties of shrimp cultivated in the world. Shrimp farming is a high-risk, capital-intensive industry that is susceptible to periodic outbreaks of diseases caused by viral and bacterial pathogens. Thus, there is a need to develop economically viable methods of disease control. The hepatopancreas of crustaceans are known to have an important role in their innate immune response. In this study, we have explored the immune response of the hepatopancreas from L. vannamei fed with trans-vp28 gene Synechocystis sp. PCC6803 using iTRAQ-based proteomics. A total of 214 differentially expressed proteins (DEPs) were identified, of which 143 were up-regulated and 71 were down-regulated. These proteins have diverse roles in the cell cytoskeleton and cell phagocytosis, antioxidant defense process and the response of immune related proteins. Among these proteins, the immunity associated with the functional annotation of L. vannamei was further analysed. In addition, 4 DEPs (act1, N/A, H and C7M84_013542) were analysed using parallel reaction monitoring (PRM). This is the first report of proteomics in the hepatopancreas of L. vannamei immunized with trans-vp28 gene Synechocystis sp. PCC6803.

A multi-parametric screening platform for photosynthetic trait characterization of microalgae and cyanobacteria under inorganic carbon limitation

Microalgae and cyanobacteria are considered as important model organisms to investigate the biology of photosynthesis; moreover, they are valuable sources of biomolecules for several biotechnological applications. Understanding the species-specific traits of photosynthetic electron transport is extremely important, because it contributes to the regulation of ATP/NADPH ratio, which has direct/indirect links to carbon fixation and other metabolic pathways and thus overall growth and biomass production. In the present work, a cuvette-based setup is developed, in which a combination of measurements of dissolved oxygen, pH, chlorophyll fluorescence and NADPH kinetics can be performed without disturbing the physiological status of the sample. The suitability of the system is demonstrated using a model cyanobacterium Synechocystis sp. PCC6803, as well as biofuel-candidate microalgae species, such as Chlorella sorokiniana, Dunaliella salina and Nannochloropsis limnetica undergoing inorganic carbon (Ci) limitation. Inorganic carbon limitation, induced by photosynthetic Ci uptake under continuous illumination, caused a decrease in the effective quantum yield of PSII (Y(II)) and loss of oxygen-evolving capacity in all species investigated here; these effects were largely recovered by the addition of NaHCO₃. Detailed analysis of the dark-light and light-dark transitions of NADPH production/uptake and changes in chlorophyll fluorescence kinetics revealed species- and condition-specific responses. These responses indicate that the impact of decreased Calvin-Benson cycle activity on photosynthetic electron transport pathways involving several sections of the electron transport chain (such as electron transfer via the Q_A-Q_B-plastoquinone pool, the redox state of the plastoquinone pool) can be analyzed with high sensitivity in a comparative manner. Therefore, the integrated system presented here can be applied for screening for specific traits in several significant species at different stages of inorganic carbon limitation, a condition that strongly impacts primary productivity.

Testing the Potential of Regulatory Sigma Factor Mutants for Wastewater Purification or Bioreactor Run in High Light

It is shown that a freshly inoculated culture of the model cyanobacterium Synechocystis sp. PCC 6803 consumed almost all phosphate and 50% of nitrate within 6 days from the nutrient-rich BG-11 growth medium, indicating potential of cyanobacteria to purify wastewaters. Synechocystis sp. PCC 6803 control strain also collected nutrients efficiently from a landfill leachate wastewater KA2 (5.9-6.9 mM ammonium and 0.073-0.077 mM phosphate). Wastewaters might induce oxidative stress to microalgae, which prompted us to test growth of sigma factor inactivation strains, as ΔsigBCE and ΔsigCDE strains show superior growth in chemically induced oxidative stress. All cyanobacterial strains, including a stress-sensitive strain ΔsigBCDE, grew well in KA2 for four days, indicating that KA2 did not cause immediate oxidative stress. Completely arrested growth and bleaching of ΔsigBCDE cells after one week in KA2 wastewater point to the importance of group 2 sigma factor-mediated changes in gene expression during wastewater treatment. The growth of ΔsigBCD was arrested early in un-buffered and Hepes buffered (pH 7.5) KA2. In ΔsigBCD, all phosphate transporter genes are upregulated in standard conditions, and ΔsigBCD cells showed growth defects in low-phosphate BG-11 medium. ΔsigBCD cells removed phosphate slower from KA2 than the control strain, but phosphate supplementation of KA2 did not improve growth of ΔsigBCD. The ΔsigBCE strain showed superior growth in a laboratory-scale bioreactor in bright light and removed phosphate even slightly more efficiently than the control strain if KA2 was Hepes buffered although ΔsigBCE grew slowly in un-buffered KA2 and in low-phosphate BG-11 medium. The results indicate that engineering expression of regulatory group 2 sigma factor(s) might be useful for practical applications.

Exploiting Day- and Night-Time Metabolism of Synechocystis sp. PCC 6803 for Fitness-Coupled Fumarate Production around the Clock

Cyanobacterial cell factories are widely researched for the sustainable production of compounds directly from CO2. Their application, however, has been limited for two reasons. First, traditional approaches have been shown to lead to unstable cell factories that lose their production capability when scaled to industrial levels. Second, the alternative approaches developed so far are mostly limited to growing conditions, which are not always the case in industry, where nongrowth periods tend to occur (e.g., darkness). We tackled both by generalizing the concept of growth-coupled production to fitness coupling. The feasibility of this new approach is demonstrated for the production of fumarate by constructing the first stable dual-strategy cell factory. We exploited circadian metabolism using both systems and synthetic biology tools, resulting in the obligatorily coupling of fumarate to either biomass or energy production. Resorting to laboratory evolution experiments, we show that this engineering approach is more stable than conventional methods.

Exploring the low photosynthetic efficiency of cyanobacteria in blue light using a mutant lacking phycobilisomes

The ubiquitous chlorophyll a (Chl a) pigment absorbs both blue and red light. Yet, in contrast to green algae and higher plants, most cyanobacteria have much lower photosynthetic rates in blue than in red light. A plausible but not yet well-supported hypothesis is that blue light results in limited energy transfer to photosystem II (PSII), because cyanobacteria invest most Chl a in photosystem I (PSI), whereas their phycobilisomes (PBS) are mostly associated with PSII but do not absorb blue photons. In this paper, we compare the photosynthetic performance in blue and orange-red light of wildtype Synechocystis sp. PCC 6803 and a PBS-deficient mutant. Our results show that the wildtype had much lower biomass, Chl a content, PSI:PSII ratio and O₂ production rate per PSII in blue light than in orange-red light, whereas the PBS-deficient mutant had a low biomass, Chl a content, PSI:PSII ratio, and O₂ production rate per PSII in both light colors. More specifically, the wildtype displayed a similar low photosynthetic efficiency in blue light as the PBS-deficient mutant in both light colors. Our results demonstrate that the absorption of light energy by PBS and subsequent transfer to PSII are crucial for efficient photosynthesis in cyanobacteria, which may explain both the low photosynthetic efficiency of PBS-containing cyanobacteria and the evolutionary success of chlorophyll-based light-harvesting antennae in environments dominated by blue light.

The Synthetic Biology Toolkit for Photosynthetic Microorganisms

Photosynthetic microorganisms offer novel characteristics as synthetic biology chassis, and the toolbox of components and techniques for cyanobacteria and algae is rapidly increasing.

