CO<Subscript>2</Subscript>-concentrating mechanism in cyanobacterial photosynthesis: organization,physiological role,and evolutionary origin

The cellular and molecular organization of the CO₂-concentrating mechanism (CCM) of cyanobacteria is reviewed. The primary processes of uptake, translocation, and accumulation of inorganic carbon (C_i) near the active site of carbon assimilation by the enzyme ribulose-1,5-bisphosphate carboxylase in the C₃ cycle in cyanobacteria are described as one of the specialized forms of CO₂ concentration which occurs in some photoautotrophic cells. The existence of this form of CO₂ concentration expands our understanding of photosynthetic C_i assimilation. The means of supplying C_i to the C₃ cycle in cyanobacteria is not by simple diffusion into the cell, but it is the result of coordinated functions of high-affinity systems for the uptake of CO₂ and bicarbonate, as well as intracellular CO₂/HCO₃ ^? interconversions by carbonic anhydrases. These biochemical events are under genetic control, and they serve to maintain cellular homeostasis and adaptation to CO₂ limitation. Here we describe the organization of the CCM in cyanobacteria with a special focus on the CCM of relict halo- and alkaliphilic cyanobacteria of soda lakes. We also assess the role of the CCM at the levels of the organism, the biosphere, and evolution.     

Characterisation of Cyanobacterial Bicarbonate Transporters in E. coli Shows that SbtA Homologs Are Functional in This Heterologous Expression System

Cyanobacterial HCO₃ ^- transporters BCT1, SbtA and BicA are important components of cyanobacterial CO₂-concentration mechanisms. They also show potential in applications aimed at improving photosynthetic rates and yield when expressed in the chloroplasts of C3 crop species. The present study investigated the feasibility of using Escherichia coli to assess function of a range of SbtA and BicA transporters in a heterologous expression system, ultimately for selection of transporters suitable for chloroplast expression. Here, we demonstrate that six β-forms of SbtA are active in E. coli, although other tested bicarbonate transporters were inactive. The sbtA clones were derived from Synechococcus sp. WH5701, Cyanobium sp. PCC7001, Cyanobium sp. PCC6307, Synechococcus elongatus PCC7942, Synechocystis sp. PCC6803, and Synechococcus sp. PCC7002. The six SbtA homologs varied in bicarbonate uptake kinetics and sodium requirements in E. coli. In particular, SbtA from PCC7001 showed the lowest uptake affinity and highest flux rate and was capable of increasing the internal inorganic carbon pool by more than 8 mM relative to controls lacking transporters. Importantly, we were able to show that the SbtB protein (encoded by a companion gene near sbtA) binds to SbtA and suppresses bicarbonate uptake function of SbtA in E. coli, suggesting a role in post-translational regulation of SbtA, possibly as an inhibitor in the dark. This study established E. coli as a heterologous expression and analysis system for HCO₃ ^- transporters from cyanobacteria, and identified several SbtA transporters as useful for expression in the chloroplast inner envelope membranes of higher plants.     

A chloroplast pump model for the CO2 concentrating mechanism in the diatom Phaeodactylum tricornutum

Prior analysis of inorganic carbon (C_i) fluxes in the diatom Phaeodactylum tricornutum has indicated that transport of C_i into the chloroplast from the cytoplasm is the major C_i flux in the cell and the primary driving force for the CO₂ concentrating mechanism (CCM). This flux drives the accumulation of C_i in the chloroplast stroma and generates a CO₂ deficit in the cytoplasm, inducing CO₂ influx into the cell. Here, the “chloroplast pump” model of the CCM in P. tricornutum is formalized and its consistency with data on CO₂ and HCO₃ ^? uptake rates, carbonic anhydrase (CA) activity, intracellular C_i concentration, intracellular pH, and RubisCO characteristics is assessed. The chloroplast pump model can account for the major features of the data. Analysis of photosynthetic and C_i uptake rates as a function of external C_i concentration shows that the model has the most difficulty obtaining sufficiently low cytoplasmic CO₂ concentrations to support observed CO₂ uptake rates at low external C_i concentrations and achieving high rates of photosynthesis. There are multiple ways in which model parameters can be varied, within a plausible range, to match measured rates of photosynthesis and CO₂ uptake. To increase CO₂ uptake rates, CA activity can be increased, kinetic characteristics of the putative chloroplast pump can be enhanced to increase HCO₃ ^? export, or the cytoplasmic pH can be raised. To increase the photosynthetic rate, the permeability of the pyrenoid to CO₂ can be reduced or RubisCO content can be increased.     

