Model of the carbon concentrating mechanism in chloroplasts of eukaryotic algae

Modeling with uncertainty quantification reveals the essentials of a non-canonical algal carbon-concentrating mechanism

The thermoacidophilic red alga Cyanidioschyzon merolae survives its challenging environment likely in part by operating a carbon-concentrating mechanism (CCM). Here, we demonstrated that C. merolae's cellular affinity for CO2 is stronger than the affinity of its rubisco for CO2. This finding provided additional evidence that C. merolae operates a CCM while lacking the structures and functions characteristic of CCMs in other organisms. To test how such a CCM could function, we created a mathematical compartmental model of a simple CCM, distinct from those we have seen previously described in detail. The results of our modeling supported the feasibility of this proposed minimal and non-canonical CCM in C. merolae. To facilitate the robust modeling of this process, we measured and incorporated physiological and enzymatic parameters into the model. Additionally, we trained a surrogate machine-learning model to emulate the mechanistic model and characterized the effects of model parameters on key outputs. This parameter exploration enabled us to identify model features that influenced whether the model met the experimentally derived criteria for functional carbon concentration and efficient energy usage. Such parameters included cytosolic pH, bicarbonate pumping cost and kinetics, cell radius, carboxylation velocity, number of thylakoid membranes, and CO2 membrane permeability. Our exploration thus suggested that a non-canonical CCM could exist in C. merolae and illuminated the essential features generally necessary for CCMs to function.

Energy crosstalk between photosynthesis and the algal CO2-concentrating mechanisms

Microalgal photosynthesis is responsible for nearly half of the CO2 annually captured by Earth's ecosystems. In aquatic environments where the CO2 availability is low, the CO2-fixing efficiency of microalgae greatly relies on mechanisms - called CO2-concentrating mechanisms (CCMs) - for concentrating CO2 at the catalytic site of the CO2-fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). While the transport of inorganic carbon (Ci) across membrane bilayers against a concentration gradient consumes part of the chemical energy generated by photosynthesis, the bioenergetics and cellular mechanisms involved are only beginning to be elucidated. Here, we review the current knowledge relating to the energy requirement of CCMs in the light of recent advances in photosynthesis regulatory mechanisms and the spatial organization of CCM components.

Extracellular carbonic anhydrase activity promotes a carbon concentration mechanism in metazoan calcifying cells

Many calcifying organisms utilize metabolic CO₂ to generate CaCO₃ minerals to harden their shells and skeletons. Carbonic anhydrases are evolutionary ancient enzymes that have been proposed to play a key role in the calcification process, with the underlying mechanisms being little understood. Here, we used the calcifying primary mesenchyme cells (PMCs) of sea urchin larva to study the role of cytosolic (iCAs) and extracellular carbonic anhydrases (eCAs) in the cellular carbon concentration mechanism (CCM). Molecular analyses identified iCAs and eCAs in PMCs and highlight the prominent expression of a glycosylphosphatidylinositol-anchored membrane-bound CA (Cara7). Intracellular pH recordings in combination with CO₂ pulse experiments demonstrated iCA activity in PMCs. iCA activity measurements, together with pharmacological approaches, revealed an opposing contribution of iCAs and eCAs on the CCM. H⁺-selective electrodes were used to demonstrate eCA-catalyzed CO₂ hydration rates at the cell surface. Knockdown of Cara7 reduced extracellular CO₂ hydration rates accompanied by impaired formation of specific skeletal segments. Finally, reduced pH_i regulatory capacities during inhibition and knockdown of Cara7 underscore a role of this eCA in cellular HCO₃^- uptake. This work reveals the function of CAs in the cellular CCM of a marine calcifying animal. Extracellular hydration of metabolic CO₂ by Cara7 coupled to HCO₃^- uptake mechanisms mitigates the loss of carbon and reduces the cellular proton load during the mineralization process. The findings of this work provide insights into the cellular mechanisms of an ancient biological process that is capable of utilizing CO₂ to generate a versatile construction material.

