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

Synthetic biology approaches to improve Rubisco carboxylation efficiency in C3 Plants: Direct and Indirect Strategies

Food security remains a pressing issue due to the growing global population and climate change, including the global warming along with increased atmospheric CO2 levels, which can negatively impact C3 crop yields. A major limitation in C3 plants is the inefficiency of Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) due to its low carboxylation activity and competing oxygenase activity. Improving Rubisco efficiency in C3 plants is thus essential for improving photosynthetic performance. Recent advances in synthetic biology have introduced promising strategies to overcome these limitations. This review highlights the latest synthetic biology and gene transformation techniques aimed at optimizing Rubsico carboxylation efficiency. Next, direct approaches such as engineering Rubisco subunits by replacing plant Rubisco with proteins from other organisms are discussed. Additionally, indirect strategies involve modifications of Rubisco-interacting proteins and adjustment of Rubisco environment. We explore CO2-concentrating mechanisms (CCMs) based on pyrenoids and carboxysomes, which increase local CO2 concentrations around Rubisco thus favouring the carboxylation reaction. Lastly, photorespiratory bypasses are also covered in this review.

Light, CO2, and carbon storage in microalgae

Microalgae exhibit remarkable adaptability to environmental changes by integrating light and CO2 signals into regulatory networks that govern energy conversion, carbon fixation, and storage. Light serves not only as an energy source for photosynthesis but also as a regulatory signal mediated by photoreceptors. Specific light spectra distinctly influence carbon allocation, driving lipid or starch biosynthesis by altering transcriptional and metabolic pathways. The ratio of ATP to NADPH imbalances significantly impact carbon allocation toward lipid or starch production. To maintain this balance, alternative electron flow pathways play critical roles, while inter-organelle redox exchanges regulate cellular energy states to support efficient carbon storage. The CO2-concentrating mechanism (CCM) enhances photosynthetic efficiency by concentrating CO2 at Rubisco, energized by ATP from photosynthetic electron transport. This review examines how light receptors, energy-producing pathways, and the CCM interact to regulate carbon metabolism in microalgae, emphasizing their collective roles in balancing energy supply and carbon storage.

In Situ, High-Resolution Quantification of CO2 Uptake Rates via Automated Off-Gas Analysis Illuminates Carbon Uptake Dynamics in Cyanobacterial Cultures

Quantification of cyanobacterial CO2 fixation rates is vital to determining their potential as industrial strains in a circular bioeconomy. Currently, however, CO2 fixation rates are most often determined through indirect and/or low-resolution methods, resulting in an incomplete picture of both dynamic behaviors and total carbon fixation potential. To address this, we developed the "Automated Carbon and CO2 Experimental Sampling System" (ACCESS); a low-cost system for in situ off-gas analysis that supports the automated acquisition of high-resolution volumetric CO2 uptake rates from multiple cyanobacterial cultures in parallel. Carbon fixation data obtained via ACCESS were first independently validated by elemental analysis of cultivated biomass. Using ACCESS, we then demonstrate how the volumetric CO2 uptake rate of two model cyanobacteria, Synechococcus sp. PCC 7002 and Synechocystis sp. PCC 6803, accelerates linearly to a maximum before then decaying monotonically to cessation by stationary phase. Furthermore, consistent with the expected stoichiometry, strong correlations were also found to exist between cell growth and carbon fixation, both in terms of rates as well as total levels. The novel insights made possible via ACCESS will aid other cyanobacterial researchers in diverse fundamental and applied research efforts.

Periplasmic carbonic anhydrase CAH1 contributes to high inorganic carbon affinity in Chlamydomonas reinhardtii

Carbonic anhydrase (CA), an enzyme conserved across species, is pivotal in the interconversion of inorganic carbon (Ci; CO2, and HCO3-). Compared to the well-studied intracellular CA, the specific role of extracellular CA in photosynthetic organisms is still not well understood. In the green alga Chlamydomonas (Chlamydomonas reinhardtii), carbonic anhydrase 1 (CAH1), located at the periplasmic space, is strongly induced under CO2-limiting conditions by the Myb transcription factor LCR1. While the lcr1 mutant shows decreased Ci-affinity, the detailed mechanisms behind this phenomenon are yet to be elucidated. In this study, we aimed to unravel the LCR1-dependent genes essential for maintaining high Ci-affinity. To achieve this, we identified a total of 12 LCR1-dependent inducible genes under CO2-limiting conditions, focusing specifically on the most prominent ones-CAH1, LCI1, LCI6, and Cre10.g426800. We then created mutants of these genes using the CRISPR-Cas9 system, all from the same parental strain, and compared their Ci-affinity. Contrary to earlier findings that reported no reduction in Ci-affinity in the cah1 mutant, our cah1-1 mutant exhibited a decrease in Ci-affinity under high HCO3-/CO2-ratio conditions. Additionally, when we treated wild-type cells with a CA inhibitor with low membrane permeability, a similar reduction in Ci-affinity was observed. Moreover, the addition of exogenous CA to the cah1 mutant rescued the decreased Ci-affinity. These results, highlighting the crucial function of the periplasmic CAH1 in maintaining high Ci-affinity in Chlamydomonas cells, provide insights into the functions of periplasmic CA in algal carbon assimilation.