Physiological Properties of Photoautotrophic Microalgae and Cyanobacteria Relevant to Industrial Biomass Production

Photoautotrophic mass culture of microalgae is currently under investigation for social implementation, since such organisms are anticipated to be resources of alternative fuels and materials for reducing global warming. Production scale-up of culture systems and economy balance are great barriers for practical usage. In order to develop new culture systems such as attachment on solid surfaces or biofilms, we investigated various characteristics of photosynthesis in Chlorella, not only in liquid but also on filter membranes. In aquatic cultures, the photosynthetic rate was almost the same as the specific exponential growth rate at over 32 °C, suggesting that highly efficient cell growth was achieved at that temperature. The algal cells could fix about 50 mmol carbons per mole photons, at cloudy-day-level light intensities, which result to produce 1.2 g dry cell weight in calculation. Moreover, Chlorella could grow on a membrane surface at almost the same rate as in liquid. Similar tolerance to water deficiency was observed in a cyanobacterium, Synechocystis, in which gene expression responded in 30 min after the stress. Such a tolerance was also observed in other species of microalgae and cyanobacteria in photosynthesis.

Mixed-species biofilms for high-cell-density application of Synechocystis sp. PCC 6803 in capillary reactors for continuous cyclohexane oxidation to cyclohexanol

Photosynthetic microorganisms have enormous potential to produce fuels and value-added compounds sustainably. Efficient cultivation concepts that enable optimal light and CO₂ supply are necessary for the realization of high cell densities (HCDs), and subsequently for process implementation. We introduce capillary biofilm reactors with a high surface to volume ratio, and thus enhanced light availability, enabling HCDs of photo-autotrophic microorganisms. However, oxygenic photosynthesis leads to O₂ accumulation in such systems, impairing biofilm growth. We combined O₂ producing Synechocystis with O₂ respiring Pseudomonas using proto-cooperation to achieve HCDs of up to 51.8 g_BDW L^-1. This concept was coupled to the challenging C-H oxyfunctionalization of cyclohexane to cyclohexanol with a remarkable conversion of >98% and selectivity of 100% (KA oil). High photoautotrophic biocatalyst concentrations were established and resulted in a productivity of 3.76 g_cyclohexanol m^-2 day^-1, which was maintained for at least one month.

Kinetic modeling of the Calvin cycle identifies flux control and stable metabolomes in Synechocystis carbon fixation

Biological fixation of atmospheric CO2 via the Calvin-Benson-Bassham cycle has massive ecological impact and offers potential for industrial exploitation, either by improving carbon fixation in plants and autotrophic bacteria, or by installation into new hosts. A kinetic model of the Calvin-Benson-Bassham cycle embedded in the central carbon metabolism of the cyanobacterium Synechocystis sp. PCC 6803 was developed to investigate its stability and underlying control mechanisms. To reduce the uncertainty associated with a single parameter set, random sampling of the steady-state metabolite concentrations and the enzyme kinetic parameters was employed, resulting in millions of parameterized models which were analyzed for flux control and stability against perturbation. Our results show that the Calvin cycle had an overall high intrinsic stability, but a high concentration of ribulose 1,5-bisphosphate was associated with unstable states. Low substrate saturation and high product saturation of enzymes involved in highly interconnected reactions correlated with increased network stability. Flux control, that is the effect that a change in one reaction rate has on the other reactions in the network, was distributed and mostly exerted by energy supply (ATP), but also by cofactor supply (NADPH). Sedoheptulose 1,7-bisphosphatase/fructose 1,6-bisphosphatase, fructose-bisphosphate aldolase, and transketolase had a weak but positive effect on overall network flux, in agreement with published observations. The identified flux control and relationships between metabolite concentrations and system stability can guide metabolic engineering. The kinetic model structure and parameterizing framework can be expanded for analysis of metabolic systems beyond the Calvin cycle.

Overexpression of Orange Carotenoid Protein Protects the Repair of PSII under Strong Light in Synechocystis sp. PCC 6803

Orange carotenoid protein (OCP) plays a vital role in the thermal dissipation of excitation energy in the photosynthetic machinery of the cyanobacterium Synechocystis sp. PCC 6803. To clarify the role of OCP in the protection of PSII from strong light, we generated an OCP-overexpressing strain of Synechocystis and examined the effects of overexpression on the photoinhibition of PSII. In OCP-overexpressing cells, thermal dissipation of energy was enhanced and the extent of photoinhibition of PSII was reduced. However, photodamage to PSII, as monitored in the presence of lincomycin, was unaffected, suggesting that overexpressed OCP protects the repair of PSII. Furthermore, the synthesis de novo of proteins in thylakoid membranes, such as the D1 protein which is required for the repair of PSII, was enhanced in OCP-overexpressing cells under strong light, while the production of singlet oxygen was suppressed. Thus, the enhanced thermal dissipation of energy via overexpressed OCP might support the repair of PSII by protecting protein synthesis from oxidative damage by singlet oxygen under strong light, with the resultant mitigation of photoinhibition of PSII.

Group 2 Sigma Factors are Central Regulators of Oxidative Stress Acclimation in Cyanobacteria

Regulatory σ factors of the RNA polymerase (RNAP) adjust gene expression according to environmental cues when the cyanobacterium Synechocystis sp. PCC 6803 acclimates to suboptimal conditions. Here we show central roles of the non-essential group 2 σ factors in oxidative stress responses. Cells missing all group 2 σ factors fail to acclimate to chemically induced singlet oxygen, superoxide or H2O2 stresses, and lose pigments in high light. SigB and SigD are the major σ factors in oxidative stress, whereas SigC and SigE play only minor roles. The SigD factor is up-regulated in high light, singlet oxygen and H2O2 stresses, and overproduction of the SigD factor in the ΔsigBCE strain leads to superior growth of ΔsigBCE cells in those stress conditions. Superoxide does not induce the production of the SigD factor but instead SigB and SigC factors are moderately induced. The SigB factor alone in ΔsigCDE can support almost as fast growth in superoxide stress as the full complement of σ factors in the control strain, but an overdose of the stationary phase-related SigC factor causes growth arrest of ΔsigBDE in superoxide stress. A drastic decrease of the functional RNAP limits the transcription capacity of the cells in H2O2 stress, which explains why cyanobacteria are sensitive to H2O2. Formation of RNAP-SigB and RNAP-SigD holoenzymes is highly enhanced in H2O2 stress, and cells containing only SigB (ΔsigCDE) or SigD (ΔsigBCE) show superior growth in H2O2 stress.

