Periplasmic carbonic anhydrase structural gene (Cah1) mutant in chlamydomonas reinhardtii

Improving Crop Yield through Increasing Carbon Gain and Reducing Carbon Loss

Photosynthesis is a process where solar energy is utilized to convert atmospheric CO2 into carbohydrates, which forms the basis for plant productivity. The increasing demand for food has created a global urge to enhance yield. Earlier, the plant breeding program was targeting the yield and yield-associated traits to enhance the crop yield. However, the yield cannot be further improved without improving the leaf photosynthetic rate. Hence, in this review, various strategies to enhance leaf photosynthesis were presented. The most promising strategies were the optimization of Rubisco carboxylation efficiency, the introduction of a CO2 concentrating mechanism in C3 plants, and the manipulation of photorespiratory bypasses in C3 plants, which are discussed in detail. Improving Rubisco's carboxylation efficiency is possible by engineering targets such as Rubisco subunits, chaperones, and Rubisco activase enzyme activity. Carbon-concentrating mechanisms can be introduced in C3 plants by the adoption of pyrenoid and carboxysomes, which can increase the CO2 concentration around the Rubisco enzyme. Photorespiration is the process by which the fixed carbon is lost through an oxidative process. Different approaches to reduce carbon and nitrogen loss were discussed. Overall, the potential approaches to improve the photosynthetic process and the way forward were discussed in detail.

The pyrenoid: the eukaryotic CO2-concentrating organelle

The pyrenoid is a phase-separated organelle that enhances photosynthetic carbon assimilation in most eukaryotic algae and the land plant hornwort lineage. Pyrenoids mediate approximately one-third of global CO2 fixation, and engineering a pyrenoid into C3 crops is predicted to boost CO2 uptake and increase yields. Pyrenoids enhance the activity of the CO2-fixing enzyme Rubisco by supplying it with concentrated CO2. All pyrenoids have a dense matrix of Rubisco associated with photosynthetic thylakoid membranes that are thought to supply concentrated CO2. Many pyrenoids are also surrounded by polysaccharide structures that may slow CO2 leakage. Phylogenetic analysis and pyrenoid morphological diversity support a convergent evolutionary origin for pyrenoids. Most of the molecular understanding of pyrenoids comes from the model green alga Chlamydomonas (Chlamydomonas reinhardtii). The Chlamydomonas pyrenoid exhibits multiple liquid-like behaviors, including internal mixing, division by fission, and dissolution and condensation in response to environmental cues and during the cell cycle. Pyrenoid assembly and function are induced by CO2 availability and light, and although transcriptional regulators have been identified, posttranslational regulation remains to be characterized. Here, we summarize the current knowledge of pyrenoid function, structure, components, and dynamic regulation in Chlamydomonas and extrapolate to pyrenoids in other species.

The Chlamydomonas reinhardtii chloroplast envelope protein LCIA transports bicarbonate in planta

LCIA is a chloroplast envelope protein associated with the CO2 concentrating mechanism of the green alga Chlamydomonas reinhardtii. LCIA is postulated to be a HCO3- channel, but previous studies were unable to show that LCIA was actively transporting bicarbonate in planta. Therefore, LCIA activity was investigated more directly in two heterologous systems: an E. coli mutant (DCAKO) lacking both native carbonic anhydrases and an Arabidopsis mutant (βca5) missing the plastid carbonic anhydrase βCA5. Both DCAKO and βca5 cannot grow in ambient CO2 conditions, as they lack carbonic anhydrase-catalyzed production of the necessary HCO3- concentration for lipid and nucleic acid biosynthesis. Expression of LCIA restored growth in both systems in ambient CO2 conditions, which strongly suggests that LCIA is facilitating HCO3- uptake in each system. To our knowledge, this is the first direct evidence that LCIA moves HCO3- across membranes in bacteria and plants. Furthermore, the βca5 plant bioassay used in this study is the first system for testing HCO3- transport activity in planta, an experimental breakthrough that will be valuable for future studies aimed at improving the photosynthetic efficiency of crop plants using components from algal CO2 concentrating mechanisms.

Advances in understanding the physiological role and locations of carbonic anhydrases in C3 plant cells

The review describes the structures of plant carbonic anhydrases (CAs), enzymes catalyzing the interconversion of inorganic carbon forms and belonging to different families, as well as the interaction of inhibitors and activators of CA activity with the active sites of CAs in representatives of these families. We outline the data that shed light on the location of CAs in green cells of C3 plants, algae and angiosperms, with the emphasis on the recently obtained data. The proven and proposed functions of CAs in these organisms are listed. The possibility of the involvement of several chloroplast CAs in acceleration of the conversion of bicarbonate to CO₂ and in supply of CO₂ for fixation by Rubisco is particularly considered. Special attention is paid to CAs in various parts of thylakoids and to discussion about current knowledge of their possible physiological roles. The review states that, despite the significant progress in application of the mutants with suppressed CAs synthesis, the approach based on the use of the inhibitors of CA activity in some cases remains quite effective. Combination of these two approaches, namely determining the effect of CA activity inhibitors in plants with certain knocked-out CA genes, turns out to be very useful for understanding the functions of other CAs.

Comparative secretome analysis between salinity-tolerant and control Chlamydomonas reinhardtii strains

Secretome analysis of a salt-tolerant and control Chlamydomonas reinhardtii revealed 514 differentially expressed proteins. Membrane transport and trafficking, signal transduction and channel proteins were up-regulated in the ST secretome. Salinity is a major abiotic stress that limits crop production worldwide. Multiple adverse effects have been reported in many living organisms exposed to high-saline concentrations. Chlamydomonas reinhardtii is known for secreting proteins in response to many environmental stresses. A salinity-tolerant (ST) strain of Chlamydomonas has been developed, whose cells were able to grow at 300 mM NaCl. The current study analyzed the secretomes of ST grown in TAP medium supplemented with 300 mM NaCl and the laboratory strain CC-503 grown in TAP medium without NaCl supplement. In total, 514 secreted proteins were identified of which 203 were up-regulated and 110 were down-regulated. Bioinformatic analysis predicted 168 proteins to be secreted or in the conventional secretory pathway. Out of these, 70 were up-regulated, while 51 proteins were down-regulated. Proteins involved in membrane transport and trafficking, signal transduction and channel proteins were altered in their expression in the ST secretome, suggesting the response of saline stress acts toward not only the intracellular pool of proteins but also the extracellular proteins. This also suggested that the secreted proteins might have roles in the extracellular space. Signal peptide (SP) prediction revealed that almost 40% of the predicted secreted proteins contained a signal peptide; however, a high proportion of proteins lacked an SP, suggesting that these proteins might be secreted through an unconventional protein secretion pathway.

External α-carbonic anhydrase and solute carrier 4 are required for bicarbonate uptake in a freshwater angiosperm

The freshwater monocot Ottelia alismoides is the only known species to operate three CO2-concentrating mechanisms (CCMs): constitutive bicarbonate (HCO3-) use, C4 photosynthesis, and facultative Crassulacean acid metabolism, but the mechanism of HCO3- use is unknown. We found that the inhibitor of an anion exchange protein, 4,4'-diisothio-cyanatostilbene-2,2'-disulfonate (DIDS), prevented HCO3- use but also had a small effect on CO2 uptake. An inhibitor of external carbonic anhydrase (CA), acetazolamide (AZ), reduced the affinity for CO2 uptake but also prevented HCO3- use via an effect on the anion exchange protein. Analysis of mRNA transcripts identified a homologue of solute carrier 4 (SLC4) responsible for HCO3- transport, likely to be the target of DIDS, and a periplasmic α-carbonic anhydrase 1 (α-CA1). A model to quantify the contribution of the three different pathways involved in inorganic carbon uptake showed that passive CO2 diffusion dominates inorganic carbon uptake at high CO2 concentrations. However, as CO2 concentrations fall, two other pathways become predominant: conversion of HCO3- to CO2 at the plasmalemma by α-CA1 and transport of HCO3- across the plasmalemma by SLC4. These mechanisms allow access to a much larger proportion of the inorganic carbon pool and continued photosynthesis during periods of strong carbon depletion in productive ecosystems.