An overview on the recently discovered iota-carbonic anhydrases

Carbonic anhydrases (CAs, EC 4.2.1.1) have been studied for decades and have been classified as a superfamily of enzymes which includes, up to date, eight gene families or classes indicated with the Greek letters α, β, γ, δ, ζ, η, θ, ι. This versatile enzyme superfamily is involved in multiple physiological processes, catalysing a fundamental reaction for all living organisms, the reversible hydration of carbon dioxide to bicarbonate and a proton. Recently, the ι-CA (LCIP63) from the diatom Thalassiosira pseudonana and a bacterial ι-CA (BteCAι) identified in the genome of Burkholderia territorii were characterised. The recombinant BteCAι was observed to act as an excellent catalyst for the physiologic reaction. Very recently, the discovery of a novel ι-CAs (COG4337) in the eukaryotic microalga Bigelowiella natans and the cyanobacterium Anabaena sp. PCC7120 has brought to light an unexpected feature for this ancient superfamily: this ι-CAs was catalytically active without a metal ion cofactor, unlike the previous reported ι-CAs as well as all known CAs investigated so far. This review reports recent investigations on ι-CAs obtained in these last three years, highlighting their peculiar features, and hypothesising that possibly this new CA family shows catalytic activity without the need of metal ions.

Intraspecific variation in multiple trait responses of Alexandrium ostenfeldii towards elevated pCO2

Dissolved oceanic CO₂ concentrations are rising as result of increasing atmospheric partial pressure of CO₂ (pCO₂), which has large consequences for phytoplankton. To test how higher CO₂ availability affects different traits of the toxic dinoflagellate Alexandrium ostenfeldii, we exposed three strains of the same population to 400 and 1,000 µatm CO₂, and measured traits including growth rate, cell volume, elemental composition, ¹³C fractionation, toxin content, and volatile organic compounds (VOCs). Strains largely increased their growth rates and particulate organic carbon and nitrogen production with higher pCO₂ and showed significant changes in their VOC profile. One strain showed a significant decrease in both PSP and cyclic imine content and thereby in cellular toxicity. Fractionation against ¹³C increased in response to elevated pCO₂, which may point towards enhanced CO₂ acquisition and/or a downscaling of the carbon concentrating mechanisms. Besides consistent responses in some traits, other traits showed large variation in both direction and strength of responses towards elevated pCO₂. The observed intraspecific variation in phenotypic plasticity of important functional traits within the same population may help A. ostenfeldii to negate the effects of immediate environmental fluctuations and allow populations to adapt more quickly to changing environments.

Improving light distribution and light/dark cycle of 900 L tangential spiral-flow column photobioreactors to promote CO2 fixation with Arthrospira sp. cells

The light distribution and light/dark cycle were improved in 900 L tangential spiral-flow column photobioreactors (TSCP) to promote CO₂ fixation with Arthrospira sp. cells. Solar irradiation model was employed in CFD simulation to investigate light distribution and light/dark cycle in flow field composed of culture medium, CO2 bubbles and Arthrospira sp. cells under actual sunlight irradiation considering geolocation and time. An accurate way to divide light/dark zone based on saturate light intensity and light intensity field was adopted for the first time. When Arthrospira sp. cell concentration increased from 0.1 to 0.9 g/L, light/dark cycle frequency of cells firstly increased from 0.650 Hz to 0.868 Hz and then decreased to 0.117 Hz. Intracellular chlorophyll a content and carotenoids content of Arthrospira sp. cells in TSCP were 6% and 41% higher than those in conventional bubble column photobioreactor. This promoted cellular photosynthesis and stress resistance, which contributed to increase CO₂ fixation rate of Arthrospira sp. cells by 59%. When CO₂ aeration rate, CO₂ volume concentration, and circulating pump power were 0.210 L/min, 15%, and 30 W, chlorophyll a content, helix pitch, and CO₂ fixation rate of Arthrospira sp. cells all reached peak values of 8.769 mg/L, 78.26 μm and 0.358 g/L/d, respectively.