A diurnal flux balance model of Synechocystis sp. PCC 6803 metabolism

Phototrophic organisms such as cyanobacteria utilize the sun's energy to convert atmospheric carbon dioxide into organic carbon, resulting in diurnal variations in the cell's metabolism. Flux balance analysis is a widely accepted constraint-based optimization tool for analyzing growth and metabolism, but it is generally used in a time-invariant manner with no provisions for sequestering different biomass components at different time periods. Here we present CycleSyn, a periodic model of Synechocystis sp. PCC 6803 metabolism that spans a 12-hr light/12-hr dark cycle by segmenting it into 12 Time Point Models (TPMs) with a uniform duration of two hours. The developed framework allows for the flow of metabolites across TPMs while inventorying metabolite levels and only allowing for the utilization of currently or previously produced compounds. The 12 TPMs allow for the incorporation of time-dependent constraints that capture the cyclic nature of cellular processes. Imposing bounds on reactions informed by temporally-segmented transcriptomic data enables simulation of phototrophic growth as a single linear programming (LP) problem. The solution provides the time varying reaction fluxes over a 24-hour cycle and the accumulation/consumption of metabolites. The diurnal rhythm of metabolic gene expression driven by the circadian clock and its metabolic consequences is explored. Predicted flux and metabolite pools are in line with published studies regarding the temporal organization of phototrophic growth in Synechocystis PCC 6803 paving the way for constructing time-resolved genome-scale models (GSMs) for organisms with a circadian clock. In addition, the metabolic reorganization that would be required to enable Synechocystis PCC 6803 to temporally separate photosynthesis from oxygen-sensitive nitrogen fixation is also explored using the developed model formalism.

A unique ferredoxin acts as a player in the low-iron response of photosynthetic organisms

Iron chronically limits aquatic photosynthesis, especially in marine environments, and the correct perception and maintenance of iron homeostasis in photosynthetic bacteria, including cyanobacteria, is therefore of global significance. Multiple adaptive mechanisms, responsive promoters, and posttranscriptional regulators have been identified, which allow cyanobacteria to respond to changing iron concentrations. However, many factors remain unclear, in particular, how iron status is perceived within the cell. Here we describe a cyanobacterial ferredoxin (Fed2), with a unique C-terminal extension, that acts as a player in iron perception. Fed2 homologs are highly conserved in photosynthetic organisms from cyanobacteria to higher plants, and, although they belong to the plant type ferredoxin family of [2Fe-2S] photosynthetic electron carriers, they are not involved in photosynthetic electron transport. As deletion of fed2 appears lethal, we developed a C-terminal truncation system to attenuate protein function. Disturbed Fed2 function resulted in decreased chlorophyll accumulation, and this was exaggerated in iron-depleted medium, where different truncations led to either exaggerated or weaker responses to low iron. Despite this, iron concentrations remained the same, or were elevated in all truncation mutants. Further analysis established that, when Fed2 function was perturbed, the classical iron limitation marker IsiA failed to accumulate at transcript and protein levels. By contrast, abundance of IsiB, which shares an operon with isiA, was unaffected by loss of Fed2 function, pinpointing the site of Fed2 action in iron perception to the level of posttranscriptional regulation.

Blue light reduces photosynthetic efficiency of cyanobacteria through an imbalance between photosystems I and II

Several studies have described that cyanobacteria use blue light less efficiently for photosynthesis than most eukaryotic phototrophs, but comprehensive studies of this phenomenon are lacking. Here, we study the effect of blue (450 nm), orange (625 nm), and red (660 nm) light on growth of the model cyanobacterium Synechocystis sp. PCC 6803, the green alga Chlorella sorokiniana and other cyanobacteria containing phycocyanin or phycoerythrin. Our results demonstrate that specific growth rates of the cyanobacteria were similar in orange and red light, but much lower in blue light. Conversely, specific growth rates of the green alga C. sorokiniana were similar in blue and red light, but lower in orange light. Oxygen production rates of Synechocystis sp. PCC 6803 were five-fold lower in blue than in orange and red light at low light intensities but approached the same saturation level in all three colors at high light intensities. Measurements of 77 K fluorescence emission demonstrated a lower ratio of photosystem I to photosystem II (PSI:PSII ratio) and relatively more phycobilisomes associated with PSII (state 1) in blue light than in orange and red light. These results support the hypothesis that blue light, which is not absorbed by phycobilisomes, creates an imbalance between the two photosystems of cyanobacteria with an energy excess at PSI and a deficiency at the PSII-side of the photosynthetic electron transfer chain. Our results help to explain why phycobilisome-containing cyanobacteria use blue light less efficiently than species with chlorophyll-based light-harvesting antennae such as Prochlorococcus, green algae and terrestrial plants.

Spectrally decomposed dark-to-light transitions in Synechocystis sp. PCC 6803

Photosynthetic activity and respiration share the thylakoid membrane in cyanobacteria. We present a series of spectrally resolved fluorescence experiments where whole cells of the cyanobacterium Synechocystis sp. PCC 6803 and mutants thereof underwent a dark-to-light transition after different dark-adaptation (DA) periods. Two mutants were used: (i) a PSI-lacking mutant (ΔPSI) and (ii) M55, a mutant without NAD(P)H dehydrogenase type-1 (NDH-1). For comparison, measurements of the wild-type were also carried out. We recorded spectrally resolved fluorescence traces over several minutes with 100 ms time resolution. The excitation light was at 590 nm so as to specifically excite the phycobilisomes. In ΔPSI, DA time has no influence, and in dichlorophenyl-dimethylurea (DCMU)-treated samples we identify three main fluorescent components: PB-PSII complexes with closed (saturated) RCs, a quenched or open PB-PSII complex, and a PB-PSII 'not fully closed.' For the PSI-containing organisms without DCMU, we conclude that mainly three species contribute to the signal: a PB-PSII-PSI megacomplex with closed PSII RCs and (i) slow PB → PSI energy transfer, or (ii) fast PB → PSI energy transfer and (iii) complexes with open (photochemically quenched) PSII RCs. Furthermore, their time profiles reveal an adaptive response that we identify as a state transition. Our results suggest that deceleration of the PB → PSI energy transfer rate is the molecular mechanism underlying a state 2 to state 1 transition.

Binding of pigments to the cyanobacterial high-light-inducible protein HliC

Cyanobacteria possess a family of one-helix high-light-inducible proteins (HLIPs) that are widely viewed as ancestors of the light-harvesting antenna of plants and algae. HLIPs are essential for viability under various stress conditions, although their exact role is not fully understood. The unicellular cyanobacterium Synechocystis sp. PCC 6803 contains four HLIPs named HliA-D, and HliD has recently been isolated in a small protein complex and shown to bind chlorophyll and β-carotene. However, no HLIP has been isolated and characterized in a pure form up to now. We have developed a protocol to purify large quantities of His-tagged HliC from an engineered Synechocystis strain. Purified His-HliC is a pigmented homo-oligomer and is associated with chlorophyll and β-carotene with a 2:1 ratio. This differs from the 3:1 ratio reported for HliD. Comparison of these two HLIPs by resonance Raman spectroscopy revealed a similar conformation for their bound β-carotenes, but clear differences in their chlorophylls. We present and discuss a structural model of HliC, in which a dimeric protein binds four chlorophyll molecules and two β-carotenes.

Hydrogen Peroxide Participates in Perception and Transduction of Cold Stress Signal in Synechocystis

The double mutant ΔkatG/tpx of cyanobacterium Synechocystis sp. strain PCC 6803, defective in the anti-oxidative enzymes catalase (KatG) and thioredoxin peroxidase (Tpx), is unable to grow in the presence of exogenous H2O2. The ΔkatG/tpx mutant is shown to be extremely sensitive to very low concentrations of H2O2, especially when intensified with cold stress. Analysis of gene expression in both wild-type and ΔkatG/tpx mutant cells treated by combined cold/oxidative stress revealed that H2O2 participates in regulation of expression of cold-responsive genes, affecting either signal perception or transduction. The central role of a transmembrane stress-sensing histidine kinase Hik33 in the cold/oxidative signal transduction pathway is discussed.