Comparison of secretory signal peptides for heterologous protein expression in microalgae: Expanding the secretion portfolio for Chlamydomonas reinhardtii

Efficient protein secretion is a desirable trait for any recombinant protein expression system, together with simple, low-cost, and defined media, such as the typical media used for photosynthetic cultures of microalgae. However, low titers of secreted heterologous proteins are usually obtained, even with the most extensively studied microalga Chlamydomonas reinhardtii, preventing their industrial application. In this study, we aimed to expand and evaluate secretory signal peptides (SP) for heterologous protein secretion in C. reinhardtii by comparing previously described SP with untested sequences. We compared the SPs from arylsulfatase 1 and carbonic anhydrase 1, with those of untried SPs from binding protein 1, an ice-binding protein, and six sequences identified in silico. We identified over 2000 unique SPs using the SignalP 4.0 software. mCherry fluorescence was used to compare the protein secretion of up to 96 colonies for each construct, non-secretion construct, and parental wild-type cc1690 cells. Supernatant fluorescence varied according to the SP used, with a 10-fold difference observed between the highest and lowest secretors. Moreover, two SPs identified in silico secreted the highest amount of mCherry. Our results demonstrate that the SP should be carefully selected and that efficient sequences can be coded in the C. reinhardtii genome. The SPs described here expand the portfolio available for research on heterologous protein secretion and for biomanufacturing applications.

Absence of OsβCA1 causes a CO2 deficit and affects leaf photosynthesis and the stomatal response to CO2 in rice

Plants always adjust the opening of stomatal pores to adapt to the environment, for example CO₂ concentration ([CO₂ ]), humidity and temperature. Low [CO₂ ] will trigger the opening of stomatal pores to absorb extra CO₂ . However, little is known about how CO₂ supply affects the carbon fixation and opening of stomatal pores in rice. Here, a chloroplast-located gene coding for β-carbonic anhydrase (βCA) was found to be involved in carbon assimilation and the CO₂ -mediated stomatal pore response in rice. OsβCA1 was constitutively expressed in all tissues and its transcripts were induced by high [CO₂ ] in leaves. Both T-DNA mutant and RNA interference lines showed phenotypes of lower biomass and CA activities. Knockout of OsβCA1 obviously decreased photosynthetic capacity, as demonstrated by the increased CO₂ compensation point and decreased light saturation point in the mutant, while knockout increased the opening ratio of stomatal pores and the rate of water loss. Moreover, the mutant showed a delayed response to low [CO₂ ], and stomatal pores could not be closed to the same degree as those of wild type even though the stomatal pores could rapidly respond to high [CO₂ ]. Genome-wide gene expression analysis via RNA sequencing demonstrated that the transcript abundance of genes related to Rubisco, photosystem compounds and the opening of stomatal pores was globally upregulated in the mutant. Taken together, the inadequate CO₂ supply caused by the absence of OsβCA1 reduces photosynthetic efficiency, triggers the opening of stomatal pores and finally decreases their sensitivity to CO₂ fluctuation.

The CO2 concentrating mechanism and photosynthetic carbon assimilation in limiting CO2 : how Chlamydomonas works against the gradient

The CO2 concentrating mechanism (CCM) represents an effective strategy for carbon acquisition that enables microalgae to survive and proliferate when the CO2 concentration limits photosynthesis. The CCM improves photosynthetic performance by raising the CO2 concentration at the site of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), simultaneously enhancing carbon fixation and suppressing photorespiration. Active inorganic carbon (Ci) uptake, Rubisco sequestration and interconversion between different Ci species catalyzed by carbonic anhydrases (CAs) are key components in the CCM, and an array of molecular regulatory elements is present to facilitate the sensing of CO2 availability, to regulate the expression of the CCM and to coordinate interplay between photosynthetic carbon metabolism and other metabolic processes in response to limiting CO2 conditions. This review intends to integrate our current understanding of the eukaryotic algal CCM and its interaction with carbon assimilation, based largely on Chlamydomonas as a model, and to illustrate how Chlamydomonas acclimates to limiting CO2 conditions and how its CCM is regulated.

Size scaling of extracellular carbonic anhydrase activity in centric marine diatoms

Many microalgae have a surface-associated extracellular carbonic anhydrase (eCA) that converts HCO3 (-) to CO2 for uptake and subsequent photosynthetic fixation. We investigated eCA activity and assessed its importance for photosynthetic CO2 supply in six centric diatom species spanning nearly the full range of cell sizes for centric diatoms (equivalent spherical radius 3-67 μm). Since larger cells are more susceptible to diffusion limitation, we hypothesized that eCA activity would increase with cell size as would its importance for CO2 supply. eCA activity did increase with cell size, increasing with cell radius by a size-scaling exponent of 2.6 ± 0.3. The rapid increase in eCA activity with cell radius keeps the absolute CO2 concentration difference between bulk seawater and the cell surface very low (<~0.2 μM) allowing high rates of CO2 uptake even for large diatoms. Although inhibiting eCA did reduce photosynthesis in the diatoms, there was no overall relationship between the extent of inhibition of photosynthesis and cell size. The only indication that eCA may be more important for larger diatoms was that photosynthesis in the smallest diatoms (<4 μm radius) was only affected by eCA inhibition when CO2 concentrations were very low, while photosynthesis in some larger diatoms was affected even at typical seawater CO2 concentrations. eCA is ubiquitous in centric marine diatoms, in contrast to other taxa where its presence is irregularly distributed among different species, and plays an important role in supplying CO2 for photosynthesis across the size spectrum.

The regulation of photosynthetic structure and function during nitrogen deprivation in Chlamydomonas reinhardtii

The accumulation of carbon storage compounds by many unicellular algae after nutrient deprivation occurs despite declines in their photosynthetic apparatus. To understand the regulation and roles of photosynthesis during this potentially bioenergetically valuable process, we analyzed photosynthetic structure and function after nitrogen deprivation in the model alga Chlamydomonas reinhardtii. Transcriptomic, proteomic, metabolite, and lipid profiling and microscopic time course data were combined with multiple measures of photosynthetic function. Levels of transcripts and proteins of photosystems I and II and most antenna genes fell with differing trajectories; thylakoid membrane lipid levels decreased, while their proportions remained similar and thylakoid membrane organization appeared to be preserved. Cellular chlorophyll (Chl) content decreased more than 2-fold within 24 h, and we conclude from transcript protein and (13)C labeling rates that Chl synthesis was down-regulated both pre- and posttranslationally and that Chl levels fell because of a rapid cessation in synthesis and dilution by cellular growth rather than because of degradation. Photosynthetically driven oxygen production and the efficiency of photosystem II as well as P700(+) reduction and electrochromic shift kinetics all decreased over the time course, without evidence of substantial energy overflow. The results also indicate that linear electron flow fell approximately 15% more than cyclic flow over the first 24 h. Comparing Calvin-Benson cycle transcript and enzyme levels with changes in photosynthetic (13)CO2 incorporation rates also pointed to a coordinated multilevel down-regulation of photosynthetic fluxes during starch synthesis before the induction of high triacylglycerol accumulation rates.

