An Indexed, Mapped Mutant Library Enables Reverse Genetics Studies of Biological Processes in Chlamydomonas reinhardtii

Structural organization of the C1a-e-c supercomplex within the ciliary central apparatus

Fu et al. use a WT versus mutant comparison and cryo-electron tomography of Chlamydomonas flagella to identify central apparatus (CA) subunits and visualize their location in the native 3D CA structure. This study provides a better understanding of the CA and how it regulates ciliary motility.

Nearly all motile cilia contain a central apparatus (CA) composed of two connected singlet microtubules with attached projections that play crucial roles in regulating ciliary motility. Defects in CA assembly usually result in motility-impaired or paralyzed cilia, which in humans causes disease. Despite their importance, the protein composition and functions of the CA projections are largely unknown. Here, we integrated biochemical and genetic approaches with cryo-electron tomography to compare the CA of wild-type Chlamydomonas with CA mutants. We identified a large (>2 MD) complex, the C1a-e-c supercomplex, that requires the PF16 protein for assembly and contains the CA components FAP76, FAP81, FAP92, and FAP216. We localized these subunits within the supercomplex using nanogold labeling and show that loss of any one of them results in impaired ciliary motility. These data provide insight into the subunit organization and 3D structure of the CA, which is a prerequisite for understanding the molecular mechanisms by which the CA regulates ciliary beating.

Scaffold subunits support associated subunit assembly in the Chlamydomonas ciliary nexin-dynein regulatory complex

The nexin-dynein regulatory complex (N-DRC) in motile cilia and flagella functions as a linker between neighboring doublet microtubules, acts to stabilize the axonemal core structure, and serves as a central hub for the regulation of ciliary motility. Although the N-DRC has been studied extensively using genetic, biochemical, and structural approaches, the precise arrangement of the 11 (or more) N-DRC subunits remains unknown. Here, using cryo-electron tomography, we have compared the structure of Chlamydomonas wild-type flagella to that of strains with specific DRC subunit deletions or rescued strains with tagged DRC subunits. Our results show that DRC7 is a central linker subunit that helps connect the N-DRC to the outer dynein arms. DRC11 is required for the assembly of DRC8, and DRC8/11 form a subcomplex in the proximal lobe of the linker domain that is required to form stable contacts to the neighboring B-tubule. Gold labeling of tagged subunits determines the precise locations of the previously ambiguous N terminus of DRC4 and C terminus of DRC5. DRC4 is now shown to contribute to the core scaffold of the N-DRC. Our results reveal the overall architecture of N-DRC, with the 3 subunits DRC1/2/4 forming a core complex that serves as the scaffold for the assembly of the "functional subunits," namely DRC3/5-8/11. These findings shed light on N-DRC assembly and its role in regulating flagellar beating.

The Mars1 kinase confers photoprotection through signaling in the chloroplast unfolded protein response

In response to proteotoxic stress, chloroplasts communicate with the nuclear gene expression system through a chloroplast unfolded protein response (cpUPR). We isolated Chlamydomonas reinhardtii mutants that disrupt cpUPR signaling and identified a gene encoding a previously uncharacterized cytoplasmic protein kinase, termed Mars1-for mutant affected in chloroplast-to-nucleus retrograde signaling-as the first known component in cpUPR signal transmission. Lack of cpUPR induction in MARS1 mutant cells impaired their ability to cope with chloroplast stress, including exposure to excessive light. Conversely, transgenic activation of cpUPR signaling conferred an advantage to cells undergoing photooxidative stress. Our results indicate that the cpUPR mitigates chloroplast photodamage and that manipulation of this pathway is a potential avenue for engineering photosynthetic organisms with increased tolerance to chloroplast stress.

FAP57/WDR65 targets assembly of a subset of inner arm dyneins and connects to regulatory hubs in cilia

Ciliary motility depends on both the precise spatial organization of multiple dynein motors within the 96 nm axonemal repeat and the highly coordinated interactions between different dyneins and regulatory complexes located at the base of the radial spokes. Mutations in genes encoding cytoplasmic assembly factors, intraflagellar transport factors, docking proteins, dynein subunits, and associated regulatory proteins can all lead to defects in dynein assembly and ciliary motility. Significant progress has been made in the identification of dynein subunits and extrinsic factors required for preassembly of dynein complexes in the cytoplasm, but less is known about the docking factors that specify the unique binding sites for the different dynein isoforms on the surface of the doublet microtubules. We have used insertional mutagenesis to identify a new locus, IDA8/BOP2, required for targeting the assembly of a subset of inner dynein arms (IDAs) to a specific location in the 96 nm repeat. IDA8 encodes flagellar-associated polypeptide (FAP)57/WDR65, a highly conserved WD repeat, coiled coil domain protein. Using high resolution proteomic and structural approaches, we find that FAP57 forms a discrete complex. Cryo-electron tomography coupled with epitope tagging and gold labeling reveal that FAP57 forms an extended structure that interconnects multiple IDAs and regulatory complexes.