A Specific Glycogen Mobilization Strategy Enables Rapid Awakening of Dormant Cyanobacteria from Chlorosis

Many organisms survive stressful conditions via entry into a dormant state that can be rapidly exited when the stressor disappears; this ability provides a strong selective advantage. In the cyanobacterium Synechocystis sp. PCC 6803, the exit from nitrogen chlorosis takes less than 48 h and is enabled by the impressive metabolic flexibility of these cyanobacteria, which pass through heterotrophic and mixotrophic phases before reentering photoautotrophic growth. Switching between these states requires delicate coordination of carbohydrate oxidation, CO₂ fixation, and photosynthesis. Here, we investigated the contribution of the different carbon catabolic routes by assessing mutants of these pathways during nitrogen chlorosis and resuscitation. The addition of nitrate to nitrogen-starved cells rapidly starts the awakening program. Metabolism switches from maintenance metabolism, characterized by residual photosynthesis and low cellular ATP levels, to an initial heterotrophic phase, characterized by respiration and an immediate increase in ATP levels. This respiration relies on glycogen breakdown catalyzed by the glycogen phosphorylase GlgP2. In the following transient mixotrophic phase, photosynthesis and CO₂ fixation restart and glycogen is consumed. During the mixotrophic phase, parallel operation of the oxidative pentose phosphate cycle and the Entner-Doudoroff pathway is required for resuscitation to proceed; the glycolytic route via the Embden-Meyerhof-Parnas pathway has minor importance. Our data suggest that, during resuscitation, only the Entner-Doudoroff and oxidative pentose phosphate pathways supply the metabolic intermediates necessary for the anabolic reactions required to reconstitute a vegetative cell. Intriguingly, the key enzymes for glycogen catabolism are already expressed during the preceding chlorotic phase, in apparent preparation for rapid resuscitation.

Sorbitol production and optimization of photosynthetic supply in the cyanobacterium Synechocystis PCC 6803

Biochemicals production is a major theme in the application of photosynthesis to address global warming and organic-resource problems. Among biochemicals, sugar alcohols have attracted research attention because they are directly derived from two photosynthetic products, sugars and reductants. Here, we produced sorbitol photosynthetically by using cyanobacteria and modified the supply of its substrates through genetic engineering. Expression of an NADPH-dependent enzyme that generates sorbitol-6-phosphate, S6PDH, was highly toxic to cyanobacteria likely due to the sorbitol production, whereas expression of an NADH-dependent enzyme, SrlD2, yielded no sorbitol. The toxicity was partly overcome by introducing a theophylline-inducible riboswitch for S6PDH expression and optimizing induction, but sorbitol production was still low and severely inhibited growth. Co-expression of fructose-1,6-bisphosphatase drastically alleviated the growth inhibition, but did not increase short-term sorbitol production. The NADPH/NADP⁺ ratio decreased during sorbitol production. Overexpression of a membrane-bound transhydrogenase for NADPH generation from NADH elevated the short-term sorbitol production, but only partly alleviated the growth inhibition. Notably, a strain overexpressing all three enzymes exhibited sustainable sorbitol production at 312 mg/L, which was nearly 27-fold higher than the yield of the initial S6PDH-overexpressing strain. We discuss these results in relation to the optimization of photosynthetic supply for sorbitol production in cyanobacteria.

Measurement of the mechanical properties of single Synechocystis sp. strain PCC6803 cells in different osmotic concentrations using a robot-integrated microfluidic chip

Synechocystis sp. strain PCC6803 (Synechocystis) is a model microorganism and its mechanosensitive (MS) channels play important roles in its osmoadaptation mechanism. When the osmotic concentration of the culture environment changes, the inner pressure of the cell also changes due to the transportation of water through ion channels. Because the tension in the cell membrane relates to the inner pressure, we expect that the response of the MS channels to an osmotic concentration change could be evaluated by measuring their mechanical properties. Here, we propose a system for the measurement of the mechanical properties of a single Synechocystis cell. We developed a robot-integrated microfluidic chip combined with optical tweezers. The chip has an external actuated pushing probe and a force sensor probe. A single cell was located between the tip of both probes using the optical tweezers and was then deformed using the probes. As a result, we could measure the force and deformation and compare the Young's moduli of two groups: a group of wild type cells and a group of mutant (genetically modified) cells with a defect in the MS channels, at three different osmotic concentrations. The results showed that the Young's modulus of each group changed according to the osmotic concentration, while changes in cell size were too small to be detected. These results confirmed that the proposed evaluation method provides an understanding of the physiological function of MS channels for keeping the cell integrity of microorganisms when the cells are exposed to different external osmotic changes.

Resequencing of a mutant bearing an iron starvation recovery phenotype defines Slr1658 as a new player in the regulatory network of a model cyanobacterium

Photosynthetic microorganisms encounter an erratic nutrient environment characterized by periods of iron limitation and sufficiency. Surviving in such an environment requires mechanisms for handling these transitions. Our study identified a regulatory system involved in the process of recovery from iron limitation in cyanobacteria. We set out to study the role of bacterioferritin co-migratory proteins during transitions in iron bioavailability in the cyanobacterium Synechocystis sp. PCC 6803 using knockout strains coupled with physiological and biochemical measurements. One of the mutants displayed slow recovery from iron limitation. However, we discovered that the cause of the phenotype was not the intended knockout but rather the serendipitous selection of a mutation in an unrelated locus, slr1658. Bioinformatics analysis suggested similarities to two-component systems and a possible regulatory role. Transcriptomic analysis of the recovery from iron limitation showed that the slr1658 mutation had an extensive effect on the expression of genes encoding regulatory proteins, proteins involved in the remodeling and degradation of the photosynthetic apparatus and proteins modulating electron transport. Most significantly, expression of the cyanobacterial homologue of the cyclic electron transport protein PGR5 was upregulated 1000-fold in slr1658 disruption mutants. pgr5 transcripts in the Δslr1658 mutant retained these high levels under a range of stress and recovery conditions. The results suggest that slr1658 is part of a regulatory operon that, among other aspects, affects the regulation of alternative electron flow. Disruption of its function has deleterious results under oxidative stress promoting conditions.

Phototaxis as a Collective Phenomenon in Cyanobacterial Colonies

Cyanobacteria are a diverse group of photosynthetic bacteria that exhibit phototaxis, or motion in response to light. Cyanobacteria such as Synechocystis sp. secrete a mixture of complex polysaccharides that facilitate cell motion, while their type 4 pili allow them to physically attach to each other. Even though cells can respond individually to light, colonies are observed to move collectively towards the light source in dense finger-like projections. We present an agent-based model for cyanobacterial phototaxis that accounts for slime deposition as well as for direct physical links between bacteria, mediated through their type 4 pili. We reproduce the experimentally observed aggregation of cells at the colony boundary as a precursor to finger formation. Our model also describes the changes in colony morphology that occur when the location of the light source is abruptly changed. We find that the overall motion of cells toward light remains relatively unimpaired even if a fraction of them do not sense light, allowing heterogeneous populations to continue to mount a robust collective response to stimuli. Our work suggests that in addition to bio-chemical signalling via diffusible molecules in the context of bacterial quorum-sensing, short-ranged physical interactions may also contribute to collective effects in bacterial motility.