Dynamics of carbon-concentrating mechanism induction and protein relocalization during the dark-to-light transition in synchronized Chlamydomonas reinhardtii

In the model green alga Chlamydomonas reinhardtii, a carbon-concentrating mechanism (CCM) is induced under low CO2 in the light and comprises active inorganic carbon transport components, carbonic anhydrases, and aggregation of Rubisco in the chloroplast pyrenoid. Previous studies have focused predominantly on asynchronous cultures of cells grown under low versus high CO2. Here, we have investigated the dynamics of CCM activation in synchronized cells grown in dark/light cycles compared with induction under low CO2. The specific focus was to undertake detailed time course experiments comparing physiology and gene expression during the dark-to-light transition. First, the CCM could be fully induced 1 h before dawn, as measured by the photosynthetic affinity for inorganic carbon. This occurred in advance of maximum gene transcription and protein accumulation and contrasted with the coordinated induction observed under low CO2. Between 2 and 1 h before dawn, the proportion of Rubisco and the thylakoid lumen carbonic anhydrase in the pyrenoid rose substantially, coincident with increased CCM activity. Thus, other mechanisms are likely to activate the CCM before dawn, independent of gene transcription of known CCM components. Furthermore, this study highlights the value of using synchronized cells during the dark-to-light transition as an alternative means of investigating CCM induction.

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 (Ci). C. reinhardtii possesses a carbon concentrating mechanism (CCM) which can provide suitable amounts of Ci 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 Ci 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.

CO2 acquisition in Chlamydomonas acidophila is influenced mainly by CO2, not phosphorus, availability

The extremophilic green microalga Chlamydomonas acidophila grows in very acidic waters (pH 2.3-3.4), where CO2 is the sole inorganic carbon source. Previous work has revealed that the species can accumulate inorganic carbon (Ci) and exhibits high affinity CO2 utilization under low-CO2 (air-equilibrium) conditions, similar to organisms with an active CO2 concentrating mechanism (CCM), whereas both processes are down-regulated under high CO2 (4.5 % CO2) conditions. Responses of this species to phosphorus (Pi)-limited conditions suggested a contrasting regulation of the CCM characteristics. Therefore, we measured external carbonic anhydrase (CAext) activities and protein expression (CAH1), the internal pH, Ci accumulation, and CO2-utilization in cells adapted to high or low CO2 under Pi-replete and Pi-limited conditions. Results reveal that C. acidophila expressed CAext activity and expressed a protein cross-reacting with CAH1 (the CAext from Chlamydomonas reinhardtii). Although the function of this CA remains unclear, CAext activity and high affinity CO2 utilization were the highest under low CO2 conditions. C. acidophila accumulated Ci and expressed the CAH1 protein under all conditions tested, and C. reinhardtii also contained substantial amounts of CAH1 protein under Pi-limitation. In conclusion, Ci utilization is optimized in C. acidophila under ecologically relevant conditions, which may enable optimal survival in its extreme Ci- and Pi-limited habitat. The exact physiological and biochemical acclimation remains to be further studied.

Localization of putative carbonic anhydrases in the marine diatom, Thalassiosira pseudonana

Thirteen putative carbonic anhydrase (CA) genes have been identified in the marine multipolar centric diatom, Thalassiosira pseudonana, and two of these CAs have been localized previously. The first, an alpha CA (TpαCA1), was localized in the chloroplast stroma; the second, a zeta-type CA (TpζCA1), was localized to the periplasmic space. In the present study, cloning and localization of the remaining CAs were carried out. TpγCA2, TpγCA3, TpγCA4, TpγCA5, TpδCA1, TpδCA2, TpδCA3, and TpζCA1 were responsive to CO2 availability at the transcriptional level, being significantly reduced in cells grown at 0.4 % CO2, whereas TpαCA1, TpαCA2, TpαCA3, TpγCA1, and TpδCA4 transcript levels were constitutive with respect to CO2 concentration. Full-length cDNAs for TpγCA1, TpγCA2, TpγCA3, TpγCA4, TpδCA1, and TpδCA2 were isolated and fused with the enhanced-green fluorescent gene at their 3' termini. These GFP-fusion constructs were transformed into T. pseudonana, and the resulting GFP fusion products were localized using fluorescence microscopy. The δ-type TpδCA1 was localized on the periphery of the cell, strongly suggesting localization to the periplasmic space or the frustule. The δ-type TpδCA3 and the γ-type TpγCA2 were, respectively, localized in a periplastidal compartment and the cytosol. The δ-type TpδCA2, and the γ-types TpγCA1, 3, and 4 were localized in the mitochondria. The distribution of CAs in T. pseudonana contrasts notably with that of the raphid pennate diatom P. tricornutum, with likely consequences for CCM function including modes of CO2 acquisition, regions in which DIC is accumulated, and needs for minimizing CO2 leakage from the chloroplast.

Regulation of CCM genes in Chlamydomonas reinhardtii during conditions of light-dark cycles in synchronous cultures

We have investigated transcript level changes of CO(2)-concentrating mechanism (CCM) genes during light-dark (12 h:12 h) cycles in synchronized Chlamydomonas reinhardtii at air-level CO(2). CCM gene transcript levels vary at various times of light-dark cycles, even at same air-level CO(2). Transcripts of inorganic carbon transporter genes (HLA3, LCI1, CCP1, CCP2 and LCIA) and mitochondrial carbonic anhydrase genes (CAH4 and CAH5) are up regulated in light, following which their levels decline in dark. Contrastingly, transcripts of chloroplast carbonic anhydrases namely CAH6, CAH3 and LCIB are up regulated in dark. CAH3 and LCIB transcript levels reached maximum by the end of dark, followed by high expression into early light period. In contrast, CAH6 transcript level stayed high in dark, followed by high level even in light. Moreover, the up regulation of transcripts in dark was undone by high CO(2), suggesting that the dark induced CCM transcripts were regulated by CO(2) even in dark when CCM is absent. Thus while the CAH3 transcript level modulations appear not to positively correlate with that of CCM, the protein regulation matched with CCM status: in spite of high transcript levels in dark, CAH3 protein reached peak level only in light and localized entirely to pyrenoid, a site functionally relevant for CCM. Moreover, in dark, CAH3 protein level not only reduced but also the protein localized as a diffused pattern in chloroplast. We propose that transcription of most CCM genes, followed by protein level changes including their intracellular localization of a subset is subject to light-dark cycles.

Carbon acquisition and accumulation in microalgae Chlamydomonas: Insights from "omics" approaches

Understanding the processes and mechanisms of carbon acquisition and accumulation in microalgae is fundamental to enhance the cellular capabilities aimed to environmental and industrial applications. The "omics" approaches have greatly contributed to expanding the knowledge on these carbon-related cellular responses, reporting large data sets on microalgae transcriptome, proteome and metabolome. This review emphasizes the advances made on Chlamydomonas exploration; however, some knowledge acquired from studying this model organism, may be extrapolated to close algae species. The large data sets available for this organism revealed the identity of a vast range of genes and proteins which are integrating carbon-related mechanisms. Nevertheless, these data sets have also highlighted the need for integrative analysis in order to fully explore the information enclosed. Here, some of the main results from "omics" approaches which may contribute to the understanding of carbon acquisition and accumulation in Chlamydomonas were reviewed and possible applications were discussed.

BIOLOGICAL SIGNIFICANCE

A number of important publications in the field of "omics" technologies have been published reporting studies of the model green microalga Chlamydomonas reinhardtii and related to microalgal biomass production. However, there are only few attempts to integrate these data. Publications showing the results from "omics" approaches, such as transcriptome, metabolome and proteome, focused in the study of mechanisms of carbon acquisition and accumulation in microalgae were reviewed. This review contributes to highlight the knowledge recently generated on such "omics" studies and it discusses how these results may be important for the advance of applied sciences, such as microalgae biotechnology.