Subcellular Energetics and Carbon Storage in Chlamydomonas

Microalgae have emerged as a promising platform for production of carbon- and energy- rich molecules, notably starch and oil. Establishing an economically viable algal biotechnology sector requires a holistic understanding of algal photosynthesis, physiology, cell cycle and metabolism. Starch/oil productivity is a combined effect of their cellular content and cell division activities. Cell growth, starch and fatty acid synthesis all require carbon building blocks and a source of energy in the form of ATP and NADPH, but with a different requirement in ATP/NADPH ratio. Thus, several cellular mechanisms have been developed by microalgae to balance ATP and NADPH supply which are essentially produced by photosynthesis. Major energy management mechanisms include ATP production by the chloroplast-based cyclic electron flow and NADPH removal by water-water cycles. Furthermore, energetic coupling between chloroplast and other cellular compartments, mitochondria and peroxisome, is increasingly recognized as an important process involved in the chloroplast redox poise. Emerging literature suggests that alterations of energy management pathways affect not only cell fitness and survival, but also influence biomass content and composition. These emerging discoveries are important steps towards diverting algal photosynthetic energy to useful products for biotechnological applications.

Proteomics Analysis of Lipid Droplets from the Oleaginous Alga Chromochloris zofingiensis Reveals Novel Proteins for Lipid Metabolism

Chromochloris zofingiensis represents an industrially relevant and unique green alga, given its capability of synthesizing triacylglycerol (TAG) and astaxanthin simultaneously for storage in lipid droplets (LDs). To further decipher lipid metabolism, the nitrogen deprivation (ND)-induced LDs from C. zofingiensis were isolated, purified, and subjected to proteomic analysis. Intriguingly, many C. zofingiensis LD proteins had no orthologs present in LD proteome of the model alga Chlamydomonas reinhardtii. Seven novel LD proteins (i.e., two functionally unknown proteins, two caleosins, two lipases, and one l-gulonolactone oxidase) and the major LD protein (MLDP), which were all transcriptionally up-regulated by ND, were selected for further investigation. Heterologous expression in yeast demonstrated that all tested LD proteins were localized to LDs and all except the two functionally unknown proteins enabled yeast to produce more TAG. MLDP could restore the phenotype of mldp mutant strain and enhance TAG synthesis in wild-type strain of C. reinhardtii. Although MLDP and caleosins had a comparable abundance in LDs, they responded distinctly to ND at the transcriptional level. The two lipases, instead of functioning as TAG lipases, likely recycled polar lipids to support TAG synthesis. For the first time, we reported that l-gulonolactone oxidase was abundant in LDs and facilitated TAG accumulation. Moreover, we also proposed a novel working model for C. zofingiensis LDs. Taken together, our work unravels the unique characteristics of C. zofingiensis LDs and provides insights into algal LD biogenesis and TAG synthesis, which would facilitate genetic engineering of this alga for TAG improvement.

The Synthetic Biology Toolkit for Photosynthetic Microorganisms

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

Thylakoid localized bestrophin-like proteins are essential for the CO2 concentrating mechanism of Chlamydomonas reinhardtii

The green alga Chlamydomonas reinhardtii possesses a CO₂ concentrating mechanism (CCM) that helps in successful acclimation to low CO₂ conditions. Current models of the CCM postulate that a series of ion transporters bring HCO₃^- from outside the cell to the thylakoid lumen, where the carbonic anhydrase 3 (CAH3) dehydrates accumulated HCO₃^- to CO₂, raising the CO₂ concentration for Ribulose bisphosphate carboxylase/oxygenase (Rubisco). Previously, HCO₃^- transporters have been identified at both the plasma membrane and the chloroplast envelope, but the transporter thought to be on the thylakoid membrane has not been identified. Three paralogous genes (BST1, BST2, and BST3) belonging to the bestrophin family have been found to be up-regulated in low CO₂ conditions, and their expression is controlled by CIA5, a transcription factor that controls many CCM genes. YFP fusions demonstrate that all 3 proteins are located on the thylakoid membrane, and interactome studies indicate that they might associate with chloroplast CCM components. A single mutant defective in BST3 has near-normal growth on low CO₂, indicating that the 3 bestrophin-like proteins may have redundant functions. Therefore, an RNA interference (RNAi) approach was adopted to reduce the expression of all 3 genes at once. RNAi mutants with reduced expression of BST1-3 were unable to grow at low CO₂ concentrations, exhibited a reduced affinity to inorganic carbon (C_i) compared with the wild-type cells, and showed reduced C_i uptake. We propose that these bestrophin-like proteins are essential components of the CCM that deliver HCO₃^- accumulated in the chloroplast stroma to CAH3 inside the thylakoid lumen.