A synthetic biology approach for the treatment of pollutants with microalgae

The increase in global population and industrial development has led to a significant release of organic and inorganic pollutants into water streams, threatening human health and ecosystems. Microalgae, encompassing eukaryotic protists and prokaryotic cyanobacteria, have emerged as a sustainable and cost-effective solution for removing these pollutants and mitigating carbon emissions. Various microalgae species, such as C. vulgaris, P. tricornutum, N. oceanica, A. platensis, and C. reinhardtii, have demonstrated their ability to eliminate heavy metals, salinity, plastics, and pesticides. Synthetic biology holds the potential to enhance microalgae-based technologies by broadening the scope of treatment targets and improving pollutant removal rates. This review provides an overview of the recent advances in the synthetic biology of microalgae, focusing on genetic engineering tools to facilitate the removal of inorganic (heavy metals and salinity) and organic (pesticides and plastics) compounds. The development of these tools is crucial for enhancing pollutant removal mechanisms through gene expression manipulation, DNA introduction into cells, and the generation of mutants with altered phenotypes. Additionally, the review discusses the principles of synthetic biology tools, emphasizing the significance of genetic engineering in targeting specific metabolic pathways and creating phenotypic changes. It also explores the use of precise engineering tools, such as CRISPR/Cas9 and TALENs, to adapt genetic engineering to various microalgae species. The review concludes that there is much potential for synthetic biology based approaches for pollutant removal using microalgae, but there is a need for expansion of the tools involved, including the development of universal cloning toolkits for the efficient and rapid assembly of mutants and transgenic expression strains, and the need for adaptation of genetic engineering tools to a wider range of microalgae species.

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.

A pyrenoid-localized protein SAGA1 is necessary for Ca2+-binding protein CAS-dependent expression of nuclear genes encoding inorganic carbon transporters in Chlamydomonas reinhardtii

Microalgae induce a CO₂-concentrating mechanism (CCM) to maintain photosynthetic affinity for dissolved inorganic carbon (Ci) under CO₂-limiting conditions. In the model alga Chlamydomonas reinhardtii, the pyrenoid-localized Ca²⁺-binding protein CAS is required to express genes encoding the Ci-transporters, high-light activated 3 (HLA3), and low-CO₂-inducible protein A (LCIA). To identify new factors related to the regulation or components of the CCM, we isolated CO₂-requiring mutants KO-60 and KO-62. These mutants had insertions of a hygromycin-resistant cartridge in the StArch Granules Abnormal 1 (SAGA1) gene, which is necessary to maintain the number of pyrenoids and the structure of pyrenoid tubules in the chloroplast. In both KO-60 and the previously identified saga1 mutant, expression levels of 532 genes were significantly reduced. Among them, 10 CAS-dependent genes, including HLA3 and LCIA, were not expressed in the saga1 mutants. While CAS was expressed normally at the protein levels, the localization of CAS was dispersed through the chloroplast rather than in the pyrenoid, even under CO₂-limiting conditions. These results suggest that SAGA1 is necessary not only for maintenance of the pyrenoid structure but also for regulation of the nuclear genes encoding Ci-transporters through CAS-dependent retrograde signaling under CO₂-limiting stress.

Adapting from Low to High: An Update to CO2-Concentrating Mechanisms of Cyanobacteria and Microalgae

The intracellular accumulation of inorganic carbon (C_i) by microalgae and cyanobacteria under ambient atmospheric CO₂ levels was first documented in the 80s of the 20th Century. Hence, a third variety of the CO₂-concentrating mechanism (CCM), acting in aquatic photoautotrophs with the C₃ photosynthetic pathway, was revealed in addition to the then-known schemes of CCM, functioning in CAM and C₄ higher plants. Despite the low affinity of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) of microalgae and cyanobacteria for the CO₂ substrate and low CO₂/O₂ specificity, CCM allows them to perform efficient CO₂ fixation in the reductive pentose phosphate (RPP) cycle. CCM is based on the coordinated operation of strategically located carbonic anhydrases and CO₂/HCO₃^- uptake systems. This cooperation enables the intracellular accumulation of HCO₃^-, which is then employed to generate a high concentration of CO₂ molecules in the vicinity of Rubisco's active centers compensating up for the shortcomings of enzyme features. CCM functions as an add-on to the RPP cycle while also acting as an important regulatory link in the interaction of dark and light reactions of photosynthesis. This review summarizes recent advances in the study of CCM molecular and cellular organization in microalgae and cyanobacteria, as well as the fundamental principles of its functioning and regulation.

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.

New horizons for building pyrenoid-based CO2-concentrating mechanisms in plants to improve yields

Many photosynthetic species have evolved CO2-concentrating mechanisms (CCMs) to improve the efficiency of CO2 assimilation by Rubisco and reduce the negative impacts of photorespiration. However, the majority of plants (i.e. C3 plants) lack an active CCM. Thus, engineering a functional heterologous CCM into important C3 crops, such as rice (Oryza sativa) and wheat (Triticum aestivum), has become a key strategic ambition to enhance yield potential. Here, we review recent advances in our understanding of the pyrenoid-based CCM in the model green alga Chlamydomonas reinhardtii and engineering progress in C3 plants. We also discuss recent modeling work that has provided insights into the potential advantages of Rubisco condensation within the pyrenoid and the energetic costs of the Chlamydomonas CCM, which, together, will help to better guide future engineering approaches. Key findings include the potential benefits of Rubisco condensation for carboxylation efficiency and the need for a diffusional barrier around the pyrenoid matrix. We discuss a minimal set of components for the CCM to function and that active bicarbonate import into the chloroplast stroma may not be necessary for a functional pyrenoid-based CCM in planta. Thus, the roadmap for building a pyrenoid-based CCM into plant chloroplasts to enhance the efficiency of photosynthesis now appears clearer with new challenges and opportunities.