Quantification of extracellular carbonic anhydrase activity in two marine diatoms and investigation of its role

Many microalgae induce an extracellular carbonic anhydrase (eCA), associated with the cell surface, at low carbon dioxide (CO2) concentrations. This enzyme is thought to aid inorganic carbon uptake by generating CO2 at the cell surface, but alternative roles have been proposed. We developed a new approach to quantify eCA activity in which a reaction-diffusion model is fit to data on (18)O removal from inorganic carbon. In contrast to previous methods, eCA activity is treated as a surface process, allowing the effects of eCA on cell boundary-layer chemistry to be assessed. Using this approach, we measured eCA activity in two marine diatoms (Thalassiosira pseudonana and Thalassiosira weissflogii), characterized the kinetics of this enzyme, and studied its regulation as a function of culture pH and CO2 concentration. In support of a role for eCA in CO2 supply, eCA activity specifically responded to low CO2 rather than to changes in pH or HCO3(-), and the rates of eCA activity are nearly optimal for maintaining cell surface CO2 concentrations near those in the bulk solution. Although the CO2 gradients abolished by eCA are small (less than 0.5 μm concentration difference between bulk and cell surface), CO2 uptake in these diatoms is a passive process driven by small concentration gradients. Analysis of the effects of short-term and long-term eCA inhibition on photosynthesis and growth indicates that eCA provides a small energetic benefit by reducing the surface-to-bulk CO2 gradient. Alternative roles for eCA in CO2 recovery as HCO3(-) and surface pH regulation were investigated, but eCA was found to have minimal effects on these processes.

The proteome of copper, iron, zinc, and manganese micronutrient deficiency in Chlamydomonas reinhardtii

Trace metals such as copper, iron, zinc, and manganese play important roles in several biochemical processes, including respiration and photosynthesis. Using a label-free, quantitative proteomics strategy (MS(E)), we examined the effect of deficiencies in these micronutrients on the soluble proteome of Chlamydomonas reinhardtii. We quantified >10(3) proteins with abundances within a dynamic range of 3 to 4 orders of magnitude and demonstrated statistically significant changes in ~200 proteins in each metal-deficient growth condition relative to nutrient-replete media. Through analysis of Pearson's coefficient, we also examined the correlation between protein abundance and transcript abundance (as determined via RNA-Seq analysis) and found moderate correlations under all nutritional states. Interestingly, in a subset of transcripts known to significantly change in abundance in metal-replete and metal-deficient conditions, the correlation to protein abundance is much stronger. Examples of new discoveries highlighted in this work include the accumulation of O(2) labile, anaerobiosis-related enzymes (Hyd1, Pfr1, and Hcp2) in copper-deficient cells; co-variation of Cgl78/Ycf54 and coprogen oxidase; the loss of various stromal and lumenal photosynthesis-related proteins, including plastocyanin, in iron-limited cells; a large accumulation (from undetectable amounts to over 1,000 zmol/cell) of two COG0523 domain-containing proteins in zinc-deficient cells; and the preservation of photosynthesis proteins in manganese-deficient cells despite known losses in photosynthetic function in this condition.

Redox regulation of carbonic anhydrases via thioredoxin in chloroplast of the marine diatom Phaeodactylum tricornutum

Thioredoxins (Trxs) are important regulators of photosynthetic fixation of CO(2) and nitrogen in plant chloroplasts. To date, they have been considered to play a minor role in controlling the Calvin cycle in marine diatoms, aquatic primary producers, although diatoms possess a set of plastidic Trxs. In this study we examined the influences of the redox state and the involvement of Trxs in the enzymatic activities of pyrenoidal carbonic anhydrases, PtCA1 and PtCA2, in the marine diatom Phaeodactylum tricornutum. The recombinant mature PtCA1 and -2 (mPtCA1 and -2) were completely inactivated following oxidation by 50 μm CuCl(2), whereas DTT activated CAs in a concentration-dependent manner. The maximum activity of mPtCAs in the presence of 6 mm reduced DTT increased significantly by addition of 10 μm Trxs from Arabidopsis thaliana (AtTrx-f2 and -m2) and 5 μm Trxs from P. tricornutum (PtTrxF and -M). Analyses of mPtCA activation by Trxs in the presence of DTT revealed that the maximum mPtCA1 activity was enhanced ∼3-fold in the presence of Trx, whereas mPtCA2 was only weakly activated by Trxs, and that PtTrxs activate PtCAs more efficiently compared with AtTrxs. Site-directed mutagenesis of potential disulfide-forming cysteines in mPtCA1 and mPtCA2 resulted in a lack of oxidative inactivation of both mPtCAs. These results reveal the first direct evidence of a target of plastidic Trxs in diatoms, indicating that Trxs may participate in the redox control of inorganic carbon flow in the pyrenoid, a focal point of the CO(2)-concentrating mechanism.

Photosynthetic characteristics of a multicellular green alga Volvox carteri in response to external CO2 levels possibly regulated by CCM1/CIA5 ortholog

When CO(2) supply is limited, aquatic photosynthetic organisms induce a CO(2)-concentrating mechanism (CCM) and acclimate to the CO(2)-limiting environment. Although the CCM is well studied in unicellular green algae such as Chlamydomonas reinhardtii, physiological aspects of the CCM and its associated genes in multicellular algae are poorly understood. In this study, by measuring photosynthetic affinity for CO(2), we present physiological data in support of a CCM in a multicellular green alga, Volvox carteri. The low-CO(2)-grown Volvox cells showed much higher affinity for inorganic carbon compared with high-CO(2)-grown cells. Addition of ethoxyzolamide, a membrane-permeable carbonic anhydrase inhibitor, to the culture remarkably reduced the photosynthetic affinity of low-CO(2) grown Volvox cells, indicating that an intracellular carbonic anhydrase contributed to the Volvox CCM. We also isolated a gene encoding a protein orthologous to CCM1/CIA5, a master regulator of the CCM in Chlamydomonas, from Volvox carteri. Volvox CCM1 encoded a protein with 701 amino acid residues showing 51.1% sequence identity with Chlamydomonas CCM1. Comparison of Volvox and Chlamydomonas CCM1 revealed a highly conserved N-terminal region containing zinc-binding amino acid residues, putative nuclear localization and export signals, and a C-terminal region containing a putative LXXLL protein-protein interaction motif. Based on these results, we discuss the physiological and genetic aspects of the CCM in Chlamydomonas and Volvox.

Recent progresses on the genetic basis of the regulation of CO2 acquisition systems in response to CO2 concentration

Marine diatoms, the major primary producer in ocean environment, are known to take up both CO(2) and HCO(3)(-) in seawater and efficiently concentrate them intracellularly, which enable diatom cells to perform high-affinity photosynthesis under limiting CO(2). However, mechanisms so far proposed for the inorganic carbon acquisition in marine diatoms are significantly diverse despite that physiological studies on this aspect have been done with only limited number of species. There are two major hypotheses about this; that is, they take up and concentrate both CO(2) and HCO(3)(-) as inorganic forms, and efficiently supply CO(2) to Rubisco by an aid of carbonic anhydrases (biophysical CO(2)-concentrating mechanism: CCM); and as the other hypothesis, biochemical conversion of HCO(3)(-) into C(4) compounds may play a major role to supply concentrated CO(2) to Rubisco. At moment however, physiological evidence for these hypotheses were not related well to molecular level evidence. In this study, recent progresses in molecular studies on diatom-carbon-metabolism genes were related to the physiological aspects of carbon acquisition. Furthermore, we discussed the mechanisms regulating CO(2) acquisition systems in response to changes in pCO(2). Recent findings about the participation of cAMP in the signaling pathway of CO(2) concentration strongly suggested the occurrences of mammalian-type-signaling pathways in diatoms to respond to changes in pCO(2). In fact, there were considerable numbers of putative adenylyl cyclases, which may take part in the processes of CO(2) signal capturing.