The carbon concentrating mechanism in Chlamydomonas reinhardtii: finding the missing pieces

The photosynthetic, unicellular green alga, Chlamydomonas reinhardtii, lives in environments that often contain low concentrations of CO₂ and HCO₃ ^?, the utilizable forms of inorganic carbon (C_i). C. reinhardtii possesses a carbon concentrating mechanism (CCM) which can provide suitable amounts of C_i for growth and development. This CCM is induced when the CO₂ concentration is at air levels or lower and is comprised of a set of proteins that allow the efficient uptake of C_i into the cell as well as its directed transport to the site where Rubisco fixes CO₂ into biomolecules. While several components of the CCM have been identified in recent years, the picture is still far from complete. To further improve our knowledge of the CCM, we undertook a mutagenesis project where an antibiotic resistance cassette was randomly inserted into the C. reinhardtii genome resulting in the generation of 22,000 mutants. The mutant collection was screened using both a published PCR-based approach (Gonzalez-Ballester et al. 2011) and a phenotypic growth screen. The PCR-based screen did not rely on a colony having an altered growth phenotype and was used to identify colonies with disruptions in genes previously identified as being associated with the CCM-related gene. Eleven independent insertional mutations were identified in eight different genes showing the usefulness of this approach in generating mutations in CCM-related genes of interest as well as identifying new CCM components. Further improvements of this method are also discussed.     

Mitochondrial carbonic anhydrases are needed for optimal photosynthesis at low CO2 levels in Chlamydomonas

Chlamydomonas reinhardtii can grow photosynthetically using CO₂ or in the dark using acetate as the carbon source. In the light in air, the CO₂ concentrating mechanism (CCM) of C. reinhardtii accumulates CO₂, enhancing photosynthesis. A combination of carbonic anhydrases (CAs) and bicarbonate transporters in the CCM of C. reinhardtii increases the CO₂ concentration at Ribulose 1,5-bisphosphate carboxylase oxygenase (Rubisco) in the chloroplast pyrenoid. Previously, CAs important to the CCM have been found in the periplasmic space, surrounding the pyrenoid and inside the thylakoid lumen. Two almost identical mitochondrial CAs, CAH4 and CAH5, are also highly expressed when the CCM is made, but their role in the CCM is not understood. Here, we adopted an RNAi approach to reduce the expression of CAH4 and CAH5 to study their possible physiological functions. RNAi mutants with low expression of CAH4 and CAH5 had impaired rates of photosynthesis under ambient levels of CO₂ (0.04% CO₂ [v/v] in air). These strains were not able to grow at very low CO₂ (<0.02% CO₂ [v/v] in air), and their ability to accumulate inorganic carbon (C_i = CO₂ + HCO3−) was reduced. At low CO₂ concentrations, the CCM is needed to both deliver C_i to Rubisco and to minimize the leak of CO₂ generated by respiration and photorespiration. We hypothesize that CAH4 and CAH5 in the mitochondria convert the CO₂ released from respiration and photorespiration as well as the CO₂ leaked from the chloroplast to HCO3- thus “recapturing” this potentially lost CO₂.

Mitochondrial carbonic anhydrases CAH4 and CAH5 in Chlamydomonas reinhardtii are involved in maintaining optimal photosynthesis.     

LCIB in the Chlamydomonas CO2-concentrating mechanism

The CO₂-concentrating mechanism confers microalgae a versatile and efficient strategy for adapting to a wide range of environmental CO₂ concentrations. LCIB, which has been demonstrated as a key player in the eukaryotic algal CO₂-concentrating mechanism (CCM), is a novel protein in Chlamydomonas lacking any recognizable domain or motif, and its exact function in the CCM has not been clearly defined. The unique air-dier growth phenotype and photosynthetic characteristics in the LCIB mutants, and re-localization of LCIB between different subcellular locations in response to different levels of CO₂, have indicated that the function of LCIB is closely associated with a distinct low CO₂ acclimation state. Here, we review physiological and molecular evidence linking LCIB with inorganic carbon accumulation in the CCM and discuss the proposed function of LCIB in several inorganic carbon uptake/accumulation pathways. Several new molecular characteristics of LCIB also are presented.     