MYB gene family in the diatom Phaeodactylum tricornutum revealing their potential functions in the adaption to nitrogen deficiency and diurnal cycle

The MYB transcription factor (TF) family is one of the largest and most important TF families, regulating the growth and response of microalgae to stress. However, the gene structure and characteristics of Phaeodactylum tricornutum MYB TFs, and their functions under nitrogen deficiency, have not been explored yet. To identify all P. tricornutum MYB (PtMYB) genes, the MYB gene family was analyzed at the genome-wide level in this study. A total ofm26 PtMYB genes were identified from the genome of P. tricornutum. These PtMYB genes were divided into 5 subfamilies: 5R-MYB, 4R-MYB, R2R3-MYB, R1R2R3-MYB, and MYB-related proteins. Phylogenetical motif and gene structure analyses of MYB genes indicated that the number and proportion of MYB TFs were species-specific, and MYB genes exhibited a lot of duplication events from microalgae to higher plants. Furthermore, the differentially expressed patterns of all 26 PtMYB TFs implied that PtMYB genes might have functional specificity under nitrogen deficiency. Homology analysis of MYB genes revealed that PtMYB3, PtMYB15, and PtMYB21 might play important roles in the regulation of the diurnal cycle and response to nitrogen stress in P. tricornutum. PtMYB3, PtMYB15, and PtMYB21 genes might be used as potential candidate genes for further studying the regulatory mechanisms of P. tricornutum under nitrogen deficiency. This work provides an important foundation for the future research of the potential functions of PtMYB genes and its diurnal regulatory mechanisms under nitrogen deficiency.

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 (Ci = CO2 + HCO3-) was reduced. At low CO2 concentrations, the CCM is needed to both deliver Ci 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.

Characterization of a CO2-Concentrating Mechanism with Low Sodium Dependency in the Centric Diatom Chaetoceros gracilis

Microalgae induce a CO₂-concentrating mechanism (CCM) to overcome CO₂-limiting stress in aquatic environments by coordinating inorganic carbon (Ci) transporters and carbonic anhydrases (CAs). Two mechanisms have been suggested to facilitate Ci uptake from aqueous media: Na⁺-dependent HCO₃^- uptake by solute carrier (SLC) family transporters and accelerated dehydration of HCO₃^- to CO₂ by external CA in model diatoms. However, studies on ecologically and industrially important diatoms including Chaetoceros gracilis, a common food source in aquacultures, are still limited. Here, we characterized the CCM of C. gracilis using inhibitors and growth dependency on Na⁺ and CO₂. Addition of a membrane-impermeable SLC inhibitor, 4,4'-diisothiocyano-2,2'-stilbenedisulfonic acid (DIDS), or the transient removal of Na⁺ from the culture medium did not impair photosynthetic affinity for Ci in CO₂-limiting stress conditions, but addition of a membrane-impermeable CA inhibitor, acetazolamide, decreased Ci affinity to one-third of control cultures. In culture medium containing 0.23 mM Na⁺ C. gracilis grew photoautotrophically by aeration with air containing 5% CO₂, but not with the air containing 0.04% CO₂. These results suggested that C. gracilis utilizes external CAs in its CCM to elevate photosynthetic affinity for Ci rather than plasma-membrane SLC family transporters. In addition, it is possible that low level of Na⁺ may support the CCM in processes other than Ci-uptake at the plasma membrane specifically in CO₂-limiting conditions. Our findings provide insights into the diversity of CCMs among diatoms as well as basic information to optimize culture conditions for industrial applications.

Quantitative proteomic comparison of salt stress in Chlamydomonas reinhardtii and the snow alga Chlamydomonas nivalis reveals mechanisms for salt-triggered fatty acid accumulation via reallocation of carbon resources

BACKGROUND

Chlamydomonas reinhardtii is a model green alga strain for molecular studies; its fully sequenced genome has enabled omic-based analyses that have been applied to better understand its metabolic responses to stress. Here, we characterised physiological and proteomic changes between a low-starch C. reinhardtii strain and the snow alga Chlamydomonas nivalis, to reveal insights into their contrasting responses to salinity stress.

RESULTS

Each strain was grown in conditions tailored to their growth requirements to encourage maximal fatty acid (as a proxy measure of lipid) production, with internal controls to allow comparison points. In 0.2 M NaCl, C. nivalis accumulates carbohydrates up to 10.4% DCW at 80 h, and fatty acids up to 52.0% dry cell weight (DCW) over 12 days, however, C. reinhardtii does not show fatty acid accumulation over time, and shows limited carbohydrate accumulation up to 5.5% DCW. Analysis of the C. nivalis fatty acid profiles showed that salt stress improved the biofuel qualities over time. Photosynthesis and respiration rates are reduced in C. reinhardtii relative to C. nivalis in response to 0.2 M NaCl. De novo sequencing and homology matching was used in conjunction with iTRAQ-based quantitative analysis to identify and relatively quantify proteomic alterations in cells exposed to salt stress. There were abundance differences in proteins associated with stress, photosynthesis, carbohydrate and lipid metabolism proteins. In terms of lipid synthesis, salt stress induced an increase in dihydrolipoyl dehydrogenase in C. nivalis (1.1-fold change), whilst levels in C. reinhardtii remained unaffected; this enzyme is involved in acetyl CoA production and has been linked to TAG accumulation in microalgae. In salt-stressed C. nivalis there were decreases in the abundance of UDP-sulfoquinovose (- 1.77-fold change), which is involved in sulfoquinovosyl diacylglycerol metabolism, and in citrate synthase (- 2.7-fold change), also involved in the TCA cycle. Decreases in these enzymes have been shown to lead to increased TAG production as fatty acid biosynthesis is favoured. Data are available via ProteomeXchange with identifier PXD018148.

CONCLUSIONS

These differences in protein abundance have given greater understanding of the mechanism by which salt stress promotes fatty acid accumulation in the un-sequenced microalga C. nivalis as it switches to a non-growth state, whereas C. reinhardtii does not have this response.

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.

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.