Thylakoid localized bestrophin-like proteins are essential for the CO2 concentrating mechanism of Chlamydomonas reinhardtii

Models of the CO₂ concentrating mechanism (CCM) of green algae and diatoms postulate that chloroplast CO₂ is generated from HCO₃⁻ brought into the acidic thylakoid lumen and converted to CO₂ by specific thylakoid carbonic anhydrases. However, the identity of the transporter required for thylakoid HCO₃⁻ uptake has remained elusive. In this work, 3 bestrophin-like proteins, BST1–3, located on the thylakoid membrane have been found to be essential to the CCM of Chlamydomonas. Reduction in expression of BST1–3 markedly reduced the inorganic carbon affinity of the alga. These proteins are prime candidates to be thylakoid HCO₃⁻ transporters, a critical currently missing step of the CCM required for future engineering efforts of the Chlamydomonas CCM into plants to improve photosynthesis.

The green alga Chlamydomonas reinhardtii possesses a CO₂ concentrating mechanism (CCM) that helps in successful acclimation to low CO₂ conditions. Current models of the CCM postulate that a series of ion transporters bring HCO₃⁻ from outside the cell to the thylakoid lumen, where the carbonic anhydrase 3 (CAH3) dehydrates accumulated HCO₃⁻ to CO₂, raising the CO₂ concentration for Ribulose bisphosphate carboxylase/oxygenase (Rubisco). Previously, HCO₃⁻ transporters have been identified at both the plasma membrane and the chloroplast envelope, but the transporter thought to be on the thylakoid membrane has not been identified. Three paralogous genes (BST1, BST2, and BST3) belonging to the bestrophin family have been found to be up-regulated in low CO₂ conditions, and their expression is controlled by CIA5, a transcription factor that controls many CCM genes. YFP fusions demonstrate that all 3 proteins are located on the thylakoid membrane, and interactome studies indicate that they might associate with chloroplast CCM components. A single mutant defective in BST3 has near-normal growth on low CO₂, indicating that the 3 bestrophin-like proteins may have redundant functions. Therefore, an RNA interference (RNAi) approach was adopted to reduce the expression of all 3 genes at once. RNAi mutants with reduced expression of BST1–3 were unable to grow at low CO₂ concentrations, exhibited a reduced affinity to inorganic carbon (C_i) compared with the wild-type cells, and showed reduced C_i uptake. We propose that these bestrophin-like proteins are essential components of the CCM that deliver HCO₃⁻ accumulated in the chloroplast stroma to CAH3 inside the thylakoid lumen.

A Series of Fortunate Events: Introducing Chlamydomonas as a Reference Organism

The unicellular alga Chlamydomonas reinhardtii is a classical reference organism for studying photosynthesis, chloroplast biology, cell cycle control, and cilia structure and function. It is also an emerging model for studying sensory cilia, the production of high-value bioproducts, and in situ structural determination. Much of the early appeal of Chlamydomonas was rooted in its promise as a genetic system, but like other classic model organisms, this rise to prominence predated the discovery of the structure of DNA, whole-genome sequences, and molecular techniques for gene manipulation. The haploid genome of C. reinhardtii facilitates genetic analyses and offers many of the advantages of microbial systems applied to a photosynthetic organism. C. reinhardtii has contributed to our understanding of chloroplast-based photosynthesis and cilia biology. Despite pervasive transgene silencing, technological advances have allowed researchers to address outstanding lines of inquiry in algal research. The most thoroughly studied unicellular alga, C. reinhardtii, is the current standard for algal research, and although genome editing is still far from efficient and routine, it nevertheless serves as a template for other algae. We present a historical retrospective of the rise of C. reinhardtii to illuminate its past and present. We also present resources for current and future scientists who may wish to expand their studies to the realm of microalgae.

Advances in microalgal research and engineering development

Microalgae have been investigated for the photosynthetic production of natural products with industrial and biomedical applications. Their rapid growth offers an advantage over higher plants, while their complex metabolic capacities allow for the production of various molecules. Despite their potentials, molecular techniques are underdeveloped in microalgae compared to higher plants, fungi, and bacteria. However, recent advances in genome sequencing, strain development, and genome editing technologies, are providing thrust to enhance research on microalgal species that have branched out from several focal model organisms to encompass a great diversity of species. In this review, we highlight the recent, significant advances in microalgal research, with a focus on the development of new resources that can enhance work on model and non-model species.