Insertional suppressors of Chlamydomonas reinhardtii that restore growth of air-dier lcib mutants in low CO2

Chlamydomonas reinhardtii and other microalgae show adaptive changes to limiting CO(2) conditions by induction of CO(2)-concentrating mechanisms. The limiting-CO(2)-inducible gene, LCIB, encodes a soluble plastid protein and is proposed to play a role in trapping CO(2) released by CAH3 (thylakoid lumen carbonic anhydrase) catalyzed dehydration of accumulated Ci, especially in low CO(2) (L-CO(2); ~0.04% CO(2)) conditions. To gain further insight into the mechanisms of Ci uptake and accumulation in L-CO(2) acclimated C. reinhardtii, we performed an insertional mutagenesis screen to isolate extragenic suppressors that restore the growth of lcib mutants (pmp1 and ad1) in L-CO(2). Four independent suppressors are described here and classified by their photosynthetic affinities for Ci and expression patterns of known limiting-CO(2)-inducible transcripts. Genetic analysis of the four suppressors identified two allelic, dominant suppressors (su4 and su5), and two recessive suppressors (su1 and su8). Consistent with the suppression phenotype, both the relative affinities of photosynthetic O(2) evolution and internal Ci accumulation in all four suppressors were substantially increased relative to pmp1/ad1 in L-CO(2) acclimated cells. The relative affinities of pmp-su1 and ad-su8 for Ci were nearly the same as wild type, but that of pmp-su4/su5 was intermediate between pmp-su1 and pmp1. Also, the interactions between lcib mutations and each of the three suppressors varied over the range of CO(2) acclimation states. Our results suggest complex contributions of LCIB-dependent and independent active Ci uptake/accumulation systems in various CO(2) acclimation states and therefore provide new clues about the roles played by LCIB in limiting Ci acclimation.

Acclimation to low or limiting CO2 in non-synchronous Chlamydomonas causes a transient synchronization of the cell division cycle

Acclimation of Chlamydomonas reinhardtii (hereafter, Chlamydomonas) to low or limiting CO(2) or inorganic carbon (C(i)) has been studied fairly extensively with regard to the mechanisms underlying the inducible C(i) acquisition systems and the signal transduction pathway involved in recognizing and responding to decreased C(i) availability. Investigation of low C(i )acclimation responses typically is performed with non-synchronous cultures grown in continuous light to avoid any effects of the cell division cycle (CDC) confounding interpretation of acclimation responses. However, little is known about whether acclimation to low C(i) might affect the distribution of cells among the various stages of the CDC. To investigate the effects of a limiting-C(i) challenge on the CDC of Chlamydomonas, flow cytometry was used to monitor the distribution of cells among the CDC stages in both synchronous and non-synchronous cultures during acclimation to low or limiting C(i). When faced with C(i) limitation, non-synchronous cultures of Chlamydomonas undergo transient synchronization as those cells past the Commitment point of the CDC undergo division, while the remainder of the cells pause their growth in early G-phase, with the result that the cells all accumulate in early G-phase, appearing transiently synchronized until acclimated sufficiently to the decreased C(i) for growth to resume. This perturbation of the CDC by a limiting-C(i) challenge has important implications for the interpretation of gene expression and other responses apparently induced by low or limiting C(i).

The carbonic anhydrase isoforms of Chlamydomonas reinhardtii: intracellular location, expression, and physiological roles

Aquatic photosynthetic organisms, such as the green alga Chlamydomonas reinhardtii, respond to low CO(2) conditions by inducing a CO(2) concentrating mechanism (CCM). Carbonic anhydrases (CAs) are important components of the CCM. CAs are zinc-containing metalloenzymes that catalyze the reversible interconversion of CO(2) and HCO(3)(-). In C. reinhardtii, there are at least 12 genes that encode CA isoforms, including three alpha, six beta, and three gamma or gamma-like CAs. The expression of the three alpha and six beta genes has been measured from cells grown on elevated CO(2) (having no active CCM) versus cells growing on low levels of CO(2) (with an active CCM) using northern blots, differential hybridization to DNA chips and quantitative RT-PCR. Recent RNA-seq profiles add to our knowledge of the expression of all of the CA genes. In addition, protein content for some of the CA isoforms was estimated using antibodies corresponding to the specific CA isoforms: CAH1/2, CAH3, CAH4/5, CAH6, and CAH7. The intracellular location of each of the CA isoforms was elucidated using immunolocalization and cell fractionation techniques. Combining these results with previous studies using CA mutant strains, we will discuss possible physiological roles of the CA isoforms concentrating on how these CAs might contribute to the acquisition and retention of CO(2) in C. reinhardtii.

Expression of a low CO₂-inducible protein, LCI1, increases inorganic carbon uptake in the green alga Chlamydomonas reinhardtii

Aquatic photosynthetic organisms can modulate their photosynthesis to acclimate to CO₂-limiting stress by inducing a carbon-concentrating mechanism (CCM) that includes carbonic anhydrases and inorganic carbon (Ci) transporters. However, to date, Ci-specific transporters have not been well characterized in eukaryotic algae. Previously, a Chlamydomonas reinhardtii mutant (lcr1) was identified that was missing a Myb transcription factor. This mutant had reduced light-dependent CO₂ gas exchange (LCE) activity when grown under CO₂-limiting conditions and did not induce the CAH1 gene encoding a periplasmic carbonic anhydrase, as well as two as yet uncharacterized genes, LCI1 and LCI6. In this study, LCI1 was placed under the control of the nitrate reductase promoter, allowing for the induction of LCI1 expression by nitrate in the absence of other CCM components. When the expression of LCI1 was induced in the lcr1 mutant under CO₂-enriched conditions, the cells showed an increase in LCE activity, internal Ci accumulation, and photosynthetic affinity for Ci. From experiments using indirect immunofluorescence, LCI1-green fluorescent protein fusions, and cell fractionation procedures, it appears that LCI1 is mainly localized to the plasma membrane. These results provide strong evidence that LCI1 may contribute to the CCM as a component of the Ci transport machinery in the plasma membrane.

Thylakoid lumen carbonic anhydrase (CAH3) mutation suppresses air-Dier phenotype of LCIB mutant in Chlamydomonas reinhardtii

An active CO2-concentrating mechanism is induced when Chlamydomonas reinhardtii acclimates to limiting inorganic carbon (Ci), either low-CO2 (L-CO2; air level; approximately 0.04% CO2) or very low-CO2 (VL-CO2; approximately 0.01% CO2) conditions. A mutant, ad1, which is defective in the limiting-CO2-inducible, plastid-localized LCIB, can grow in high-CO2 or VL-CO2 conditions but dies in L-CO2, indicating a deficiency in a L-CO2-specific Ci uptake and accumulation system. In this study, we identified two ad1 suppressors that can grow in L-CO2 but die in VL-CO2. Molecular analyses revealed that both suppressors have mutations in the CAH3 gene, which encodes a thylakoid lumen localized carbonic anhydrase. Photosynthetic rates of L-CO2-acclimated suppressors under acclimation CO2 concentrations were more than 2-fold higher than ad1, apparently resulting from a more than 20-fold increase in the intracellular concentration of Ci as measured by direct Ci uptake. However, photosynthetic rates of VL-CO2-acclimated cells under acclimation CO2 concentrations were too low to support growth in spite of a significantly elevated intracellular Ci concentration. We conclude that LCIB functions downstream of CAH3 in the CO2-concentrating mechanism and probably plays a role in trapping CO2 released by CAH3 dehydration of accumulated Ci. Apparently dehydration by the chloroplast stromal carbonic anhydrase CAH6 of the very high internal Ci caused by the defect in CAH3 provides Rubisco sufficient CO2 to support growth in L-CO2-acclimated cells, but not in VL-CO2-acclimated cells, even in the absence of LCIB.