Prospects for Engineering Biophysical CO2 Concentrating Mechanisms into Land Plants to Enhance Yields

Although cyanobacteria and algae represent a small fraction of the biomass of all primary producers, their photosynthetic activity accounts for roughly half of the daily CO₂ fixation that occurs on Earth. These microorganisms are able to accomplish this feat by enhancing the activity of the CO₂-fixing enzyme Rubisco using biophysical CO₂ concentrating mechanisms (CCMs). Biophysical CCMs operate by concentrating bicarbonate and converting it into CO₂ in a compartment that houses Rubisco (in contrast with other CCMs that concentrate CO₂ via an organic intermediate, such as malate in the case of C₄ CCMs). This activity provides Rubisco with a high concentration of its substrate, thereby increasing its reaction rate. The genetic engineering of a biophysical CCM into land plants is being pursued as a strategy to increase crop yields. This review focuses on the progress toward understanding the molecular components of cyanobacterial and algal CCMs, as well as recent advances toward engineering these components into land plants.

Diatom Molecular Research Comes of Age: Model Species for Studying Phytoplankton Biology and Diversity

Diatoms are the world's most diverse group of algae, comprising at least 100,000 species. Contributing ∼20% of annual global carbon fixation, they underpin major aquatic food webs and drive global biogeochemical cycles. Over the past two decades, Thalassiosira pseudonana and Phaeodactylum tricornutum have become the most important model systems for diatom molecular research, ranging from cell biology to ecophysiology, due to their rapid growth rates, small genomes, and the cumulative wealth of associated genetic resources. To explore the evolutionary divergence of diatoms, additional model species are emerging, such as Fragilariopsis cylindrus and Pseudo-nitzschia multistriata Here, we describe how functional genomics and reverse genetics have contributed to our understanding of this important class of microalgae in the context of evolution, cell biology, and metabolic adaptations. Our review will also highlight promising areas of investigation into the diversity of these photosynthetic organisms, including the discovery of new molecular pathways governing the life of secondary plastid-bearing organisms in aquatic environments.

Differential proteomic analyses of green microalga Ettlia sp. at various dehydration levels

Water deprivation could be a lethal stress for aquatic and aero-terrestrial organisms. Ettlia sp. is a unicellular photosynthetic freshwater microalga. In the present study, proteomic alterations and physiological characteristics of Ettlia sp. were analyzed to comprehend the molecular changes in dehydrated conditions. Varying levels of dehydration were achieved by incubating drained Ettlia sp. in different relative humidity environments for 24  hours. Using a comparative proteomic analysis, 52 differentially expressed protein spots were identified that could be divided into eight functional groups. The PCA analysis of normalized protein expression values demonstrated a clear segregation of protein expression profiles among different dehydration levels. Identified proteins could be grouped into four clusters based on their expression profiles. Proteins relating to photosynthesis comprised the largest group with 25% of the identified proteins that were decreased in dehydrated samples and belonged to cluster I. The photosynthetic activities were measured with rehydrated Ettlia sp. These results revealed that photosynthesis remained inhibited over extended time in response to dehydration. The expressions of reactive oxygen species (ROS) scavenger proteins increased in strong dehydration and were assigned to cluster III. Carbon metabolism proteins were suppressed, which might limit energy consumption, whereas glycolysis was activated at mild dehydration. The accumulation of desiccation-associated late embryogenesis proteins might inhibit the aggregation of housekeeping proteins. DNA protective proteins were expressed higher in the dehydrated state, which might reduce DNA damage, and membrane-stabilizing proteins increased in abundance in desiccation. These findings provide an understanding of Ettlia's adaptation and survival capabilities in a dehydrated state.

Ion and metabolite transport in the chloroplast of algae: lessons from land plants

Chloroplasts are endosymbiotic organelles and play crucial roles in energy supply and metabolism of eukaryotic photosynthetic organisms (algae and land plants). They harbor channels and transporters in the envelope and thylakoid membranes, mediating the exchange of ions and metabolites with the cytosol and the chloroplast stroma and between the different chloroplast subcompartments. In secondarily evolved algae, three or four envelope membranes surround the chloroplast, making more complex the exchange of ions and metabolites. Despite the importance of transport proteins for the optimal functioning of the chloroplast in algae, and that many land plant homologues have been predicted, experimental evidence and molecular characterization are missing in most cases. Here, we provide an overview of the current knowledge about ion and metabolite transport in the chloroplast from algae. The main aspects reviewed are localization and activity of the transport proteins from algae and/or of homologues from other organisms including land plants. Most chloroplast transporters were identified in the green alga Chlamydomonas reinhardtii, reside in the envelope and participate in carbon acquisition and metabolism. Only a few identified algal transporters are located in the thylakoid membrane and play role in ion transport. The presence of genes for putative transporters in green algae, red algae, diatoms, glaucophytes and cryptophytes is discussed, and roles in the chloroplast are suggested. A deep knowledge in this field is required because algae represent a potential source of biomass and valuable metabolites for industry, medicine and agriculture.

Transport and Use of Bicarbonate in Plants: Current Knowledge and Challenges Ahead

Bicarbonate plays a fundamental role in the cell pH status in all organisms. In autotrophs, HCO₃− may further contribute to carbon concentration mechanisms (CCM). This is especially relevant in the CO₂-poor habitats of cyanobacteria, aquatic microalgae, and macrophytes. Photosynthesis of terrestrial plants can also benefit from CCM as evidenced by the evolution of C₄ and Crassulacean Acid Metabolism (CAM). The presence of HCO₃− in all organisms leads to more questions regarding the mechanisms of uptake and membrane transport in these different biological systems. This review aims to provide an overview of the transport and metabolic processes related to HCO₃− in microalgae, macroalgae, seagrasses, and terrestrial plants. HCO₃− transport in cyanobacteria and human cells is much better documented and is included for comparison. We further comment on the metabolic roles of HCO₃− in plants by focusing on the diversity and functions of carbonic anhydrases and PEP carboxylases as well as on the signaling role of CO₂/HCO₃− in stomatal guard cells. Plant responses to excess soil HCO₃− is briefly addressed. In conclusion, there are still considerable gaps in our knowledge of HCO₃− uptake and transport in plants that hamper the development of breeding strategies for both more efficient CCM and better HCO₃− tolerance in crop plants.