Modeling and mutagenesis of amino acid residues critical for CO2 hydration by specialized NDH-1 complexes in cyanobacteria

The uptake of inorganic carbon in cyanobacteria is facilitated by an energetically intensive CO₂-concentrating mechanism (CCM). This includes specialized Type-1 NDH complexes that function to couple photosynthetic redox energy to CO₂ hydration forming the bicarbonate that accumulates to high cytoplasmic concentrations during the operation of the CCM, required for effective carbon fixation. Here we used a Synechococcus PCC7942 expression system to investigate the role of conserved histidine and cysteine residues in the CupB (also designated, ChpX) protein, which has been hypothesized to participate in a vectoral CO₂ hydration reaction near the interface between CupB protein and the proton-pumping subunits of the NDH-1 complex. A homology model has been constructed and most of the targeted conserved residues are in the vicinity of a Zn ion modeled to form the catalytic site of deprotonation and CO₂ hydration. Growth and CO₂ uptake assays show that the most severe defects in activity among the targeted residues are due to a substitution of the predicted Zn ligand, CupB-His86. Mutations at other sites produced intermediate effects. Proteomic analysis revealed that some amino acid substitution mutations of CupB caused the induction of bicarbonate uptake proteins to a greater extent than complete deletion of CupB, despite growth under CO₂-enriched conditions. The results are discussed in terms of hypotheses on the catalytic function of this unusual enzyme.     

Responses of macroalgae to CO2 enrichment cannot be inferred solely from their inorganic carbon uptake strategy

Increased plant biomass is observed in terrestrial systems due to rising levels of atmospheric CO₂, but responses of marine macroalgae to CO₂ enrichment are unclear. The 200% increase in CO₂ by 2100 is predicted to enhance the productivity of fleshy macroalgae that acquire inorganic carbon solely as CO₂ (non‐carbon dioxide‐concentrating mechanism [CCM] species—i.e., species without a carbon dioxide‐concentrating mechanism), whereas those that additionally uptake bicarbonate (CCM species) are predicted to respond neutrally or positively depending on their affinity for bicarbonate. Previous studies, however, show that fleshy macroalgae exhibit a broad variety of responses to CO₂ enrichment and the underlying mechanisms are largely unknown. This physiological study compared the responses of a CCM species (Lomentaria australis) with a non‐CCM species (Craspedocarpus ramentaceus) to CO₂ enrichment with regards to growth, net photosynthesis, and biochemistry. Contrary to expectations, there was no enrichment effect for the non‐CCM species, whereas the CCM species had a twofold greater growth rate, likely driven by a downregulation of the energetically costly CCM(s). This saved energy was invested into new growth rather than storage lipids and fatty acids. In addition, we conducted a comprehensive literature synthesis to examine the extent to which the growth and photosynthetic responses of fleshy macroalgae to elevated CO₂ are related to their carbon acquisition strategies. Findings highlight that the responses of macroalgae to CO₂ enrichment cannot be inferred solely from their carbon uptake strategy, and targeted physiological experiments on a wider range of species are needed to better predict responses of macroalgae to future oceanic change.     

On-line stable isotope gas exchange reveals an inducible but leaky carbon concentrating mechanism in Nannochloropsis salina

Carbon concentrating mechanisms (CCMs) are common among microalgae, but their regulation and even existence in some of the most promising biofuel production strains is poorly understood. This is partly because screening for new strains does not commonly include assessment of CCM function or regulation despite its fundamental role in primary carbon metabolism. In addition, the inducible nature of many microalgal CCMs means that environmental conditions should be considered when assessing CCM function and its potential impact on biofuels. In this study, we address the effect of environmental conditions by combining novel, high frequency, on-line ¹³CO₂ gas exchange screen with microscope-based lipid characterization to assess CCM function in Nannochloropsis salina and its interaction with lipid production. Regulation of CCM function was explored by changing the concentration of CO₂ provided to continuous cultures in airlift bioreactors where cell density was kept constant across conditions by controlling the rate of media supply. Our isotopic gas exchange results were consistent with N. salina having an inducible “pump-leak” style CCM similar to that of Nannochloropsis gaditana. Though cells grew faster at high CO₂ and had higher rates of net CO₂ uptake, we did not observe significant differences in lipid content between conditions. Since the rate of CO₂ supply was much higher for the high CO₂ conditions, we calculated that growing cells bubbled with low CO₂ is about 40 % more efficient for carbon capture than bubbling with high CO₂. We attribute this higher efficiency to the activity of a CCM under low CO₂ conditions.     