Phenotypic characterization of Synechocystis sp. PCC 6803 substrains reveals differences in sensitivity to abiotic stress

Synechocystis sp. PCC 6803 is a widely used model cyanobacterium, whose substrains can vary on both genotype and phenotype levels. Previously described phenotypic variations include ability of mixotrophic growth, ability of movement on agar plates and variations in pigments composition or cell size. In this study, we report for the first time significant variation among Synechocystis substrains in complex cellular traits such as growth rate, photosynthesis efficiency, cellular dry weight and cellular composition (including protein or carbohydrates content). We also confirmed previously reported differences in cell size. Synechocystis cultures were cultivated in controlled environment of flat panel photobioreactors under red, blue and white light of intensities up to 790 μmol(photons) m^-2 s^-1, temperatures 23°C–60°C, input CO₂ concentrations ranging from 400 to 15 000 ppm and in BG11 cultivation medium with and without addition of NaCl. Three Synechocystis substrains were used for the comparative experiments: GT-L, GT-B (Brno, CZ) and PCC-B (Brno, CZ). Growth rates of Synechocystis GT-B were inhibited under high intensities of red light (585–670 nm), and growth rates of both substrains GT-B and PCC-B were inhibited under photons of wavelengths 485–585 nm and 670–700 nm. Synechocystis GT-B was more sensitive to low temperatures than the other two tested substrains, and Synechocystis GT-L was sensitive to the presence of NaCl in the cultivation media. The results suggest that stress sensitivity of commonly used Synechocystis substrains can strongly vary, similarly as glucose tolerance or motility as reported previously. Our study further supports the previous statement that emphasizes importance of proper Synechocystis substrains selection and awareness of phenotypical differences among Synechocystis substrains which is crucial for comparative and reproducible research. This is highly relevant for studies related to stress physiology and development of sustainable biotechnological applications.

Characterization of the sulfur-formation (suf) genes in Synechocystis sp. PCC 6803 under photoautotrophic and heterotrophic growth conditions

The sulfur-formation ( suf ) genes play important roles in both photosynthesis and respiration of cyanobacteria, but the organism prioritizes Fe-S clusters for respiration at the expense of photosynthesis. Iron-sulfur (Fe-S) clusters are important to all living organisms, but their assembly mechanism is poorly understood in photosynthetic organisms. Unlike non-photosynthetic bacteria that rely on the iron-sulfur cluster system, Synechocystis sp. PCC 6803 uses the Sulfur-Formation (SUF) system as its major Fe-S cluster assembly pathway. The co-expression of suf genes and the direct interactions among SUF subunits indicate that Fe-S assembly is a complex process in which no suf genes can be knocked out completely. In this study, we developed a condition-controlled SUF Knockdown mutant by inserting the petE promoter, which is regulated by Cu²⁺ concentration, in front of the suf operon. Limited amount of the SUF system resulted in decreased chlorophyll contents and photosystem activities, and a lower PSI/PSII ratio. Unexpectedly, increased cyclic electron transport and a decreased dark respiration rate were only observed under photoautotrophic growth conditions. No visible effects on the phenotype of SUF Knockdown mutant were observed under heterotrophic culture conditions. The phylogenetic distribution of the SUF system indicates that it has a co-evolutionary relationship with photosynthetic energy storing pathways.

Membrane fluidity controls redox-regulated cold stress responses in cyanobacteria

Membrane fluidity is the important regulator of cellular responses to changing ambient temperature. Bacteria perceive cold by the transmembrane histidine kinases that sense changes in thickness of the cytoplasmic membrane due to its rigidification. In the cyanobacterium Synechocystis, about a half of cold-responsive genes is controlled by the light-dependent transmembrane histidine kinase Hik33, which also partially controls the responses to osmotic, salt, and oxidative stress. This implies the existence of some universal, but yet unknown signal that triggers adaptive gene expression in response to various stressors. Here we selectively probed the components of photosynthetic machinery and functionally characterized the thermodynamics of cyanobacterial photosynthetic membranes with genetically altered fluidity. We show that the rate of oxidation of the quinone pool (PQ), which interacts with both photosynthetic and respiratory electron transport chains, depends on membrane fluidity. Inhibitor-induced stimulation of redox changes in PQ triggers cold-induced gene expression. Thus, the fluidity-dependent changes in the redox state of PQ may universally trigger cellular responses to stressors that affect membrane properties.

Membrane fluidity controls redox-regulated cold stress responses in cyanobacteria

Membrane fluidity is the important regulator of cellular responses to changing ambient temperature. Bacteria perceive cold by the transmembrane histidine kinases that sense changes in thickness of the cytoplasmic membrane due to its rigidification. In the cyanobacterium Synechocystis, about a half of cold-responsive genes is controlled by the light-dependent transmembrane histidine kinase Hik33, which also partially controls the responses to osmotic, salt, and oxidative stress. This implies the existence of some universal, but yet unknown signal that triggers adaptive gene expression in response to various stressors. Here we selectively probed the components of photosynthetic machinery and functionally characterized the thermodynamics of cyanobacterial photosynthetic membranes with genetically altered fluidity. We show that the rate of oxidation of the quinone pool (PQ), which interacts with both photosynthetic and respiratory electron transport chains, depends on membrane fluidity. Inhibitor-induced stimulation of redox changes in PQ triggers cold-induced gene expression. Thus, the fluidity-dependent changes in the redox state of PQ may universally trigger cellular responses to stressors that affect membrane properties.

A Novel Mechanism, Linked to Cell Density, Largely Controls Cell Division in Synechocystis

Many studies have investigated the various genetic and environmental factors regulating cyanobacterial growth. Here, we investigated the growth and metabolism of Synechocystis sp. PCC 6803 under different nitrogen sources, light intensities, and CO₂ concentrations. Cells grown on urea showed the highest growth rates. However, for all conditions tested, the daily growth rates in batch cultures decreased steadily over time, and stationary phase was obtained with similar cell densities. Unexpectedly, metabolic and physiological analyses showed that growth rates during log phase were not controlled primarily by the availability of photoassimilates. Further physiological investigations indicated that nutrient limitation, quorum sensing, light quality, and light intensity (self-shading) were not the main factors responsible for the decrease in the growth rate and the onset of the stationary phase. Moreover, cell division rates in fed-batch cultures were positively correlated with the dilution rates. Hence, not only light, CO₂, and nutrients can affect growth but also a cell-cell interaction. Accordingly, we propose that cell-cell interaction may be a factor responsible for the gradual decrease of growth rates in batch cultures during log phase, culminating with the onset of stationary phase.

Cyanobacteria in motion

Cyanobacteria are able to move directly towards or away from a light source, a process called phototaxis. Recent studies have revealed that the spherical unicellular cyanobacterium Synechocystis sp. PCC 6803 exhibits a cell polarity in response to unidirectional illumination and that micro-optic properties of cyanobacterial cells are the basis of their directional light sensing. Further functional and physiological studies highlight a very complex control of cyanobacterial phototaxis by sensory proteins, histidine kinases and response regulators. Notably, PATAN domain response regulators appear to participate in directional control of phototaxis in the cyanobacterium Synechocystis sp. PCC 6803. In this review we explain the problem of directional light sensing at the small scale of bacteria and discuss our current understanding of signal transduction in cyanobacterial phototaxis.