Cyanobacterial removal by a red soil-based flocculant and its effect on zooplankton: an experiment with deep enclosures in a tropical reservoir in China

As one kind of cheap, environmentally-friendly and efficient treatment materials for direct control of cyanobacterial blooms, modified clays have been widely concerned. The present study evaluated cyanobaterial removal by a red soil-based flocculant (RSBF) with a large enclosure experiment in a tropical mesotrophic reservoir, in which phytoplankton community was dominated by Microcystis spp. and Anabaena spp. The flocculant was composed of red soil, chitosan and FeCl₃. Twelve enclosures were used in the experiment: three replicates for each of one control and three treatments RSBF₁₅ (15 mg FeCl₃ l^-1), RSBF₂₅ (25 mg FeCl₃ l^-1), and RSBF₃₅ (35 mg FeCl₃ l^-1). The results showed that the red soil-based flocculant can significantly remove cyanobacterial biomass and reduce concentrations of nutrients including total nitrogen, nitrate, ammonia, total phosphorus, and orthophosphate. Biomass of Microcystis spp. and Anabaena spp. was reduced more efficiently (95%) than other filamentous cyanobacteria (50%). In the RSBF₁₅ treatment, phytoplankton biomass recovered to the level of the control group after 12 days and cyanobacteria quickly dominated. Phytoplankton biomass in the RSBF₂₅ treatment also recovered after 12 days, but green algae co-dominated with cyanobacteria. A much later recovery of phytoplankton until the day of 28 was observed under RSBF₃₅ treatment, and cyanobacteria did no longer dominate the phytoplankton community. The application of red soil-based flocculant greatly reduces zooplankton, especially rotifers, however, Copepods and Cladocera recovered fast. Generally, the red soil-based flocculant can be effective for urgent treatments at local scales in cyanobacteria dominating systems.

Meta-analysis reveals enhanced growth of marine harmful algae from temperate regions with warming and elevated CO2 levels

Elevated pCO₂ and warming may promote algal growth and toxin production, and thereby possibly support the proliferation and toxicity of harmful algal blooms (HABs). Here, we tested whether empirical data support this hypothesis using a meta-analytic approach and investigated the responses of growth rate and toxin content or toxicity of numerous marine and estuarine HAB species to elevated pCO₂ and warming. Most of the available data on HAB responses towards the two tested climate change variables concern dinoflagellates, as many members of this phytoplankton group are known to cause HAB outbreaks. Toxin content and toxicity did not reveal a consistent response towards both tested climate change variables, while growth rate increased consistently with elevated pCO₂ . Warming also led to higher growth rates, but only for species isolated at higher latitudes. The observed gradient in temperature growth responses shows the potential for enhanced development of HABs at higher latitudes. Increases in growth rates with more CO₂ may present an additional competitive advantage for HAB species, particularly as CO₂ was not shown to enhance growth rate of other non-HAB phytoplankton species. However, this may also be related to the difference in representation of dinoflagellate and diatom species in the respective HAB and non-HAB phytoplankton groups. Since the proliferation of HAB species may strongly depend on their growth rates, our results warn for a greater potential of dinoflagellate HAB development in future coastal waters, particularly in temperate regions.

A comparison of species specific sensitivities to changing light and carbonate chemistry in calcifying marine phytoplankton

Coccolithophores are unicellular marine phytoplankton and important contributors to global carbon cycling. Most work on coccolithophore sensitivity to climate change has been on the small, abundant bloom-forming species Emiliania huxleyi and Gephyrocapsa oceanica. However, large coccolithophore species can be major contributors to coccolithophore community production even in low abundances. Here we fit an analytical equation, accounting for simultaneous changes in CO₂ and light intensity, to rates of photosynthesis, calcification and growth in Scyphosphaera apsteinii. Comparison of responses to G. oceanica and E. huxleyi revealed S. apsteinii is a low-light adapted species and, in contrast, becomes more sensitive to changing environmental conditions when exposed to unfavourable CO₂ or light. Additionally, all three species decreased their light requirement for optimal growth as CO₂ levels increased. Our analysis suggests that this is driven by a drop in maximum rates and, in G. oceanica, increased substrate uptake efficiency. Increasing light intensity resulted in a higher proportion of muroliths (plate-shaped) to lopadoliths (vase shaped) and liths became richer in calcium carbonate as calcification rates increased. Light and CO₂ driven changes in response sensitivity and maximum rates are likely to considerably alter coccolithophore community structure and productivity under future climate conditions.