An external delta-carbonic anhydrase in a free-living marine dinoflagellate may circumvent diffusion-limited carbon acquisition

The oceans globally constitute an important sink for carbon dioxide (CO(2)) due to phytoplankton photosynthesis. However, the marine environment imposes serious restraints to carbon fixation. First, the equilibrium between CO(2) and bicarbonate (HCO(3)(-)) is pH dependent, and, in normal, slightly alkaline seawater, [CO(2)] is typically low (approximately 10 mum). Second, the rate of CO(2) diffusion in seawater is slow, so, for any cells unable to take up bicarbonate efficiently, photosynthesis could become carbon limited due to depletion of CO(2) from their immediate vicinity. This may be especially problematic for those dinoflagellates using a form II Rubisco because this form is less oxygen tolerant than the usually found form I enzyme. We have identified a carbonic anhydrase (CA) from the free-living marine dinoflagellate Lingulodinium polyedrum that appears to play a role in carbon acquisition. This CA shares 60% sequence identity with delta-class CAs, isoforms so far found only in marine algae. Immunoelectron microscopy indicates that this enzyme is associated exclusively with the plasma membrane. Furthermore, this enzyme appears to be exposed to the external medium as determined by whole-cell CA assays and vectorial labeling of cell surface proteins with (125)I. The fixation of (14)CO(2) is strongly pH dependent, suggesting preferential uptake of CO(2) rather than HCO(3)(-), and photosynthetic rates decrease in the presence of 1 mm acetazolamide, a non-membrane-permeable CA inhibitor. This constitutes the first CA identified in the dinoflagellates, and, taken together, our results suggest that this enzyme may help to increase CO(2) availability at the cell surface.

Localization and targeting mechanisms of two chloroplastic beta-carbonic anhydrases in the marine diatom Phaeodactylum tricornutum

Two beta-CA genes, ptca1 and ptca2, were previously isolated from the marine diatom Phaeodactylum tricornutum and shown to be regulated by ambient [CO(2)] at the transcriptional levels. The product of ptca1, PtCA1, was also shown to be localized to the chloroplast as clumped particles. Both ptca1 and 2 encode putative N-terminal signal peptides of 19 amino acids. In the present study, the C-terminal region of the 46 amino acid presequence of PtCA1 (Pre46AA) was truncated to investigate the function of this region. DNA sequences, which encode the N-terminal 19, 23, 24, 34 or 44 polypeptides of Pre46AA, were fused with the sequence that encodes the mature protein, PtCA1. These constructs were fused with the enhanced-green fluorescent protein gene, egfp, and expressed in P. tricornutum. Fluorescent microscopy of expressed green fluorescent protein (GFP) showed that presequences of PtCA1 longer than the initial N-terminal 23 amino acids successfully sorted the PtCA1::GFP fusion into chloroplasts, whereas those shorter than 23 amino acids did not. These results indicate that the four amino acids after the endoplasmic reticulum signal peptide cleavage site are required as a chloroplast-targeting signal. Ala(19) Phe(20) is known to be the highly conserved transit motif among presequences of nuclear-encoded chloroplastic proteins in diatoms; however, the corresponding amino acid sequence deduced from the ptca2 was Ala(19) Leu(20). Substitution of Phe(20) in PtCA1 with Leu did not alter the localization of PtCA1, indicating that the chloroplast-targeting motif possesses some alternative pattern and that PtCA2 could be sorted to chloroplast via a process similar to that of PtCA1. The ptca2 cDNA was isolated, fused at the 3' terminus with the egfp and introduced into P. tricornutum cells. Expressed PtCA2::GFP fusion was clearly localized by chlorophyll fluorescence in the chloroplast of P. tricornutum as clumped particles, which was strikingly similar to the localization of PtCA1.

Identification and characterization of two closely related beta-carbonic anhydrases from Chlamydomonas reinhardtii

Aquatic photosynthetic organisms such as the green alga Chlamydomonas reinhardtii respond to low-CO(2) conditions by inducing a CO(2) concentrating mechanism (CCM). Important components of the CCM are the carbonic anhydrases (CAs), zinc metalloenzymes that catalyze the interconversion of CO(2) and HCO(-)(3). Six CAs have previously been identified in C. reinhardtii. Here, we identify and characterize two additional beta-type CAs. These two CAs are closely related beta-type CAs and have been designated as CAH7 and CAH8. Conceptual translation shows that CAH7 and CAH8 encode proteins of 399 and 333 amino acids, respectively, and they contain targeting sequences. An unusual characteristic of these two CAs is that they have carboxy-terminal extensions containing a hydrophobic sequence. Both these CAs are constitutively expressed at the transcript and protein level. The CAH7 and CAH8 open reading frames were cloned in the overexpression vector pMal-c2x and expressed as recombinant proteins. Activity assays showed that CAH7 and CAH8 are both active CAs. Antibodies were raised against both CAH7 and CAH8, and immunolocalization studies showed that CAH8 was localized in the periplasmic space. A possible role for CAH8 in the inorganic carbon acquisition by C. reinhardtii is discussed.

Characterization and expression analysis of genes encoding alpha and beta carbonic anhydrases in Arabidopsis

Carbonic anhydrases (CAs) are Zn-containing metalloenzymes that catalyse the reversible hydration of CO(2). We investigated the alphaCA and betaCA families in Arabidopsis, which contain eight alphaCA (At alphaCA1-8) and six betaCA genes (At betaCA1-6). Analyses of expressed sequence tags (ESTs) from The Arabidopsis Information Resource (TAIR) database indicate that all the betaCA encoding sequences, but only three of the At alphaCA, are expressed. Using semi-quantitative PCR experiments, functional CA genes were more strongly expressed in green tissue, but strong expression was also found in roots for betaCA3, betaCA6 and alphaCA2. Two alphaCA genes were shown to respond to the CO(2) environment, while the others were unresponsive. Using the green fluorescent reporter protein gene fused with cDNA sequences coding for betaCAs, we provided evidence that betaCAs were targeted to specific subcellular compartments: betaCA1 and betaCA5 were targeted to the chloroplast, betaCA2 and betaCA3 to the cytosol, betaCA4 to the plasma membrane and betaCA6 to the mitochondria. The targeting and the pattern of gene expression suggest that CA isoforms play specific roles in subcellular compartments, tissues and organs. The data indicate that other CA isoforms than the well-characterized betaCA1 may contribute to the CO(2) transfer in the cell to the catalytic site of ribulose 1.5-bisphosphate carboxylase/oxygenase (Rubisco).