Transition from exponential to linear photoautotrophic growth changes the physiology of Synechocystis sp. PCC 6803

Phototrophic microorganisms like cyanobacteria show growth curves in batch culture that differ from the corresponding growth curves of chemotrophic bacteria. Instead of the usual three phases, i.e., lag-, log-, and stationary phase, phototrophs display four distinct phases. The extra growth phase is a phase of linear, light-limited growth that follows the exponential phase and is often ignored as being different. Results of this study demonstrate marked growth phase-dependent alterations in the photophysiology of the cyanobacterium Synechocystis sp. PCC 6803 between cells harvested from the exponential and the linear growth phase. Notable differences are a gradual shift in the energy transfer of the light-harvesting phycobilisomes to the photosystems and a distinct change in the redox state of the plastoquinone pool. These differences will likely affect the result of physiological studies and the efficiency of product formation of Synechocystis in biotechnological applications. Our study also demonstrates that the length of the period of exponential growth can be extended by a gradually stronger incident light intensity that matches the increase of the cell density of the culture.

Alternating Current-Dielectrophoresis Collection and Chaining of Phytoplankton on Chip: Comparison of Individual Species and Artificial Communities

The capability of alternating current (AC) dielectrophoresis (DEP) for on-chip capture and chaining of the three species representative of freshwater phytoplankton was evaluated. The effects of the AC field intensity, frequency and duration on the chaining efficiency and chain lengths of green alga Chlamydomonas reinhardtii, cyanobacterium Synechocystis sp. and diatom Cyclotella meneghiniana were characterized systematically. C. reinhardtii showed an increase of the chaining efficiency from 100 Hz to 500 kHz at all field intensities; C. meneghiniana presented a decrease of chaining efficiency from 100 Hz to 1 kHz followed by a significant increase from 1 kHz to 500 kHz, while Synechocystis sp. exhibited low chaining tendency at all frequencies and all field intensities. The experimentally-determined DEP response and cell alignment of each microorganism were in agreement with their effective polarizability. Mixtures of cells in equal proportion or 10-times excess of Synechocystis sp. showed important differences in terms of chaining efficiency and length of the chains compared with the results obtained when the cells were alone in suspension. While a constant degree of chaining was observed with the mixture of C. reinhardtii and C. meneghiniana, the presence of Synechocystis sp. in each mixture suppressed the formation of chains for the two other phytoplankton species. All of these results prove the potential of DEP to discriminate different phytoplankton species depending on their effective polarizability and to enable their manipulation, such as specific collection or separation in freshwater.

A comparative study of three signaling forms of the orange carotenoid protein

Orange carotenoid protein (OCP) is a water-soluble photoactive protein responsible for a photoprotective mechanism of nonphotochemical quenching in cyanobacteria. Under blue-green illumination, OCP converts from the stable orange into the signaling red quenching form; however, the latter form could also be obtained by chemical activation with high concentrations of sodium thiocyanate (NaSCN) or point mutations. In this work, we show that a single replacement of tryptophan-288, normally involved in protein-chromophore interactions, by alanine, results in formation of a new protein form, hereinafter referred to as purple carotenoid protein (PCP). Comparison of resonance Raman spectra of the native photoactivated red form, chemically activated OCP, and PCP reveals that carotenoid conformation is sensitive to the structure of the C-domain, implicating that the chromophore retains some interactions with this part of the protein in the active red form. Combination of differential scanning fluorimetry and picosecond time-resolved fluorescence anisotropy measurements allowed us to compare the stability of different OCP forms and to estimate relative differences in protein rotation rates. These results were corroborated by hydrodynamic analysis of proteins by dynamic light scattering and analytical size-exclusion chromatography, indicating that the light-induced conversion of the protein is accompanied by a significant increase in its size. On the whole, our data support the idea that the red form of OCP is a molten globule-like protein in which, however, interactions between the carotenoid and the C-terminal domain are preserved.

Synechocystis mutants defective in manganese uptake regulatory system, ManSR, are hypersensitive to strong light

High affinity transport of manganese ions (Mn²⁺) in cyanobacteria is carried by an ABC-type transporter, encoded by the mntCAB operon, which is derepressed by the deficiency of Mn²⁺. Transcription of this operon is negatively regulated by the two-component system consisting of a sensory histidine kinase ManS and DNA-binding response regulator ManR. In this study, we examined two Synechocystis mutants, defective in ManS and ManR. These mutants were unable to grow on high concentrations of manganese. Furthermore, they were sensitive to high light intensity and unable to recover after short-term photoinhibition. Under standard illumination and Mn²⁺ concentration, mutant cells revealed the elevated levels of transcripts of genes involved in the formation of Photosystem II (psbA, psbD, psbC, pap-operon). This finding suggests that, in mutant cells, the PSII is sensitive to high concentrations of Mn²⁺ even at relatively low light intensity.

β-Carotene influences the phycobilisome antenna of cyanobacterium Synechocystis sp. PCC 6803

We investigated the relation between the carotenoid composition and the structure of phycobilisome (PBS) antenna of cyanobacterium Synechocystis sp. PCC 6803. PBS is a large soluble protein complex enhances the light harvesting efficiency of the cells. It is composed of a central allophycocyanin core and radial phycocyanin rods, but it does not contain carotenoids. However, the absence or low level of carotenoids were previously shown to lead the co-existence of unconnected rod units and assembled PBS with shorter peripheral rods. Here we show that the lack of β-carotene, but not of xanthophylls or the distortion of photosystem structure, evoked unconnected rods. Thus, these essential β-carotene molecules are not bound by Photosystem I or Photosystem II. Our results do not show correlation between the reactive oxygen species (ROS) and PBS distortion despite the higher singlet oxygen producing capacity and light sensitivity of the mutant cells. Reduced cellular level of those linker proteins attaching the rod units together was also observed, but the direct damage of the linkers by ROS are not supported by our data. Enzymatic PBS proteolysis induced by nitrogen starvation in carotenoid mutant cells revealed a retarded degradation of the unconnected rod units.

CyAbrB2 Contributes to the Transcriptional Regulation of Low CO2 Acclimation in Synechocystis sp. PCC 6803

Acclimation to low CO₂ conditions in cyanobacteria involves the co-ordinated regulation of genes mainly encoding components of the carbon-concentrating mechanism (CCM). Making use of several independent microarray data sets, a core set of CO₂-regulated genes was defined for the model strain Synechocystis sp. PCC 6803. On the transcriptional level, the CCM is mainly regulated by the well-characterized transcriptional regulators NdhR (= CcmR) and CmpR. However, the role of an additional regulatory protein, namely cyAbrB2 belonging to the widely distributed AbrB regulator family that was originally characterized in the genus Bacillus, is less defined. Here we present results of transcriptomic and metabolic profiling of the wild type and a ΔcyabrB2 mutant of Synechocystis sp. PCC 6803 after shifts from high CO₂ (5% in air, HC) to low CO₂ (0.04%, LC). Evaluation of the transcriptomic data revealed that cyAbrB2 is involved in the regulation of several CCM-related genes such as sbtA/B, ndhF3/ndhD3/cupA and cmpABCD under LC conditions, but apparently acts supplementary to NdhR and CmpR. Under HC conditions, cyAbrB2 deletion affects the transcript abundance of PSII subunits, light-harvesting components and Calvin-Benson-Bassham cycle enzymes. These changes are also reflected by down-regulation of primary metabolite pools. The data suggest a role for cyAbrB2 in adjusting primary carbon and nitrogen metabolism to photosynthetic activity under fluctuating environmental conditions. The findings were integrated into the current knowledge about the acquisition of inorganic carbon (Ci), the CCM and parts of its regulation on the transcriptional level.