Transcriptome and key genes expression related to carbon fixation pathways in Chlorella PY-ZU1 cells and their growth under high concentrations of CO2

BACKGROUND

The biomass yield of Chlorella PY-ZU1 drastically increased when cultivated under high CO₂ condition compared with that cultivated under air condition. However, less attention has been given to the microalgae photosynthetic mechanisms response to different CO₂ concentrations. The genetic reasons for the higher growth rate, CO₂ fixation rate, and photosynthetic efficiency of microalgal cells under higher CO₂ concentration have not been clearly defined yet.

RESULTS

In this study, the Illumina sequencing and de novo transcriptome assembly of Chlorella PY-ZU1 cells cultivated under 15% CO₂ were performed and compared with those of cells grown under air. It was found that carbonic anhydrase (CAs, enzyme for interconversion of bicarbonate to CO₂) dramatically decreased to near 0 in 15% CO₂-grown cells, which indicated that CO₂ molecules directly permeated into cells under high CO₂ stress without CO₂-concentrating mechanism. Extrapolating from the growth conditions and quantitative Real-Time PCR of CCM-related genes, the K_m (CO₂) (the minimum intracellular CO₂ concentration that rubisco required) of Chlorella PY-ZU1 might be in the range of 80-192 μM. More adenosine triphosphates was saved for carbon fixation-related pathways. The transcript abundance of rubisco (the most important enzyme of CO₂ fixation reaction) was 16.3 times higher in 15% CO₂-grown cells than that under air. Besides, the transcript abundances of most key genes involved in carbon fixation pathways were also enhanced in 15% CO₂-grown cells.

CONCLUSIONS

Carbon fixation and nitrogen metabolism are the two most important metabolisms in the photosynthetic cells. These genes related to the two most metabolisms with significantly differential expressions were beneficial for microalgal growth (2.85 g L^-1) under 15% CO₂ concentration. Considering the micro and macro growth phenomena of Chlorella PY-ZU1 under different concentrations of CO₂ (0.04-60%), CO₂ transport pathways responses to different CO₂ (0.04-60%) concentrations was reconstructed.

Warming and Ocean Acidification Effects on Phytoplankton--From Species Shifts to Size Shifts within Species in a Mesocosm Experiment

While the isolated responses of marine phytoplankton to climate warming and to ocean acidification have been studied intensively, studies on the combined effect of both aspects of Global Change are still scarce. Therefore, we performed a mesocosm experiment with a factorial combination of temperature (9 and 15 °C) and pCO2 (means: 439 ppm and 1040 ppm) with a natural autumn plankton community from the western Baltic Sea. Temporal trajectories of total biomass and of the biomass of the most important higher taxa followed similar patterns in all treatments. When averaging over the entire time course, phytoplankton biomass decreased with warming and increased with CO2 under warm conditions. The contribution of the two dominant higher phytoplankton taxa (diatoms and cryptophytes) and of the 4 most important species (3 diatoms, 1 cryptophyte) did not respond to the experimental treatments. Taxonomic composition of phytoplankton showed only responses at the level of subdominant and rare species. Phytoplankton cell sizes increased with CO2 addition and decreased with warming. Both effects were stronger for larger species. Warming effects were stronger than CO2 effects and tended to counteract each other. Phytoplankton communities without calcifying species and exposed to short-term variation of CO2 seem to be rather resistant to ocean acidification.