Molecular characterization of Chlamydomonas reinhardtii telomeres and telomerase mutants

This study characterizes the sequence, end structure, and length distribution of Chlamydomonas reinhardtii telomeres and shows that telomerase mutants are defective in telomere maintenance.

Telomeres are repeated sequences found at the end of the linear chromosomes of most eukaryotes and are required for chromosome integrity. Expression of the reverse-transcriptase telomerase allows for extension of telomeric repeats to counteract natural telomere shortening. Although Chlamydomonas reinhardtii, a photosynthetic unicellular green alga, is widely used as a model organism in photosynthesis and flagella research, and for biotechnological applications, the biology of its telomeres has not been investigated in depth. Here, we show that the C. reinhardtii (TTTTAGGG)_n telomeric repeats are mostly nondegenerate and that the telomeres form a protective structure, with a subset ending with a 3′ overhang and another subset presenting a blunt end. Although telomere size and length distributions are stable under various standard growth conditions, they vary substantially between 12 genetically close reference strains. Finally, we identify CrTERT, the gene encoding the catalytic subunit of telomerase and show that telomeres shorten progressively in mutants of this gene. Telomerase mutants eventually enter replicative senescence, demonstrating that telomerase is required for long-term maintenance of telomeres in C. reinhardtii.

LIP4 Is Involved in Triacylglycerol Degradation in Chlamydomonas reinhardtii

Degradation of the storage compound triacylglycerol (TAG) is a crucial process in response to environmental stimuli. In microalgae, this process is important for re-growth when conditions become favorable after cells have experienced stresses. Mobilization of TAG is initiated by actions of lipases causing the release of glycerol and free fatty acids, which can be further broken down for energy production or recycled to synthesize membrane lipids. Although key enzymes in the process, TAG lipases remain to be characterized in the model green alga Chlamydomonas reinhardtii. Here, we describe the functional analysis of a putative TAG lipase, i.e. LIP4, which shares 44% amino acid identity with the major TAG lipase in Arabidopsis (SUGAR DEPENDENT1-SDP1). The LIP4 transcript level was downregulated during nitrogen deprivation when TAG accumulates, but was upregulated during nitrogen resupply (NR) when TAG was degraded. Both artificial microRNA and insertional mutants showed a delay in TAG mobilization during NR. The difference in TAG degradation was more pronounced when the cultures were incubated without acetate in the dark. Furthermore, the lip4 insertional mutants over-accumulated TAG during optimal growth conditions. Taken together, the results suggest to us that LIP4 likely acts as a TAG lipase and plays a role in TAG homeostasis in Chlamydomonas.

Characterization of the GPR1/FUN34/YaaH protein family in the green microalga Chlamydomonas suggests their role as intracellular membrane acetate channels

The unicellular green microalga Chlamydomonas reinhardtii is a powerful photosynthetic model organism which is capable of heterotrophic growth on acetate as a sole carbon source. This capacity has enabled its use for investigations of perturbations in photosynthetic machinery as mutants can be recovered heterotrophically. Fixation of acetate into cellular carbon metabolism occurs first by its conversion into acetyl-CoA by a respective synthase and the generation of succinate by the glyoxylate cycle. These metabolic steps have been recently determined to largely occur in the peroxisomes of this alga; however, little is known about the trafficking and import of acetate or its subcellular compartmentalization. Recently, the genes of five proteins belonging to the GPR1/FUN34/YaaH (GFY) superfamily were observed to exhibit increased expression in C. reinhardtii upon acetate addition, however, no further characterization has been reported. Here, we provide several lines of evidence to implicate Cr GFY1-5 as channels which share structural homology with bacterial succinate-acetate channels and specifically localize to microbodies, which are surprisingly distinct from the glyoxylate cycle-containing peroxisomes. We demonstrate structural models, gene expression profiling, and in vivo fluorescence localization of all five isoforms in the algal cell to further support this role.

Molecular Genetic Tools and Emerging Synthetic Biology Strategies to Increase Cellular Oil Content in Chlamydomonas reinhardtii

Microalgae constitute a highly diverse group of eukaryotic and photosynthetic microorganisms that have developed extremely efficient systems for harvesting and transforming solar energy into energy-rich molecules such as lipids. Although microalgae are considered to be one of the most promising platforms for the sustainable production of liquid oil, the oil content of these organisms is naturally low, and algal oil production is currently not economically viable. Chlamydomonas reinhardtii (Chlamydomonas) is an established algal model due to its fast growth, high transformation efficiency, and well-understood physiology and to the availability of detailed genome information and versatile molecular tools for this organism. In this review, we summarize recent advances in the development of genetic manipulation tools for Chlamydomonas, from gene delivery methods to state-of-the-art genome-editing technologies and fluorescent dye-based high-throughput mutant screening approaches. Furthermore, we discuss practical strategies and toolkits that enhance transgene expression, such as choice of expression vector and background strain. We then provide examples of how advanced genetic tools have been used to increase oil content in Chlamydomonas. Collectively, the current literature indicates that microalgal oil content can be increased by overexpressing key enzymes that catalyze lipid biosynthesis, blocking lipid degradation, silencing metabolic pathways that compete with lipid biosynthesis and modulating redox state. The tools and knowledge generated through metabolic engineering studies should pave the way for developing a synthetic biological approach to enhance lipid productivity in microalgae.