ENHANCED TRANSPORT OF INORGANIC CARBON INTO ALGAL CELLS AND ITS IMPLICATIONS FOR THE BIOLOGICAL FIXATION OF CARBON1,2

Kinetics of uptake of inorganic carbon by the freshwater green alga Chlamydomonas reinhardtii Dang. suggest that rates of fixation may be enhanced at low tensions of CO₂ by transport of bicarbonate from the cell surface to the chloroplast. Results are evaluated in the context of models that treat diffusion and reaction of dissolved inorganic carbon across a 3 dimensional finite boundary layer, and they are consistent with the claim that CO₂ alone is the substrate used during carbon fixation. An alternative hypothesis, which presumes that both CO₂ and bicarbonate are used as substrates, yields predictions which are inconsistent with the data. Instead, bicarbonate seems to act only as a vehicle for the transport of inorganic carbon into the cell, thereby adding its flux to that of CO₂, and enhancing rates of synthesis that would otherwise be restricted by uptake of CO₂ alone.     

Diversity of carbon use strategies in a kelp forest community: implications for a high CO2 ocean

Mechanisms for inorganic carbon acquisition in macroalgal assemblages today could indicate how coastal ecosystems will respond to predicted changes in ocean chemistry due to elevated carbon dioxide (CO₂). We identified the proportion of noncalcifying macroalgae with particular carbon use strategies using the natural abundance of carbon isotopes and pH drift experiments in a kelp forest. We also identified all calcifying macroalgae in this system; these were the dominant component of the benthos (by % cover) at all depths and seasons while cover of noncalcareous macroalgae increased at shallower depths and during summer. All large canopy‐forming macroalgae had attributes suggestive of active uptake of inorganic carbon and the presence of a CO₂ concentration mechanism (CCM). CCM species covered, on average, 15–45% of the benthos and were most common at shallow depths and during summer. There was a high level of variability in carbon isotope discrimination within CCM species, probably a result of energetic constraints on active carbon uptake in a low light environment. Over 50% of red noncalcifying species exhibited values below ?30‰ suggesting a reliance on diffusive CO₂ uptake and no functional CCM. Non‐CCM macroalgae covered on average 0–8.9% of rock surfaces and were most common in deep, low light habitats. Elevated CO₂ has the potential to influence competition between dominant coralline species (that will be negatively affected by increased CO₂) and noncalcareous CCM macroalgae (neutral or positive effects) and relatively rare (on a % cover basis) non‐CCM species (positive effects). Responses of macroalgae to elevated CO₂ will be strongly modified by light and any responses are likely to be different at times or locations where energy constrains photosynthesis. Increased growth and competitive ability of noncalcareous macroalgae alongside negative impacts of acidification on calcifying species could have major implications for the functioning of coastal reef systems at elevated CO₂ concentrations.     

Structure and function of LCI1: a plasma membrane CO2 channel in the Chlamydomonas CO2 concentrating mechanism

Microalgae and cyanobacteria contribute roughly half of the global photosynthetic carbon assimilation. Faced with limited access to CO₂ in aquatic environments, which can vary daily or hourly, these microorganisms have evolved use of an efficient CO₂ concentrating mechanism (CCM) to accumulate high internal concentrations of inorganic carbon (C_i) to maintain photosynthetic performance. For eukaryotic algae, a combination of molecular, genetic and physiological studies using the model organism Chlamydomonas reinhardtii, have revealed the function and molecular characteristics of many CCM components, including active C_i uptake systems. Fundamental to eukaryotic C_i uptake systems are C_i transporters/channels located in membranes of various cell compartments, which together facilitate the movement of C_i from the environment into the chloroplast, where primary CO₂ assimilation occurs. Two putative plasma membrane C_i transporters, HLA3 and LCI1, are reportedly involved in active C_i uptake. Based on previous studies, HLA3 clearly plays a meaningful role in HCO₃^? transport, but the function of LCI1 has not yet been thoroughly investigated so remains somewhat obscure. Here we report a crystal structure of the full‐length LCI1 membrane protein to reveal LCI1 structural characteristics, as well as in vivo physiological studies in an LCI1 loss‐of‐function mutant to reveal the C_i species preference for LCI1. Together, these new studies demonstrate LCI1 plays an important role in active CO₂ uptake and that LCI1 likely functions as a plasma membrane CO₂ channel, possibly a gated channel.     