Comparative proteomics of high light stress in the model algaChlamydomonas reinhardtii

High light (HL) stress adversely affects growth, productivity and viability of photosynthetic organisms. The green alga Chlamydomonas reinhardtii is a model system to study photosynthesis and light stress. Comparative proteomics of wild-type and two very high light (VHL)-resistant mutants, VHL(R)-S4 and VHL(R)-S9, revealed complex alterations in response to excess light. A two-dimensional reference map of the soluble subproteome was constructed representing about 1500 proteins. A total of 83 proteins from various metabolic pathways were identified by peptide mass fingerprinting. Quantitative comparisons of 444 proteins showed 105 significantly changed proteins between wild type and mutants under different light conditions. Commonly, more proteins were decreased than increased, but different proteins were affected in each genotype. Proteins uniquely altered in either VHL(R) mutant may be involved in VHL resistance. Such candidate proteins similarly altered without light stress, thus possibly contributing to "pre-adaptation" of mutants to VHL, included decreased levels of a DEAD box RNA helicase (VHL(R)-S4) and NAB1 and RB38 proteins (VHL(R)-S9), and increased levels of an oxygen evolving enhancer 1 (OEE1) isoform and an unknown protein (VHL(R)-S4). Changes from increased levels in HL to decreased levels in excess light, included OEE1 (VHL(R)-S9) or the reverse change for NAB1, RB38, beta-carbonic anhydrase and an ABC transporter-like protein (VHL(R)-S4).

The carbonic anhydrase gene families ofChlamydomonas reinhardtii

Carbonic anhydrases (CAs) are zinc-containing metalloenzymes that catalyze the reversible interconversion of CO2and HCO3–. Aquatic photosynthetic organisms have evolved different forms of CO2-concentrating mechanisms to aid Rubisco in capturing CO2from the surrounding environment. One aspect of all CO2-concentrating mechanisms is the critical roles played by various specially localized extracellular and intracellular CAs. There are three evolutionarily unrelated CA families designated α-, β-, and γ-CA. In the green alga, Chlamydomonas reinhardtii Dangeard, eight CAs have now been identified, including three α-CAs and five β-CAs. In addition, C. reinhardtii has another CA-like gene, Glp1 that is similar to known γ-CAs. To characterize these different CA isoforms, some of the CA genes have been overexpressed to determine whether the proteins have CA activity and to generate antibodies for in vivo immunolocalization. The CA proteins Cah3, Cah6, and Cah8, and the γ-CA-like protein, Glp1, have been overexpressed. Cah3, Cah6, and Cah8 have CA activity, but Glp1 does not. At least two of these proteins, Cah3 and Cah6, are localized to the chloroplast. Using immunolocalization and sequence analyses, we have determined that Cah6 is located to the chloroplast stroma and confirmed that Cah3 is localized to the chloroplast thylakoid lumen. Activity assays show that Cah3 is 100 times more sensitive to sulfonamides than Cah6. We present a model on how these two chloroplast CAs might participate in the CO2-concentrating mechanism of C. reinhardtii. Key words: carbonic anhydrase, CO2-concentrating mechanism, Chlamydomonas, immunolocalization.

Identification and characterization of a new carbonic anhydrase in the marine diatom Phaeodactylum tricornutum

A cDNA encoding a new isoenzyme of β-type carbonic anhydrase (CA; EC 4.2.1.1) in the marine diatom Phaeodactylum tricornutum Bohlin has been cloned. The cDNA contained an open reading frame of 819 bp, which encodes a polypeptide of 273 amino acids. This gene, which is designated as ptca2, was found to be highly homologous (83% at the nucleotide level) to the previously isolated intracellular β-CA gene from Phaeodactylum tricornutum (ptca1). Comparison of the deduced amino acid sequence of ptca2 with β-CAs from other sources demonstrated that PtCA2 possesses the completely conserved zinc coordination residues of β-CA. The N-terminus 19 amino acid sequence of PtCA2 was predicted to be an endoplasmic reticulum-targeting signal, suggesting localization of the protein in an organelle or in the periplasmic space. Quantitative analysis of mRNA accumulation of ptca2 using real-time polymerase chain reaction revealed a significant level of mRNA accumulation even under 5% CO2 and a 3.5-fold increase in accumulation upon acclimation of the diatom to air. This indicates that ptca2 belongs to a constitutive class of enzyme that responds only weakly to the ambient CO2 concentration. The sequences of both ptca1 and ptca2 were shown to be grouped into a phylogeny that is composed of mixture of sequences from the eucarya and procarya domains, including sequences from the red alga Porphyridium purpureum, the green alga Coccomyxa, the red mold Neurospora crassa, and the yeast Saccharomyces cerevisiae.Key words: carbonic anhydrase, marine diatom, inorganic carbon concentrating mechanism (CCM), Phaeodactylum tricornutum.

Disruption of the glycolate dehydrogenase gene in the high-CO2-requiring mutant HCR89 ofChlamydomonas reinhardtii

One of the most notable contrasts between the photorespiratory pathway of higher plants and that of many of the green algae including Chlamydomonas reinhardtii lies in the enzymes that serve for oxidation of glycolate to glyoxylate. The gene disrupted by insertional mutagenesis in a high-CO2-requiring mutant, HCR89, of C. reinhardtii was determined to encode glycolate dehydrogenase (EC 1.1.99.14), which serves as the counterpart of glycolate oxidase (EC 1.1.3.15) in classical higher plant photorespiration. Neither glycolate nor D-lactate oxidation from the membrane fraction of HCR89 was detected. Excretion of over-accumulated glycolate into media due to the absence of glycolate dehydrogenase activity was observed for HCR89 under both high- and low-CO2conditions. Chlamydomonas glycolate dehydrogenase, CrGDH, with a molecular mass of 118 851 Da, comprises a relatively hydrophobic N-terminal region, a FAD-containing domain homologous to the D subunit of the glycolate oxidase complex from Escherischia coli, and an iron–sulfur cluster containing domain homologous to the C subunit of anaerobic glycerol-3-phosphate dehydrogenase complex from Escherichia coli. The second Cys residue in the second iron–sulfur cluster motif of CrGDH is replaced by Asp, as CxxDxxCxxxCP, indicating the second iron–sulfur cluster coordinates most likely 3Fe–4S instead of 4Fe–4S. The membrane association of the glycolate dehydrogenase activity agrees with three predicted transmembrane regions on the iron–sulfur domain.Key words: algae, Chlamydomonas, CO2, glycolate, lactate, mitochondria, photorespiration, photosynthesis.

Growth, photosynthesis, and gene expression in Chlamydomonas over a range of CO2 concentrations and CO2/O2 ratios: CO2 regulates multiple acclimation states

Growth, photosynthesis, and induction of two low CO2-inducible genes of Chlamydomonas reinhardtii Dangeard strain CC125 were quantified in a range of physiologically relevant CO2 and O2 concentrations (5%–0.005% CO2 and 20% or 2% O2) using airlift bioreactors to facilitate the simultaneous measurement of both growth and in situ photosynthetic rates. Within these CO2 concentration ranges, O2 concentrations (20% vs. 2%) had no discernable effect on growth, photosynthetic rate, or induction of the periplasmic carbonic anhydrase (Cah1) and glycolate dehydrogenase (Gdh) genes in wild-type C. reinhardtii. These results failed to support the hypothesis that the CO2/O2 ratio plays any role in signaling for the up-regulation of limiting CO2-induced genes and (or) of the CO2-concentrating mechanism (CCM). The mRNA abundance of the Cah1 and Gdh genes appeared to be regulated in concert, suggesting co-regulation by the same signaling pathway, which, because of a lack of an O2 effect, seems unlikely to involve photorespiration or a photorespiratory metabolite. Instead, it appeared that the CO2 concentration alone was responsible for regulation of limiting CO2 acclimation responses. Based on growth, photosynthesis, and gene expression characteristics, three distinct CO2-regulated physiological states were recognized within the studied parameters, a high CO2 (5%–0.5%) state, a low CO2 (0.4%–0.03%) state, and a very low CO2 (0.01%–0.005%) state. Induction of Cah1 expression and Gdh up-regulation occurred at a CO2 concentration between 0.5% and 0.4% CO2, delineating the high from the low CO2 states. Photosynthetic characteristics also were distinct in the three CO2-regulated physiological states, e.g., the estimated K0.5(CO2) of the high CO2, low CO2, and very low CO2 states were 72, 10, and 0.9 µmol·L–1 CO2, respectively. In addition to a greater photosynthetic CO2 affinity, the very low CO2 state could be distinguished from the low CO2 state by an increased cell-doubling time and a smaller cell size.Key words: algae, Chlamydomonas, CO2, gene expression, induction, photorespiration, photosynthesis.