PACRG and FAP20 form the inner junction of axonemal doublet microtubules and regulate ciliary motility

We previously demonstrated that PACRG plays a role in regulating dynein-driven microtubule sliding in motile cilia. To expand our understanding of the role of PACRG in ciliary assembly and motility, we used a combination of functional and structural studies, including newly identified Chlamydomonas pacrg mutants. Using cryo-electron tomography we show that PACRG and FAP20 form the inner junction between the A- and B-tubule along the length of all nine ciliary doublet microtubules. The lack of PACRG and FAP20 also results in reduced assembly of inner-arm dynein IDA b and the beak-MIP structures. In addition, our functional studies reveal that loss of PACRG and/or FAP20 causes severe cell motility defects and reduced in vitro microtubule sliding velocities. Interestingly, the addition of exogenous PACRG and/or FAP20 protein to isolated mutant axonemes restores microtubule sliding velocities, but not ciliary beating. Taken together, these studies show that PACRG and FAP20 comprise the inner junction bridge that serves as a hub for both directly modulating dynein-driven microtubule sliding, as well as for the assembly of additional ciliary components that play essential roles in generating coordinated ciliary beating.

Proteome of the central apparatus of a ciliary axoneme

The central apparatus is an essential component of “9+2” cilia. Zhao et al. identify more than 40 new potential components of the central apparatus of Chlamydomonas. Many are conserved and will facilitate genetic screening of patients with a form of primary ciliary dyskinesia that is difficult to diagnose.

Nearly all motile cilia have a “9+2” axoneme containing a central apparatus (CA), consisting of two central microtubules with projections, that is essential for motility. To date, only 22 proteins are known to be CA components. To identify new candidate CA proteins, we used mass spectrometry to compare axonemes of wild-type Chlamydomonas and a CA-less mutant. We identified 44 novel candidate CA proteins, of which 13 are conserved in humans. Five of the latter were studied more closely, and all five localized to the CA; therefore, most of the other candidates are likely to also be CA components. Our results reveal that the CA is far more compositionally complex than previously recognized and provide a greatly expanded knowledge base for studies to understand the architecture of the CA and how it functions. The discovery of the new conserved CA proteins will facilitate genetic screening to identify patients with a form of primary ciliary dyskinesia that has been difficult to diagnose.

Electrical energy storage with engineered biological systems

The availability of renewable energy technologies is increasing dramatically across the globe thanks to their growing maturity. However, large scale electrical energy storage and retrieval will almost certainly be a required in order to raise the penetration of renewable sources into the grid. No present energy storage technology has the perfect combination of high power and energy density, low financial and environmental cost, lack of site restrictions, long cycle and calendar lifespan, easy materials availability, and fast response time. Engineered electroactive microbes could address many of the limitations of current energy storage technologies by enabling rewired carbon fixation, a process that spatially separates reactions that are normally carried out together in a photosynthetic cell and replaces the least efficient with non-biological equivalents. If successful, this could allow storage of renewable electricity through electrochemical or enzymatic fixation of carbon dioxide and subsequent storage as carbon-based energy storage molecules including hydrocarbons and non-volatile polymers at high efficiency. In this article we compile performance data on biological and non-biological component choices for rewired carbon fixation systems and identify pressing research and engineering challenges.

The bZIP1 Transcription Factor Regulates Lipid Remodeling and Contributes to ER Stress Management in Chlamydomonas reinhardtii

Endoplasmic reticulum (ER) stress is caused by the stress-induced accumulation of unfolded proteins in the ER. Here, we identified proteins and lipids that function downstream of the ER stress sensor INOSITOL-REQUIRING ENZYME1 (CrIRE1) that contributes to ER stress tolerance in Chlamydomonas (Chlamydomonas reinhardtii). Treatment with the ER stress inducer tunicamycin resulted in the splicing of a 32-nucleotide fragment of a basic leucine zipper 1 (bZIP1) transcription factor (CrbZIP1) mRNA by CrIRE1 that, in turn, resulted in the loss of the transmembrane domain in CrbZIP1, and the translocation of CrbZIP1 from the ER to the nucleus. Mutants deficient in CrbZIP1 failed to induce the expression of the unfolded protein response genes and grew poorly under ER stress. Levels of diacylglyceryltrimethylhomoserine (DGTS) and pinolenic acid (18:3Δ5,9,12) increased in the parental strains but decreased in the crbzip1 mutants under ER stress. A yeast one-hybrid assay revealed that CrbZIP1 activated the expression of enzymes catalyzing the biosynthesis of DGTS and pinolenic acid. Moreover, two lines harboring independent mutant alleles of Chlamydomonas desaturase (CrDES) failed to synthesize pinolenic acid and were more sensitive to ER stress than were their parental lines. Together, these results indicate that CrbZIP1 is a critical component of the ER stress response mediated by CrIRE1 in Chlamydomonas that acts via lipid remodeling.