Synthetic DNA system for structure-function studies of the high affinity CO2 uptake NDH-13 protein complex in cyanobacteria

The CO₂-concentrating mechanism (CCM) in cyanobacteria supports high rates of photosynthesis by greatly increasing the concentration of CO₂ around the major carbon fixing enzyme, Rubisco. However, the CCM remains poorly understood, especially in regards to the enigmatic CO₂-hydration enzymes which couple photosynthetically generated redox energy to the hydration of CO₂ to bicarbonate. This CO₂-hydration reaction is catalysed by specialized forms of NDH-1 thylakoid membrane complexes that contain phylogenetically unique extrinsic proteins that appear to couple CO₂ hydration to NDH-1 proton pumping. The development of the first molecular genetic system to probe structure-function relationships of this important enzyme system is described. A CO₂-hydration deficient strain was constructed as a recipient for DNA constructs containing different forms of the CO₂-hydration system. This was tested by introducing a construct to an ectopic location that gives constitutive expression, rather than native inducible expression, of the ndhF3-ndhD3-cupA-cupS, (cupA operon) encoding high affinity CO₂-hydration complex, NDH-1₃. Uptake assays show the restoration of high affinity for CO₂ uptake, but demonstrate that the CupA complex can drive only modest uptake fluxes, underlining the importance of its tandem operation with the CupB-containing complex NDH-1₄, the complementary high flux, low affinity CO₂ hydration system. Experiments with the carbonic anhydrase inhibitor, ethoxyzolamide, indicate that the NDH-1₃ complex is strongly inhibited, yet the remaining NDH-1₄ activity in the wild-type is less so, suggesting structural differences between the low affinity and high affinity CO₂–hydration systems. This new construct will be an important tool to study and better understand cyanobacterial CO₂ uptake systems.     

The Bicarbonate Transporter Is Essential for Bacillus anthracis Lethality

In the pathogenic bacterium Bacillus anthracis, virulence requires induced expression of the anthrax toxin and capsule genes. Elevated CO₂/bicarbonate levels, an indicator of the host environment, provide a signal ex vivo to increase expression of virulence factors, but the mechanism underlying induction and its relevance in vivo are unknown. We identified a previously uncharacterized ABC transporter (BAS2714-12) similar to bicarbonate transporters in photosynthetic cyanobacteria, which is essential to the bicarbonate induction of virulence gene expression. Deletion of the genes for the transporter abolished induction of toxin gene expression and strongly decreased the rate of bicarbonate uptake ex vivo, demonstrating that the BAS2714-12 locus encodes a bicarbonate ABC transporter. The bicarbonate transporter deletion strain was avirulent in the A/J mouse model of infection. Carbonic anhydrase inhibitors, which prevent the interconversion of CO₂ and bicarbonate, significantly affected toxin expression only in the absence of bicarbonate or the bicarbonate transporter, suggesting that carbonic anhydrase activity is not essential to virulence factor induction and that bicarbonate, and not CO₂, is the signal essential for virulence induction. The identification of this novel bicarbonate transporter essential to virulence of B. anthracis may be of relevance to other pathogens, such as Streptococcus pyogenes, Escherichia coli, Borrelia burgdorferi, and Vibrio cholera that regulate virulence factor expression in response to CO₂/bicarbonate, and suggests it may be a target for antibacterial intervention.     

LCI1, a Chlamydomonas reinhardtii plasma membrane protein,functions in active CO2 uptake under low CO2

In response to high CO₂ environmental variability, green algae, such as Chlamydomonas reinhardtii, have evolved multiple physiological states dictated by external CO₂ concentration. Genetic and physiological studies demonstrated that at least three CO₂ physiological states, a high CO₂ (0.5–5% CO₂), a low CO₂ (0.03–0.4% CO₂) and a very low CO₂ (< 0.02% CO₂) state, exist in Chlamydomonas. To acclimate in the low and very low CO₂ states, Chlamydomonas induces a sophisticated strategy known as a CO₂‐concentrating mechanism (CCM) that enables proliferation and survival in these unfavorable CO₂ environments. Active uptake of C_i from the environment is a fundamental aspect in the Chlamydomonas CCM, and consists of CO₂ and HCO₃^– uptake systems that play distinct roles in low and very low CO₂ acclimation states. LCI1, a putative plasma membrane C_i transporter, has been linked through conditional overexpression to active C_i uptake. However, both the role of LCI1 in various CO₂ acclimation states and the species of C_i, HCO₃^– or CO₂, that LCI1 transports remain obscure. Here we report the impact of an LCI1 loss‐of‐function mutant on growth and photosynthesis in different genetic backgrounds at multiple pH values. These studies show that LCI1 appears to be associated with active CO₂ uptake in low CO₂, especially above air‐level CO₂, and that any LCI1 role in very low CO₂ is minimal.