Overexpressed Superoxide Dismutase and Catalase Act Synergistically to Protect the Repair of PSII during Photoinhibition in Synechococcus elongatus PCC 7942

The repair of PSII under strong light is particularly sensitive to reactive oxygen species (ROS), such as the superoxide radical and hydrogen peroxide, and these ROS are efficiently scavenged by superoxide dismutase (SOD) and catalase. In the present study, we generated transformants of the cyanobacterium Synechococcus elongatus PCC 7942 that overexpressed an iron superoxide dismutase (Fe-SOD) from Synechocystis sp. PCC 6803; a highly active catalase (VktA) from Vibrio rumoiensis; and both enzymes together. Then we examined the sensitivity of PSII to photoinhibition in the three strains. In cells that overexpressed either Fe-SOD or VktA, PSII was more tolerant to strong light than it was in wild-type cells. Moreover, in cells that overexpressed both Fe-SOD and VktA, PSII was even more tolerant to strong light. However, the rate of photodamage to PSII, as monitored in the presence of chloramphenicol, was similar in all three transformant strains and in wild-type cells, suggesting that the overexpression of these ROS-scavenging enzymes might not protect PSII from photodamage but might protect the repair of PSII. Under strong light, intracellular levels of ROS fell significantly, and the synthesis de novo of proteins that are required for the repair of PSII, such as the D1 protein, was enhanced. Our observations suggest that overexpressed Fe-SOD and VktA might act synergistically to alleviate the photoinhibition of PSII by reducing intracellular levels of ROS, with resultant protection of the repair of PSII from oxidative inhibition.

Ethylene Regulates the Physiology of the Cyanobacterium Synechocystis sp. PCC 6803 via an Ethylene Receptor

Ethylene is a plant hormone that plays a crucial role in the growth and development of plants. The ethylene receptors in plants are well studied, and it is generally assumed that they are found only in plants. In a search of sequenced genomes, we found that many bacterial species contain putative ethylene receptors. Plants acquired many proteins from cyanobacteria as a result of the endosymbiotic event that led to chloroplasts. We provide data that the cyanobacterium Synechocystis (Synechocystis sp. PCC 6803) has a functional receptor for ethylene, Synechocystis Ethylene Response1 (SynEtr1). We first show that SynEtr1 directly binds ethylene. Second, we demonstrate that application of ethylene to Synechocystis cells or disruption of the SynEtr1 gene affects several processes, including phototaxis, type IV pilus biosynthesis, photosystem II levels, biofilm formation, and spontaneous cell sedimentation. Our data suggest a model where SynEtr1 inhibits downstream signaling and ethylene inhibits SynEtr1. This is similar to the inverse-agonist model of ethylene receptor signaling proposed for plants and suggests a conservation of structure and function that possibly originated over 1 billion years ago. Prior research showed that SynEtr1 also contains a light-responsive phytochrome-like domain. Thus, SynEtr1 is a bifunctional receptor that mediates responses to both light and ethylene. To our knowledge, this is the first demonstration of a functional ethylene receptor in a nonplant species and suggests that that the perception of ethylene is more widespread than previously thought.

Construction and application of the Synechocystis sp. PCC6803-ftnA in microbial contamination control in a coupled cultivation and wastewater treatment

Inspired by iron fertilization experiments in HNLC (high-nitrate, low-chlorophyll) sea areas, we proposed the use of iron-rich engineered microalgae for microbial contaminant control in iron-free culture media. Based on the genome sequence and natural transformation system of Synechocystis sp. PCC6803, ftnA (encoding ferritin) was selected as our target gene and was cloned into wild-type Synechocystis sp. PCC6803. Tests at the molecular level confirmed the successful construction of the engineered Synechocystis sp. PCC6803-ftnA. After Fe(3+)-EDTA pulsing, the intracellular iron content of Synechocystis sp. PCC6803-ftnA was significantly enhanced, and the algae was used in the microbial contamination control system. In the coupled Synechocystis sp. PCC6803-ftnA production and municipal wastewater (MW, including Scenedesmus obliquus and Bacillus) treatment, Synechocystis sp. PCC6803-ftnA accounted for all of the microbial activity and significantly increased from 70% of the microbial community to 95%. These results revealed that while the stored iron in the Synechocystis sp. PCC6803-ftnA cells was used for growth and reproduction of this microalga in the MW, the growth of other microbes was inhibited because of the iron limitation, and these results provide a new method for microbial contamination control during a coupling process.

The Cyanobacterial Ribosomal-Associated Protein LrtA Is Involved in Post-Stress Survival in Synechocystis sp. PCC 6803

A light-repressed transcript encodes the LrtA protein in cyanobacteria. We show that half-life of lrtA transcript from Synechocystis sp. PCC 6803 is higher in dark-treated cells as compared to light-grown cells, suggesting post-transcriptional control of lrtA expression. The lrtA 5´ untranslated leader region is involved in that darkness-dependent regulation. We also found that Synechocystis sp. PCC 6803 LrtA is a ribosome-associated protein present in both 30S and 70S ribosomal particles. In order to investigate the function of this protein we have constructed a deletion mutant of the lrtA gene. Cells lacking LrtA (∆lrtA) had significantly lower amount of 70S particles and a greater amount of 30S and 50S particles, suggesting a role of LrtA in stabilizing 70S particles. Synechocystis strains with different amounts of LrtA protein: wild-type, ∆lrtA, and LrtAS (overexpressing lrtA) showed no differences in their growth rate under standard laboratory conditions. However, a clear LrtA dose-dependent effect was observed in the presence of the antibiotic tylosin, being the LrtAS strains the most sensitive. Similar results were obtained under hyperosmotic stress caused by sorbitol. Conversely, after prolonged periods of starvation, ∆lrtA strains were delayed in their growth with respect to the wild-type and the LrtAS strains. A positive role of LrtA protein in post-stress survival is proposed.

The Flavodiiron Protein Flv3 Functions as a Homo-Oligomer During Stress Acclimation and is Distinct from the Flv1/Flv3 Hetero-Oligomer Specific to the O2 Photoreduction Pathway

The flavodiiron proteins (FDPs) Flv1 and Flv3 in cyanobacteria function in photoreduction of O2 to H2O, without concomitant formation of reactive oxygen species, known as the Mehler-like reaction. Both Flv1 and Flv3 are essential for growth under fluctuating light (FL) intensities, providing protection for PSI. Here we compared the global transcript profiles of the wild type (WT), Δflv1 and Δflv1/Δflv3 grown under constant light (GL) and FL. In the WT, FL induced the largest down-regulation in transcripts involved in carbon-concentrating mechanisms (CCMs), while those of the nitrogen assimilation pathways increased as compared with GL. Already under GL the Δflv1/Δflv3 double mutant demonstrated a partial down-regulation of transcripts for CCM and nitrogen metabolism, while in FL conditions the transcripts for nitrogen assimilation were strongly down-regulated. Many alterations were specific only for Δflv1/Δflv3, and not detected in Δflv1, suggesting that certain transcripts are affected primarily because of the lack of flv3 By constructing the strains overproducing solely either Flv1 or Flv3, we demonstrate that the homo-oligomers of these proteins also function in acclimation of cells to FL, by catalyzing reactions with as yet unidentified components, while the presence of both Flv1 and Flv3 is a prerequisite for the Mehler-like reaction and thus the electron transfer to O2 Considering the low expression of flv1, it is unlikely that the Flv1 homo-oligomer is present in the WT.