Skeletonema marinoi as a new genetic model for marine chain-forming diatoms

Diatoms are ubiquitous primary producers in marine ecosystems and freshwater habitats. Due to their complex evolutionary history, much remains unknown about the specific gene functions in diatoms that underlie their broad ecological success. In this study, we have genetically transformed the centric diatom Skeletonema marinoi, a dominant phytoplankton species in temperate coastal regions. Transformation of S. marinoi is the first for a true chain-forming diatom, with the random genomic integration via nonhomologous recombination of a linear DNA construct expressing the resistance gene to the antibiotic zeocin. A set of molecular tools were developed for reliably identifying the genomic insertion site within each transformant, many of which disrupt recognizable genes and constitute null or knock-down mutations. We now propose S. marinoi as a new genetic model for marine diatoms, representing true chain-forming species that play a central role in global photosynthetic carbon sequestration and the biogeochemical cycling of silicates and various nutrients, as well as having potential biotechnological applications.

Branched-Chain Amino Acid Catabolism Impacts Triacylglycerol Homeostasis in Chlamydomonas reinhardtii

Nitrogen (N) starvation-induced triacylglycerol (TAG) synthesis, and its complex relationship with starch metabolism in algal cells, has been intensively studied; however, few studies have examined the interaction between amino acid metabolism and TAG biosynthesis. Here, via a forward genetic screen for TAG homeostasis, we isolated a Chlamydomonas (Chlamydomonas reinhardtii) mutant (bkdE1α) that is deficient in the E1α subunit of the branched-chain ketoacid dehydrogenase (BCKDH) complex. Metabolomics analysis revealed a defect in the catabolism of branched-chain amino acids in bkdE1α Furthermore, this mutant accumulated 30% less TAG than the parental strain during N starvation and was compromised in TAG remobilization upon N resupply. Intriguingly, the rate of mitochondrial respiration was 20% to 35% lower in bkdE1α compared with the parental strains. Three additional knockout mutants of the other components of the BCKDH complex exhibited phenotypes similar to that of bkdE1α Transcriptional responses of BCKDH to different N status were consistent with its role in TAG homeostasis. Collectively, these results indicate that branched-chain amino acid catabolism contributes to TAG metabolism by providing carbon precursors and ATP, thus highlighting the complex interplay between distinct subcellular metabolisms for oil storage in green microalgae.

A genome-wide algal mutant library and functional screen identifies genes required for eukaryotic photosynthesis

Photosynthetic organisms provide food and energy for nearly all life on Earth, yet half of their protein-coding genes remain uncharacterized^1,2. Characterization of these genes could be greatly accelerated by new genetic resources for unicellular organisms. Here we generated a genome-wide, indexed library of mapped insertion mutants for the unicellular alga Chlamydomonas reinhardtii. The 62,389 mutants in the library, covering 83% of nuclear protein-coding genes, are available to the community. Each mutant contains unique DNA barcodes, allowing the collection to be screened as a pool. We performed a genome-wide survey of genes required for photosynthesis, which identified 303 candidate genes. Characterization of one of these genes, the conserved predicted phosphatase-encoding gene CPL3, showed that it is important for accumulation of multiple photosynthetic protein complexes. Notably, 21 of the 43 higher-confidence genes are novel, opening new opportunities for advances in understanding of this biogeochemically fundamental process. This library will accelerate the characterization of thousands of genes in algae, plants, and animals.

Identifying RNA splicing factors using IFT genes in Chlamydomonas reinhardtii

Intraflagellar transport moves proteins in and out of flagella/cilia and it is essential for the assembly of these organelles. Using whole-genome sequencing, we identified splice site mutations in two IFT genes, IFT81 (fla9) and IFT121 (ift121-2), which lead to flagellar assembly defects in the unicellular green alga Chlamydomonas reinhardtii. The splicing defects in these ift mutants are partially corrected by mutations in two conserved spliceosome proteins, DGR14 and FRA10. We identified a dgr14 deletion mutant, which suppresses the 3′ splice site mutation in IFT81, and a frameshift mutant of FRA10, which suppresses the 5′ splice site mutation in IFT121. Surprisingly, we found dgr14-1 and fra10 mutations suppress both splice site mutations. We suggest these two proteins are involved in facilitating splice site recognition/interaction; in their absence some splice site mutations are tolerated. Nonsense mutations in SMG1, which is involved in nonsense-mediated decay, lead to accumulation of aberrant transcripts and partial restoration of flagellar assembly in the ift mutants. The high density of introns and the conservation of noncore splicing factors, together with the ease of scoring the ift mutant phenotype, make Chlamydomonas an attractive organism to identify new proteins involved in splicing through suppressor screening.