Simulating the effects of light intensity and carbonate system composition on particulate organic and inorganic carbon production in Emiliania huxleyi

Coccolithophores play an important role in the marine carbon cycle. Variations in light intensity and external carbonate system composition alter intracellular carbon fluxes and therewith the production rates of particulate organic and inorganic carbon. Aiming to find a mechanistic explanation for the interrelation between dissolved inorganic carbon fluxes and particulate carbon production rates, we develop a numerical cell model for Emiliania huxleyi, one of the most abundant coccolithophore species. The model consists of four cellular compartments, for each of which the carbonate system is resolved dynamically. The compartments are connected to each other and to the external medium via substrate fluxes across the compartment-confining membranes. By means of the model we are able to explain several pattern observed in particulate organic and inorganic carbon production rates for different strains and under different acclimation conditions. Particulate organic and inorganic carbon production rates for instance decrease at very low external CO2 concentrations. Our model suggests that this effect is caused mainly by reduced HCO3(-) uptake rates, not by CO2 limitation. The often observed decrease in particulate inorganic carbon production rates under Ocean Acidification is explained by a downregulation of cellular HCO3(-) uptake.

CO(2)-cAMP-responsive cis-elements targeted by a transcription factor with CREB/ATF-like basic zipper domain in the marine diatom Phaeodactylum tricornutum

Expression controls of the carbon acquisition system in marine diatoms in response to environmental factors are an essential issue to understand the changes in marine primary productivity. A pyrenoidal β-carbonic anhydrase, PtCA1, is one of the most important candidates to investigate the control mechanisms of the CO(2) acquisition system in the marine diatom Phaeodactylum tricornutum. A detailed functional assay was carried out on the putative core regulatory region of the ptca1 promoter using a β-glucuronidase reporter in P. tricornutum cells under changing CO(2) conditions. A set of loss-of-function assays led to the identification of three CO(2)-responsive elements, TGACGT, ACGTCA, and TGACGC, at a region -86 to -42 relative to the transcription start site. Treatment with a cyclic (c)AMP analog, dibutyryl cAMP, revealed these three elements to be under the control of cAMP; thus, we designated them, from 5' to 3', as CO(2)-cAMP-Responsive Element1 (CCRE1), CCRE2, and CCRE3. Because the sequence TGACGT is known to be a typical target of human Activating Transcription Factor6 (ATF6), we searched for genes containing a basic zipper (bZIP) region homologous to that of ATF6 in the genome of P. tricornutum. Gel-shift assays using CCRE pentamers as labeled probes showed that at least one candidate of bZIP proteins, PtbZIP11, bound specifically to CCREs. A series of gain-of-function assays with CCREs fused to a minimal promoter strongly suggested that the alternative combination of CCRE1/2 or CCRE2/3 at proper distances from the minimal promoter is required as a potential target of PtbZIP11 for an effective CO(2) response of the ptca1 gene.

Inorganic carbon acquisition in potentially toxic and non-toxic diatoms: the effect of pH-induced changes in seawater carbonate chemistry

The effects of pH-induced changes in seawater carbonate chemistry on inorganic carbon (C(i)) acquisition and domoic acid (DA) production were studied in two potentially toxic diatom species, Pseudo-nitzschia multiseries and Nitzschia navis-varingica, and the non-toxic Stellarima stellaris. In vivo activities of carbonic anhydrase (CA), photosynthetic O(2) evolution and CO(2) and HCO(3)(-) uptake rates were measured by membrane inlet MS in cells acclimated to low (7.9) and high pH (8.4 or 8.9). Species-specific differences in the mode of carbon acquisition were found. While extracellular carbonic anhydrase (eCA) activities increased with pH in P. multiseries and S. stellaris, N. navis-varingica exhibited low eCA activities independent of pH. Half-saturation concentrations (K(1/2)) for photosynthetic O(2) evolution, which were highest in S. stellaris and lowest in P. multiseries, generally decreased with increasing pH. In terms of carbon source, all species took up both CO(2) and HCO(3)(-). K(1/2) values for inorganic carbon uptake decreased with increasing pH in two species, while in N. navis-varingica apparent affinities did not change. While the contribution of HCO(3)(-) to net fixation was more than 85% in S. stellaris, it was about 55% in P. multiseries and only approximately 30% in N. navis-varingica. The intracellular content of DA increased in P. multiseries and N. navis-varingica with increasing pH. Based on our data, we propose a novel role for eCA acting as C(i)-recycling mechanism. With regard to pH-dependence of growth, the 'HCO(3)(-) user' S. stellaris was as sensitive as the 'CO(2) user' N. navis-varingica. The suggested relationship between DA and carbon acquisition/C(i) limitation could not be confirmed.