The Chlamydomonas CO2 -concentrating mechanism and its potential for engineering photosynthesis in plants

Contents Summary I. Introduction 54 II. Recent advances in our understanding of the Chlamydomonas CCM 55 III. Current gaps in our understanding of the Chlamydomonas CCM 58 IV. Approaches to rapidly advance our understanding of the Chlamydomonas CCM 58 V. Engineering a CCM into higher plants 58 VI. Conclusion and outlook 59 Acknowledgements 60 References 60 SUMMARY: To meet the food demands of a rising global population, innovative strategies are required to increase crop yields. Improvements in plant photosynthesis by genetic engineering show considerable potential towards this goal. One prospective approach is to introduce a CO₂ -concentrating mechanism into crop plants to increase carbon fixation by supplying the central carbon-fixing enzyme, Rubisco, with a higher concentration of its substrate, CO₂ . A promising donor organism for the molecular machinery of this mechanism is the eukaryotic alga Chlamydomonas reinhardtii. This review summarizes the recent advances in our understanding of carbon concentration in Chlamydomonas, outlines the most pressing gaps in our knowledge and discusses strategies to transfer a CO₂ -concentrating mechanism into higher plants to increase photosynthetic performance.

A Spatial Interactome Reveals the Protein Organization of the Algal CO2-Concentrating Mechanism

Approximately one-third of global CO2 fixation is performed by eukaryotic algae. Nearly all algae enhance their carbon assimilation by operating a CO2-concentrating mechanism (CCM) built around an organelle called the pyrenoid, whose protein composition is largely unknown. Here, we developed tools in the model alga Chlamydomonas reinhardtii to determine the localizations of 135 candidate CCM proteins and physical interactors of 38 of these proteins. Our data reveal the identity of 89 pyrenoid proteins, including Rubisco-interacting proteins, photosystem I assembly factor candidates, and inorganic carbon flux components. We identify three previously undescribed protein layers of the pyrenoid: a plate-like layer, a mesh layer, and a punctate layer. We find that the carbonic anhydrase CAH6 is in the flagella, not in the stroma that surrounds the pyrenoid as in current models. These results provide an overview of proteins operating in the eukaryotic algal CCM, a key process that drives global carbon fixation.

Identification and characterization of a solute carrier, CIA8, involved in inorganic carbon acclimation in Chlamydomonas reinhardtii

The supply of inorganic carbon (Ci) at the site of fixation by Rubisco is a key parameter for efficient CO2 fixation in aquatic organisms including the green alga, Chlamydomonas reinhardtii. Chlamydomonas reinhardtii cells, when grown on limiting CO2, have a CO2-concentrating mechanism (CCM) that functions to concentrate CO2 at the site of Rubisco. Proteins thought to be involved in inorganic carbon uptake have been identified and localized to the plasma membrane or chloroplast envelope. However, current CCM models suggest that additional molecular components are involved in Ci uptake. In this study, the gene Cia8 was identified in an insertional mutagenesis screen and characterized. The protein encoded by Cia8 belongs to the sodium bile acid symporter subfamily. Transcript levels for this gene were significantly up-regulated when the cells were grown on low CO2. The cia8 mutant exhibited reduced growth and reduced affinity for Ci when grown in limiting CO2 conditions. Prediction programs localize this protein to the chloroplast. Ci uptake and the photosynthetic rate, particularly at high external pH, were reduced in the mutant. The results are consistent with the model that CIA8 is involved in Ci uptake in C. reinhardtii.

Evolutionarily distinct strategies for the acquisition of inorganic carbon from seawater in marine diatoms

The acquisition of dissolved inorganic carbon (DIC) in CO2-limited seawater is a central issue to understand in marine primary production. We previously demonstrated the occurrence of direct HCO3- uptake by solute carrier (SLC) 4 transporters in a diatom, a major marine primary producer. Homologs of SLC are found in both centric and pennate marine diatoms, suggesting that SLC transporters are generally conserved. Here, the generality of SLC-mediated DIC uptake in diatoms was examined using an SLC inhibitor, diisothiocyano-2,2'-stilbenedisulfonic acid (DIDS), and an inhibitor of external carbonic anhydrase, acetazolamide. DIDS suppressed high-DIC-affinity photosynthesis in the pennate diatom Phaeodactylum tricornutum and the centric diatom Chaetoceros muelleri, but there was no effect on either the pennate Cylindrotheca fusiformis or the centric Thalassiosira pseudonana. Interestingly, the DIC affinity of DIDS-insensitive strains was sensitive to treatment with up to 100 μM acetazolamide, displaying a 2-4-fold increase in K0.5[DIC]. In contrast, acetazolamide did not affect the DIDS-sensitive group. These results indicate the occurrence of two distinct strategies for DIC uptake-one primarily facilitated by SLC and the other being passive CO2 entry facilitated by external carbonic anhydrase. The phylogenetic independence of these strategies suggests that environmental demands drove the evolution of distinct DIC uptake mechanisms in diatoms.

Progress and challenges of engineering a biophysical CO2-concentrating mechanism into higher plants

Growth and productivity in important crop plants is limited by the inefficiencies of the C3 photosynthetic pathway. Introducing CO2-concentrating mechanisms (CCMs) into C3 plants could overcome these limitations and lead to increased yields. Many unicellular microautotrophs, such as cyanobacteria and green algae, possess highly efficient biophysical CCMs that increase CO2 concentrations around the primary carboxylase enzyme, Rubisco, to enhance CO2 assimilation rates. Algal and cyanobacterial CCMs utilize distinct molecular components, but share several functional commonalities. Here we outline the recent progress and current challenges of engineering biophysical CCMs into C3 plants. We review the predicted requirements for a functional biophysical CCM based on current knowledge of cyanobacterial and algal CCMs, the molecular engineering tools and research pipelines required to translate our theoretical knowledge into practice, and the current challenges to achieving these goals.