Roles of Group 2 Sigma Factors in Acclimation of the Cyanobacterium Synechocystis sp. PCC 6803 to Nitrogen Deficiency

Acclimation of cyanobacteria to environmental conditions is mainly controlled at the transcriptional level, and σ factors of the RNA polymerase have a central role in this process. The model cyanobacterium Synechocystis sp. PCC 6803 has four non-essential group 2 σ factors (SigB, SigC, SigD and SigE) that regulate global metabolic responses to various adverse environmental conditions. Here we show that although none of the group 2 σ factors is essential for the major metabolic realignments induced by a short period of nitrogen starvation, the quadruple mutant without any group 2 σ factors and triple mutants missing both SigB and SigD grow slowly in BG-11 medium containing only 5% of the nitrate present in standard BG-11. These ΔsigBCDE, ΔsigBCD and ΔsigBDE strains lost PSII activity rapidly in low nitrogen and accumulated less glycogen than the control strain. An abnormally high glycogen content was detected in ΔsigBCE (SigD is active), while the carotenoid content became high in ΔsigCDE (SigB is active), indicating that SigB and SigD regulate the partitioning of carbon skeletons in low nitrogen. Long-term survival and recovery of the cells after nitrogen deficiency was strongly dependent on group 2 σ factors. The quadruple mutant and the ΔsigBDE strain (only SigC is active) recovered more slowly from nitrogen deficiency than the control strain, and ΔsigBCDE in particular lost viability during nitrogen starvation. Nitrogen deficiency-induced changes in the pigment content of the control strain recovered essentially in 1 d in nitrogen-replete medium, but little recovery occurred in ΔsigBCDE and ΔsigBDE.

Involvement of Potassium Transport Systems in the Response of Synechocystis PCC 6803 Cyanobacteria to External pH Change, High-Intensity Light Stress and Heavy Metal Stress

The unicellular photosynthetic cyanobacterium, able to survive in varying environments, is the only prokaryote that directly converts solar energy and CO2 into organic material and is thus relevant for primary production in many ecosystems. To maintain the intracellular and intrathylakoid ion homeostasis upon different environmental challenges, the concentration of potassium as a major intracellular cation has to be optimized by various K(+)uptake-mediated transport systems. We reveal here the specific and concerted physiological function of three K(+)transporters of the plasma and thylakoid membranes, namely of SynK (K(+)channel), KtrB (Ktr/Trk/HKT) and KdpA (Kdp) in Synechocystis sp. strain PCC 6803, under specific stress conditions. The behavior of the wild type, single, double and triple mutants was compared, revealing that only Synk contributes to heavy metal-induced stress, while only Ktr/Kdp is involved in osmotic and salt stress adaptation. With regards to pH shifts in the external medium, the Kdp/Ktr uptake systems play an important role in the adaptation to acidic pH. Ktr, by affecting the CO2 concentration mechanism via its action on the bicarbonate transporter SbtA, might also be responsible for the observed effects concerning high-light stress and calcification. In the case of illumination with high-intensity light, a synergistic action of Kdr/Ktp and SynK is required in order to avoid oxidative stress and ensure cell viability. In summary, this study dissects, using growth tests, measurement of photosynthetic activity and analysis of ultrastructure, the physiological role of three K(+)transporters in adaptation of the cyanobacteria to various environmental changes.

A Feed-Forward Loop Consisting of the Response Regulator RpaB and the Small RNA PsrR1 Controls Light Acclimation of Photosystem I Gene Expression in the Cyanobacterium Synechocystis sp. PCC 6803

Since cyanobacteria need to decrease PSI content to avoid absorption of excess light energy, down-regulation of PSI gene expression is one of the key characteristics of the high-light (HL) acclimation response. The transcriptional regulator RpaB and the small RNA PsrR1 (photosynthesis regulatory RNA1) have been suggested to be the two most critical factors for this response in Synechocystis sp. PCC 6803. In this study, we found that the HLR1 DNA-binding motif, the recognition sequence for RpaB, is highly conserved in the core promoter region of the psrR1 gene among cyanobacterial species. Gel mobility shift assay revealed that RpaB binds to the HLR1 sequence of psrR1 in vitro. RNA gel blot analysis together with chromatin affinity purification (ChAP) analysis suggested that PSI genes are activated and the psrR1 gene is repressed by the binding of RpaB under low-light (LL) conditions. A decrease in DNA binding affinity of RpaB occurs within 5 min after the shift from LL to HL conditions, leading to the prompt decrease in PSI promoter activity together with derepression of psrR1 gene expression. Accumulating PsrR1 molecules then prevent translation from pre-existing PSI transcripts. By this dual repression at transcriptional and post-transcriptional levels, rapid and strict down-regulation of PSI expression under HL is secured. Our findings suggest that RpaB and PsrR1 constitute a feed-forward loop for the regulation of PSI gene expression to achieve a rapid acclimation response to the damaging HL conditions.

Maintenance of motility bias during cyanobacterial phototaxis

Signal transduction in bacteria is complex, ranging across scales from molecular signal detectors and effectors to cellular and community responses to stimuli. The unicellular, photosynthetic cyanobacterium Synechocystis sp. PCC6803 transduces a light stimulus into directional movement known as phototaxis. This response occurs via a biased random walk toward or away from a directional light source, which is sensed by intracellular photoreceptors and mediated by Type IV pili. It is unknown how quickly cells can respond to changes in the presence or directionality of light, or how photoreceptors affect single-cell motility behavior. In this study, we use time-lapse microscopy coupled with quantitative single-cell tracking to investigate the timescale of the cellular response to various light conditions and to characterize the contribution of the photoreceptor TaxD1 (PixJ1) to phototaxis. We first demonstrate that a community of cells exhibits both spatial and population heterogeneity in its phototactic response. We then show that individual cells respond within minutes to changes in light conditions, and that movement directionality is conferred only by the current light directionality, rather than by a long-term memory of previous conditions. Our measurements indicate that motility bias likely results from the polarization of pilus activity, yielding variable levels of movement in different directions. Experiments with a photoreceptor (taxD1) mutant suggest a supplementary role of TaxD1 in enhancing movement directionality, in addition to its previously identified role in promoting positive phototaxis. Motivated by the behavior of the taxD1 mutant, we demonstrate using a reaction-diffusion model that diffusion anisotropy is sufficient to produce the observed changes in the pattern of collective motility. Taken together, our results establish that single-cell tracking can be used to determine the factors that affect motility bias, which can then be coupled with biophysical simulations to connect changes in motility behaviors at the cellular scale with group dynamics.