Fast cadmium inhibition of photosynthesis in cyanobacteria in vivo and in vitro studies using perturbed angular correlation of γ-rays

The effect of cadmium on the photosynthetic activity of Synechocystis PCC 6803 was monitored in this study. The oxygen evolving capacity of Synechocystis treated with 40 muM CdCl(2) was depressed to 10% of the maximum in 15 min, indicating that Cd(2+) penetrated rapidly into the cells and blocked the photosynthetic activity. However, neither photosystem II (PSII) nor photosystem I (PSI) activity showed a significant short-term decrease which would explain this fast decrease in the whole-chain electron transport. Thermoluminescence measurements have shown that the charge separation and stabilization in PSII remains essentially unchanged during the first few hours following the Cd(2+) treatment. The electron flow through PSI was monitored by following the redox changes of the P700 reaction centers of PSI. Alterations in the oxidation kinetics of P700 in the Cd(2+)-treated cells indicated that Cd(2+) treatment might affect the available electron acceptor pool of P700, including the CO(2) reduction and accumulation in the cells. Perturbed angular correlation of gamma-rays (PAC) using the radioactive (111m)Cd isotope was used to follow the Cd(2+) uptake at a molecular level. The most plausible interpretation of the PAC data is that Cd(2+) is taken up by one or more Zn proteins replacing Zn(2+) in Synechocystis PCC 6803. Using the radioactive (109)Cd isotope, a protein of approximately 30 kDa that binds Cd(2+) could be observed in sodium dodecyl sulfate polyacrylamide gel electrophoresis. The results indicate that Cd(2+) might inactivate different metal-containing enzymes, including carbonic anhydrase, by replacing the zinc ion, which would explain the rapid and almost full inhibition of the photosynthetic activity in cyanobacteria.

An anaplerotic role for mitochondrial carbonic anhydrase in Chlamydomonas reinhardtii

Previous studies of the mitochondrial carbonic anhydrase (mtCA) of Chlamydomonas reinhardtii showed that expression of the two genes encoding this enzyme activity required photosynthetically active radiation and a low CO(2) concentration. These studies suggested that the mtCA was involved in the inorganic carbon-concentrating mechanism. We have now shown that the expression of the mtCA at low CO(2) concentrations decreases when the external NH(4)(+) concentration decreases, to the point of being undetectable when NH(4)(+) supply restricts the rate of photoautotrophic growth. The expression of mtCA can also be induced at supra-atmospheric partial pressure of CO(2) by increasing the NH(4)(+) concentration in the growth medium. Conditions that favor mtCA expression usually also stimulate anaplerosis. We therefore propose that the mtCA is involved in supplying HCO(3)(-) for anaplerotic assimilation catalyzed by phosphoenolpyruvate carboxylase, which provides C skeletons for N assimilation under some circumstances.

Hydrogen bonds and the catalytic mechanism of human carbonic anhydrase II

A new model for catalysis of human carbonic anhydrase II is suggested. The model is based on the X-ray structure of the hydrogen bond network in the catalytic site. The outer part of the network is proposed to adjust the p K(a) of the catalytic site to the experimentally observed value of about 7. The inner part of the network is proposed to become a low-barrier hydrogen bond network in the transition state. The energy released in forming the low-barrier hydrogen bond network is used to catalyse the interconversion of CO(2) and HCO(3)(-). The suggested molecular mechanism is consistent with the generally accepted kinetic scheme for human carbonic anhydrase II.