Construction of Marker-Free Transgenic Strains of Chlamydomonas reinhardtii Using a Cre/loxP-Mediated Recombinase System

The Escherichia coli bacteriophage P1 encodes a site-specific recombinase called Cre and two 34-bp target sites of Cre recombinase called loxP. The Cre/loxP system has been used to achieve targeted insertion and precise deletion in many animal and plant genomes. The Cre/loxP system has particularly been used for the removal of selectable marker genes to create marker-free transgenic organisms. For the first time, we applied the Cre/loxP-mediated site-specific recombination system to Chlamydomonas reinhardtii to construct marker-free transgenic strains. Specifically, C. reinhardtii strains cc4350 and cc124 carrying an aphVIII expression cassette flanked by two direct repeats of loxP were constructed. Separately, a synthetic Cre recombinase gene (CrCRE), the codons of which were optimized for expression in C. reinhardtii, was synthesized, and a CrCRE expression cassette was introduced into strain cc4350 carrying a single copy of the loxP-flanked aphVIII expression cassette. Among 46 transformants carrying the CrCRE expression cassette stably, the excision of aphVIII by CrCre recombinase was observed only in one transformant. We then constructed an expression cassette of an in-frame fusion of ble to CrCRE via a short linker peptide. The product of ble (Ble) is a bleomycin-binding protein that confers resistance to bleomycin-related antibiotics such as Zeocin and localizes in the nucleus. Therefore, the ble-(linker)-CrCRE fusion protein is expected to localize in the nucleus. When the ble-(linker)-CrCRE expression cassette was integrated into the genome of strain cc4350 carrying a single copy of the loxP-flanked aphVIII expression cassette, CrCre recombinase-mediated excision of the aphVIII expression cassette was observed at a frequency higher than that in stable transformants of the CrCRE expression cassette. Similarly, from strain cc124 carrying a single loxP-flanked aphVIII expression cassette, the aphVIII expression cassette was successfully excised after introduction of the ble-(linker)-CrCRE expression cassette. The ble-(linker)-CrCRE expression cassette remained in the genome after excision of the aphVIII expression cassette, and it was subsequently removed by crossing with the wild-type strain. This precise Cre-mediated deletion method applicable to transgenic C. reinhardtii could further increase the potential of this organism for use in basic and applied research.

Will an algal CO2-concentrating mechanism work in higher plants?

Many algae use a biophysical carbon concentrating mechanism for active accumulation and retention of inorganic carbon within chloroplasts, with CO2 fixation by RuBisCO within a micro-compartment, the pyrenoid. Engineering such mechanisms into higher plant chloroplasts is a possible route to augment RuBisCO operating efficiency and photosynthetic rates. Significant progress has been made recently in characterising key algal transporters and identifying factors responsible for the aggregation of RuBisCO into the pyrenoid. Several transporters have now also been successfully incorporated into higher plant chloroplasts. Consistent with the predictions from modelling, regulation of higher plant plastidic carbonic anhydrases and some form of RuBisCO aggregation will be needed before the mechanism delivers potential benefits. Key research priorities include a better understanding of the regulation of the algal carbon concentrating mechanism, advancing the fundamental characterisation of known components, evaluating whether higher plant chloroplasts can accommodate a pyrenoid, and, ultimately, testing transgenic lines under realistic growth conditions.

Introducing an algal carbon-concentrating mechanism into higher plants: location and incorporation of key components

Many eukaryotic green algae possess biophysical carbon-concentrating mechanisms (CCMs) that enhance photosynthetic efficiency and thus permit high growth rates at low CO2 concentrations. They are thus an attractive option for improving productivity in higher plants. In this study, the intracellular locations of ten CCM components in the unicellular green alga Chlamydomonas reinhardtii were confirmed. When expressed in tobacco, all of these components except chloroplastic carbonic anhydrases CAH3 and CAH6 had the same intracellular locations as in Chlamydomonas. CAH6 could be directed to the chloroplast by fusion to an Arabidopsis chloroplast transit peptide. Similarly, the putative inorganic carbon (Ci) transporter LCI1 was directed to the chloroplast from its native location on the plasma membrane. CCP1 and CCP2 proteins, putative Ci transporters previously reported to be in the chloroplast envelope, localized to mitochondria in both Chlamydomonas and tobacco, suggesting that the algal CCM model requires expansion to include a role for mitochondria. For the Ci transporters LCIA and HLA3, membrane location and Ci transport capacity were confirmed by heterologous expression and H(14) CO3 (-) uptake assays in Xenopus oocytes. Both were expressed in Arabidopsis resulting in growth comparable with that of wild-type plants. We conclude that CCM components from Chlamydomonas can be expressed both transiently (in tobacco) and stably (in Arabidopsis) and retargeted to appropriate locations in higher plant cells. As expression of individual Ci transporters did not enhance Arabidopsis growth, stacking of further CCM components will probably be required to achieve a significant increase in photosynthetic efficiency in this species.