CO2 concentrating mechanisms in algae: mechanisms, environmental modulation, and evolution

The evolution of organisms capable of oxygenic photosynthesis paralleled a long-term reduction in atmospheric CO2 and the increase in O2. Consequently, the competition between O2 and CO2 for the active sites of RUBISCO became more and more restrictive to the rate of photosynthesis. In coping with this situation, many algae and some higher plants acquired mechanisms that use energy to increase the CO2 concentrations (CO2 concentrating mechanisms, CCMs) in the proximity of RUBISCO. A number of CCM variants are now found among the different groups of algae. Modulating the CCMs may be crucial in the energetic and nutritional budgets of a cell, and a multitude of environmental factors can exert regulatory effects on the expression of the CCM components. We discuss the diversity of CCMs, their evolutionary origins, and the role of the environment in CCM modulation.

Expression profiling-based identification of CO2-responsive genes regulated by CCM1 controlling a carbon-concentrating mechanism in Chlamydomonas reinhardtii

Photosynthetic acclimation to CO2-limiting stress is associated with control of genetic and physiological responses through a signal transduction pathway, followed by integrated monitoring of the environmental changes. Although several CO2-responsive genes have been previously isolated, genome-wide analysis has not been applied to the isolation of CO2-responsive genes that may function as part of a carbon-concentrating mechanism (CCM) in photosynthetic eukaryotes. By comparing expression profiles of cells grown under CO2-rich conditions with those of cells grown under CO2-limiting conditions using a cDNA membrane array containing 10,368 expressed sequence tags, 51 low-CO2 inducible genes and 32 genes repressed by low CO2 whose mRNA levels were changed more than 2.5-fold in Chlamydomonas reinhardtii Dangeard were detected. The fact that the induction of almost all low-CO2 inducible genes was impaired in the ccm1 mutant suggests that CCM1 is a master regulator of CCM through putative low-CO2 signal transduction pathways. Among low-CO2 inducible genes, two novel genes, LciA and LciB, were identified, which may be involved in inorganic carbon transport. Possible functions of low-CO2 inducible and/or CCM1-regulated genes are discussed in relation to the CCM.

The novel Myb transcription factor LCR1 regulates the CO2-responsive gene Cah1, encoding a periplasmic carbonic anhydrase in Chlamydomonas reinhardtii

Chlamydomonas reinhardtii acclimates to CO2-limiting stress by inducing a set of genes for a carbon-concentrating mechanism (CCM). This set includes the gene Cah1, which encodes a periplasmic carbonic anhydrase. Although physiological aspects of CO2response have been extensively studied, regulatory components, such as transcription factors involved in the acclimation, have not been well described in eukaryotic microalgae. Using an arylsulfatase gene driven by the Cah1 promoter, a regulatory mutant of Cah1 was isolated and named lcr1 (for low-CO2 stress response). The photosynthetic affinity for inorganic carbon of lcr1 was reduced compared with that of wild-type cells. Expression of three low-CO2-inducible genes, Cah1, Lci1, and Lci6, were regulated by LCR1 as shown by cDNA array and RNA gel blot analyses. The Lcr1 gene encodes a protein of 602 amino acids containing a single Myb domain, which binds to the Cah1-promoter region. Expression of Lcr1 was induced by lowering CO2 levels and controlled by the regulatory factor CCM1. These results suggest that LCR1 transmits the low CO2 signal to at least three CO2-responsive genes and then fully induces CCM.

The Chlamydomonas reinhardtii cia3 mutant lacking a thylakoid lumen-localized carbonic anhydrase is limited by CO2 supply to rubisco and not photosystem II function in vivo

The Chlamydomonas reinhardtii cia3 mutant has a phenotype indicating that it requires high-CO(2) levels for effective photosynthesis and growth. It was initially proposed that this mutant was defective in a carbonic anhydrase (CA) that was a key component of the photosynthetic CO(2)-concentrating mechanism (CCM). However, more recent identification of the genetic lesion as a defect in a lumenal CA associated with photosystem II (PSII) has raised questions about the role of this CA in either the CCM or PSII function. To resolve the role of this lumenal CA, we re-examined the physiology of the cia3 mutant. We confirmed and extended previous gas exchange analyses by using membrane-inlet mass spectrometry to monitor(16)O(2),(18)O(2), and CO(2) fluxes in vivo. The results demonstrate that PSII electron transport is not limited in the cia3 mutant at low inorganic carbon (Ci). We also measured metabolite pools sizes and showed that the RuBP pool does not fall to abnormally low levels at low Ci as might be expected by a photosynthetic electron transport or ATP generation limitation. Overall, the results demonstrate that under low Ci conditions, the mutant lacks the ability to supply Rubisco with adequate CO(2) for effective CO(2) fixation and is not limited directly by any aspect of PSII function. We conclude that the thylakoid CA is primarily required for the proper functioning of the CCM at low Ci by providing an ample supply of CO(2) for Rubisco.

Isolation and characterisation of Chlamydomonas reinhardtii mutants with an impaired CO2-concentrating mechanism

In order to identify new genes involved in the carbon-concentrating mechanism of Chlamydomonas reinhardtii (Dangeard), high-CO2-requiring mutants were isolated by insertional mutagenesis after transformation of strain CC1618 with a plasmid carrying Arg7 as a selectable marker gene. Six mutants were classified by their growth behaviour under ambient CO2, the affinity of the CO2-concentrating mechanism for inorganic carbon and the expression of known low-CO2-inducible proteins. The mass-spectrometric measurement of carbonic anhydrase activity and CO2/HCO3- transport revealed that four of the mutants are unable to induce a high-affinity carbon-concentrating mechanism. The expression of various carbonic anhydrases and chloroplast inner envelope polypeptides was examined with Western Blots. While three high-CO2-requiring mutants showed abnormal expression patterns, one matched the wild type. With Southern blots the total number and structure of the insertion events were determined to select possible candidates for plasmid recovery. Abnormal structures of thylakoid lamellae traversing the pyrenoid were detected by electron microscopy in some of the high-CO2-requiring mutants. Our characterisations of the insertionally generated mutants revealed phenotypes that have not been published before and therefore might be useful tools to obtain new insights on the molecular background of the CO2-concentrating mechanism and its regulation.

The roles of carbonic anhydrases in photosynthetic CO(2) concentrating mechanisms

Cyanobacteria, algae, aquatic angiosperms and higher plants have all developed their own unique versions of photosynthetic CO(2) concentrating mechanisms (CCMs) to aid Rubisco in efficient CO(2) capture. An important aspect of all CCMs is the critical roles that the specialised location and function that various carbonic anhydrase enzymes play in the overall process, participating the interconversion of CO(2) and HCO(3) (-) species both inside and outside the cell. This review examines what we currently understand about the nature of the carbonic anhydrase enzymes, their localisation and roles in the various CCMs that have been studied in detail.