A genome-wide algal mutant library and functional screen identifies genes required for eukaryotic photosynthesis

Photosynthetic organisms provide food and energy for nearly all life on Earth, yet half of their protein-coding genes remain uncharacterized^1,2. Characterization of these genes could be greatly accelerated by new genetic resources for unicellular organisms. Here, we generated a genome-wide, indexed library of mapped insertion mutants for the unicellular alga Chlamydomonas reinhardtii. The 62,389 mutants in the library, covering 83% of nuclear, protein-coding genes, are available to the community. Each mutant contains unique DNA barcodes, allowing the collection to be screened as a pool. We performed a genome-wide survey of genes required for photosynthesis, which identified 303 candidate genes. Characterization of one of these genes, the conserved predicted phosphatase-encoding gene CPL3, showed it is important for accumulation of multiple photosynthetic protein complexes. Notably, 21 of the 43 highest-confidence genes are novel, opening new opportunities for advances in our understanding of this biogeochemically fundamental process. This library will accelerate the characterization of thousands of genes in algae, plants and animals.

Generation of a library of 62,389 mapped insertion mutants for the unicellular alga Chlamydomonas reinhardtii enables screening for genes required for photosynthesis and the identification of 303 candidate genes.

The dynamin-like protein Fzl promotes thylakoid fusion and resistance to light stress in Chlamydomonas reinhardtii

Large GTPases of the Dynamin Related Proteins (DRP) family shape lipid bilayers through membrane fission or fusion processes. Despite the highly organized photosynthetic membranes of thylakoids, a single DRP is known to be targeted inside the chloroplast. Fzl from the land plant Arabidopsis thaliana is inserted in the inner envelope and thylakoid membranes to regulate their morphology. Fzl may promote the fusion of thylakoids but this remains to be proven. Moreover, the physiological requirement for fusing thylakoids is currently unknown. Here, we find that the unicellular microalga Chlamydomonas reinhardtii encodes an Fzl ortholog (CrFzl) that is localized in the chloroplast where it is soluble. To explore its function, the CRISPR/Cas9 technology was employed to generate multiple CrFzl knock out strains. Phenotypic analyzes revealed a specific requirement of CrFzl for survival upon light stress. Consistent with this, strong irradiance lead to increased photoinhibition of photosynthesis in mutant cells. Fluorescence and electron microscopy analysis demonstrated that upon exposure to high light, CrFzl mutants show defects in chloroplast morphology but also large cytosolic vacuoles in close contact with the plastid. We further observe that strong irradiance induces an increased recruitment of the DRP to thylakoid membranes. Most importantly, we show that CrFzl is required for the fusion of thylakoids during mating. Together, our results suggest that thylakoids fusion may be necessary for resistance to light stress.

All eukaryotic cells are composed of compartments with defined functions. Among those, mitochondria generate the main source of energy in human and animal cells. Their capacity to generate and diffuse energy in the cell is regulated by fusion and fragmentation processes.

Together with mitochondria that produce energy from oxygen, plant cells include an additional compartment called the chloroplast that produces energy from light. The machinery that converts light into energy is more precisely located inside the chloroplast within stacks of membranes called the thylakoids. Here, we elucidate the function of CrFzl, a previously uncharacterized protein encoded by the genome of the unicellular alga Chlamydomonas reinhardtii. Algal cells that do not contain CrFzl are impaired in their capacity to grow when they receive too much light and our results indicate that CrFzl promotes the fusion of thylakoids during mating. These results suggest that membrane fusion is an essential tool for energy production in stress conditions by living organisms.