Characterization of cooperative bicarbonate uptake into chloroplast stroma in the green alga Chlamydomonas reinhardtii

The supply of inorganic carbon (Ci; CO2 and HCO3 (-)) is an environmental rate-limiting factor in aquatic photosynthetic organisms. To overcome the difficulty in acquiring Ci in limiting-CO2 conditions, an active Ci uptake system called the CO2-concentrating mechanism (CCM) is induced to increase CO2 concentrations in the chloroplast stroma. An ATP-binding cassette transporter, HLA3, and a formate/nitrite transporter homolog, LCIA, are reported to be associated with HCO3 (-) uptake [Wang and Spalding (2014) Plant Physiol 166(4):2040-2050]. However, direct evidence of the route of HCO3 (-) uptake from the outside of cells to the chloroplast stroma remains elusive owing to a lack of information on HLA3 localization and comparative analyses of the contribution of HLA3 and LCIA to the CCM. In this study, we revealed that HLA3 and LCIA are localized to the plasma membrane and chloroplast envelope, respectively. Insertion mutants of HLA3 and/or LCIA showed decreased Ci affinities/accumulation, especially in alkaline conditions where HCO3 (-) is the predominant form of Ci. HLA3 and LCIA formed protein complexes independently, and the absence of LCIA decreased HLA3 mRNA accumulation, suggesting the presence of unidentified retrograde signals from the chloroplast to the nucleus to maintain HLA3 mRNA expression. Furthermore, although single overexpression of HLA3 or LCIA in high CO2 conditions did not affect Ci affinity, simultaneous overexpression of HLA3 with LCIA significantly increased Ci affinity/accumulation. These results highlight the HLA3/LCIA-driven cooperative uptake of HCO3 (-) and a key role of LCIA in the maintenance of HLA3 stability as well as Ci affinity/accumulation in the CCM.

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.

Expression activation and functional analysis of HLA3, a putative inorganic carbon transporter in Chlamydomonas reinhardtii

The CO2 concentrating mechanism (CCM) is a key component of the carbon assimilation strategy of aquatic microalgae. Induced by limiting CO2 and tightly regulated, the CCM enables these microalgae to respond rapidly to varying environmental CO2 supplies and to perform photosynthetic CO2 assimilation in a cost-effective way. A functional CCM in eukaryotic algae requires Rubisco sequestration, rapid interconversion between CO2 and HCO3(-) catalyzed by carbonic anhydrases (CAs), and active inorganic carbon (Ci) uptake. In the model microalga Chlamydomonas reinhardtii, a membrane protein HLA3 is proposed to be involved in active Ci uptake across the plasma membrane. In this study, we use an artificially designed transcription activator-like effector (dTALE) to activate the expression of HLA3. The successful activation of HLA3 expression demonstrates dTALE as a promising tool for gene-specific activation and investigation of gene function in Chlamydomonas. Activation of HLA3 expression in high CO2 acclimated cells, where HLA3 is not expressed, resulted in increased Ci accumulation and Ci-dependent photosynthetic O2 evolution specifically in very low CO2 concentrations, which confirms that HLA3 is indeed involved in Ci uptake, and suggests it is mainly associated with HCO3(-) transport in very low CO2 concentrations, conditions in which active CO2 uptake is highly limited.

Accumulation of squalene in a microalga Chlamydomonas reinhardtii by genetic modification of squalene synthase and squalene epoxidase genes

Several microalgae accumulate high levels of squalene, and as such provide a potentially valuable source of this useful compound. However, the molecular mechanism of squalene biosynthesis in microalgae is still largely unknown. We obtained the sequences of two enzymes involved in squalene synthesis and metabolism, squalene synthase (CrSQS) and squalene epoxidase (CrSQE), from the model green alga Chlamydomonas reinhardtii. CrSQS was functionally characterized by expression in Escherichia coli and CrSQE by complementation of a budding yeast erg1 mutant. Transient expression of CrSQS and CrSQE fused with fluorescent proteins in onion epidermal tissue suggested that both proteins were co-localized in the endoplasmic reticulum. CrSQS-overexpression increased the rate of conversion of 14C-labeled farnesylpyrophosphate into squalene but did not lead to over-accumulation of squalene. Addition of terbinafine caused the accumulation of squalene and suppression of cell survival. On the other hand, in CrSQE-knockdown lines, the expression level of CrSQE was reduced by 59-76% of that in wild-type cells, and significant levels of squalene (0.9-1.1 μg mg-1 cell dry weight) accumulated without any growth inhibition. In co-transformation lines with CrSQS-overexpression and CrSQE-knockdown, the level of squalene was not increased significantly compared with that in solitary CrSQE-knockdown lines. These results indicated that partial knockdown of CrSQE is an effective strategy to increase squalene production in C. reinhardtii cells.

Impacts of CO2 concentration on growth, lipid accumulation, and carbon-concentrating-mechanism-related gene expression in oleaginous Chlorella

Biodiesel production by microalgae with photosynthetic CO2 biofixation is thought to be a feasible way in the field of bioenergy and carbon emission reduction. Knowledge of the carbon-concentrating mechanism plays an important role in improving microalgae carbon fixation efficiency. However, little information is available regarding the dramatic changes of cells suffered upon different environmental factors, such as CO2 concentration. The aim of this study was to investigate the growth, lipid accumulation, carbon fixation rate, and carbon metabolism gene expression under different CO2 concentrations in oleaginous Chlorella. It was found that Chlorella pyrenoidosa grew well under CO2 concentrations ranging from 1 to 20 %. The highest biomass and lipid productivity were 4.3 g/L and 107 mg/L/day under 5 % CO2 condition. Switch from high (5 %) to low (0.03 %, air) CO2 concentration showed significant inhibitory effect on growth and CO2 fixation rate. The amount of the saturated fatty acids was increased obviously along with the transition. Low CO2 concentration (0.03 %) was suitable for the accumulation of saturated fatty acids. Reducing the CO2 concentration could significantly decrease the polyunsaturated degree in fatty acids. Moreover, the carbon-concentrating mechanism-related gene expression revealed that most of them, especially CAH2, LCIB, and HLA3, had remarkable change after 1, 4, and 24 h of the transition, which suggests that Chlorella has similar carbon-concentrating mechanism with Chlamydomonas reinhardtii. The findings of the present study revealed that C. pyrenoidosa is an ideal candidate for mitigating CO2 and biodiesel production and is appropriate as a model for mechanism research of carbon sequestration.

Acclimation to very low CO2: contribution of limiting CO2 inducible proteins, LCIB and LCIA, to inorganic carbon uptake in Chlamydomonas reinhardtii

The limiting-CO2 inducible CO2-concentrating mechanism (CCM) of microalgae represents an effective strategy to capture CO2 when its availability is limited. At least two limiting-CO2 acclimation states, termed low CO2 and very low CO2, have been demonstrated in the model microalga Chlamydomonas reinhardtii, and many questions still remain unanswered regarding both the regulation of these acclimation states and the molecular mechanism underlying operation of the CCM in these two states. This study examines the role of two proteins, Limiting CO2 Inducible A (LCIA; also named NAR1.2) and LCIB, in the CCM of C. reinhardtii. The identification of an LCIA-LCIB double mutant based on its inability to survive in very low CO2 suggests that both LCIA and LCIB are critical for survival in very low CO2. The contrasting effects of individual mutations in LCIB and LCIA compared with the effects of LCIB-LCIA double mutations on growth and inorganic carbon-dependent photosynthetic O2 evolution reveal distinct roles of LCIA and LCIB in the CCM. Although both LCIA and LCIB are essential for very low CO2 acclimation, LCIB appears to function in a CO2 uptake system, whereas LCIA appears to be associated with a HCO3(-) transport system. The contrasting and complementary roles of LCIA and LCIB in acclimation to low CO2 and very low CO2 suggest a possible mechanism of differential regulation of the CCM based on the inhibition of HCO3(-) transporters by moderate to high levels of CO2.

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.

Isolation and characterization of mutants defective in the localization of LCIB, an essential factor for the carbon-concentrating mechanism in Chlamydomonas reinhardtii

The unicellular green alga Chlamydomonas reinhardtii acclimates to low-CO2 (LC) conditions by actively transporting inorganic carbon (Ci) into the cell, resulting in an increase in photosynthetic efficiency. This mechanism is called the carbon-concentrating mechanism (CCM), and soluble protein LCIB is essential for the CCM. LCIB is localized in the vicinity of pyrenoid, a prominent structure in the chloroplast, under LC conditions in the light. In contrast, in the dark or in high-CO2 conditions, where the CCM is inactive, LCIB diffuses away from the pyrenoid. Although the functional importance of LCIB for the CCM has been shown, the significance and mechanism of the change in suborganellar localization of LCIB remain to be elucidated. In this study, we screened 13,000 DNA-tagged mutants and isolated twelve aberrant LCIB localization (abl) mutants under LC conditions. abl-1 and abl-3 with dispersed and speckled localization of LCIB in the chloroplast showed significant decreases in Ci affinity, Ci accumulation, and CO2 fixation. Ten abl mutants (abl-1, abl-3, abl-4, abl-5, abl-6, abl-7, abl-8, abl-9, abl-11, and abl-12) showed not only aberrant LCIB localization but also reduced pyrenoid sizes. Moreover, three abl mutants (abl-10, abl-11, and abl-12) showed the increased numbers of pyrenoids per cell. These results suggested that the specific LCIB localization could be related to pyrenoid development.

Isolation and characterization of novel high-CO2-requiring mutants of Chlamydomonas reinhardtii

Aquatic microalgae induce a carbon-concentrating mechanism (CCM) to maintain photosynthetic activity in low-CO2 (LC) conditions. Although the molecular mechanism of the CCM has been investigated using the single-cell green alga Chlamydomonas reinhardtii, and several CCM-related genes have been identified by analyzing high-CO2 (HC)-requiring mutants, many aspects of the CO2-signal transduction pathways remain to be elucidated. In this study, we report the isolation of novel HC-requiring mutants defective in the induction of CCM by DNA tagging. Growth rates of 20,000 transformants grown under HC and LC conditions were compared, and three HC-requiring mutants (H24, H82, and P103) were isolated. The photosynthetic CO2-exchange activities of these mutants were significantly decreased compared with that of wild-type cells, and accumulation of HLA3 and both LCIA and HLA3 were absent in mutants H24 and H82, respectively. Although the insertion of the marker gene and the HC-requiring phenotype were linked in the tetrad progeny of H82, and a calcium-sensing receptor CAS was disrupted by the insertion, exogenous expression of CAS alone could not complement the HC-requiring phenotype.

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.

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.

Isobutanol production as an alternative metabolic sink to rescue the growth deficiency of the glycogen mutant of Synechococcus elongatus PCC 7942

Glycogen synthesis initiated by glucose-1-phosphate adenylyltransferase (glgC) represents a major carbon storage route in cyanobacteria which could divert a significant portion of assimilated carbon. Significant growth retardation in cyanobacteria with glgC knocked out (ΔglgC) has been reported in high light conditions. Here, we knocked out the glgC gene and analyzed its effects on carbon distribution in an isobutanol-producing strain of Synechococcus elongatus PCC7942 and its parental wild-type strain. We showed that isobutanol production was able to partially rescue the growth of ΔglgC mutant where the growth rescue effect positively correlated with the rate of isobutanol production. Using NaH(14)CO3 incorporation analysis, we observed a 28 % loss of total carbon fixation rate in the ΔglgC mutant compared to the wild-type. Upon expression of the isobutanol production pathway in ΔglgC mutant, the total carbon fixation rate was restored to the wild-type level. Furthermore, we showed that 52 % of the total carbon fixed was redirected into isobutanol biosynthesis in the ΔglgC mutant expressing enzymes for isobutanol production, which is 2.5 times higher than that of the wild-type expressing the same enzymes. These results suggest that biosynthesis of non-native product such as isobutanol can serve as a metabolic sink for replacing glycogen to rescue growth and restore carbon fixation rate. The rescue effect may further serve as a platform for cyanobacteria energy and carbon metabolism study.