Efficient Editing of the Nuclear APT Reporter Gene in Chlamydomonas reinhardtii via Expression of a CRISPR-Cas9 Module

The clustered regularly interspaced short palindromic repeat/CRISPR-associated protein 9 (CRISPR/Cas9) technology is a versatile and useful tool to perform genome editing in different organisms ranging from bacteria and yeast to plants and mammalian cells. For a couple of years, it was believed that the system was inefficient and toxic in the alga Chlamydomonas reinhardtii. However, recently the system has been successfully implemented in this model organism, albeit relying mostly on the electroporation of ribonucleoproteins (RNPs) into cell wall deficient strains. This requires a constant source of RNPs and limits the application of the technology to strains that are not necessarily the most relevant from a biotechnological point of view. Here, we show that transient expression of the Streptococcus pyogenes Cas9 gene and sgRNAs, targeted to the single-copy nuclear apt9 gene, encoding an adenine phosphoribosyl transferase (APT), results in efficient disruption at the expected locus. Introduction of indels to the apt9 locus results in cell insensitivity to the otherwise toxic compound 2-fluoroadenine (2-FA). We have used agitation with glass beads and particle bombardment to introduce the plasmids carrying the coding sequences for Cas9 and the sgRNAs in a cell-walled strain of C. reinhardtii (CC-125). Using sgRNAs targeting exons 1 and 3 of apt9, we obtained disruption efficiencies of 3 and 30% on preselected 2-FA resistant colonies, respectively. Our results show that transient expression of Cas9 and a sgRNA can be used for editing of the nuclear genome inexpensively and at high efficiency. Targeting of the APT gene could potentially be used as a pre-selection marker for multiplexed editing or disruption of genes of interest.

Early Evolution of the Mitogen-Activated Protein Kinase Family in the Plant Kingdom

Mitogen-activated protein kinase (MAPK) pathways are central cellular signalling mechanisms in all eukaryotes. They are key regulators of the cell cycle and stress responses, yet evolution of MAPK families took markedly different paths in the animal and plant kingdoms. Instead of the characteristic divergence of MAPK types in animals, in plants an expanded network of ERK-like MAPKs has emerged. To gain insight into the early evolution of the plant MAPK family we identified and analysed MAPKs in 13 representative species across green algae, a large and diverse early-diverging lineage within the plant kingdom. Our results reveal that the plant MAPK gene family emerged from three types of progenitor kinases, which are ubiquitously present in algae, implying their formation in an early ancestor. Low number of MAPKs is characteristic across algae, the few losses or duplications are associated with genome complexity rather than habitat ecology, despite the importance of MAPKs in environmental signalling in flowering plants. ERK-type MAPKs are associated with cell cycle regulation in opisthokont models, yet in plants their stress-signalling function is more prevalent. Unicellular microalgae offer an excellent experimental system to study the cell cycle, and MAPK gene expression profiles show CDKB-like peaks around S/M phase in synchronised Chlamydomonas reinhardtii cultures, suggesting their participation in cell cycle regulation, in line with the notion that the ancestral eukaryotic MAPK was a cell cycle regulator ERK-like kinase. Our work also highlights the scarcity of signalling knowledge in microalgae, in spite of their enormous ecological impact and emerging economic importance.

The Role of Plastidic Trigger Factor Serving Protein Biogenesis in Green Algae and Land Plants

Biochemical processes in chloroplasts are important for virtually all life forms. Tight regulation of protein homeostasis and the coordinated assembly of protein complexes, composed of both imported and locally synthesized subunits, are vital to plastid functionality. Protein biogenesis requires the action of cotranslationally acting molecular chaperones. One such chaperone is trigger factor (TF), which is known to cotranslationally bind most newly synthesized proteins in bacteria, thereby assisting their correct folding and maturation. However, how these processes are regulated in chloroplasts remains poorly understood. We report here functional investigation of chloroplast-localized TF (TIG1) in the green alga (Chlamydomonas reinhardtii) and the vascular land plant Arabidopsis (Arabidopsis thaliana). We show that chloroplastic TIG1 evolved as a specialized chaperone. Unlike other plastidic chaperones that are functionally interchangeable with their prokaryotic counterpart, TIG1 was not able to complement the broadly acting ortholog in Escherichia coli. Whereas general chaperone properties such as the prevention of aggregates or substrate recognition seems to be conserved between bacterial and plastidic TFs, plant TIG1s differed by associating with only a relatively small population of translating ribosomes. Furthermore, a reduction of plastidic TIG1 levels leads to deregulated protein biogenesis at the expense of increased translation, thereby disrupting the chloroplast energy household. This suggests a central role of TIG1 in protein biogenesis in the chloroplast.

miRNA-Mediated Regulation of Synthetic Gene Circuits in the Green Alga Chlamydomonas reinhardtii

MicroRNAs (miRNAs), small RNA molecules of 20-24 nts, have many features that make them useful tools for gene expression regulation-small size, flexible design, target predictability, and action at a late stage of the gene expression pipeline. In addition, their role in fine-tuning gene expression can be harnessed to increase robustness of synthetic gene networks. In this work, we apply a synthetic biology approach to characterize miRNA-mediated gene expression regulation in the unicellular green alga Chlamydomonas reinhardtii. This characterization is then used to build tools based on miRNAs, such as synthetic miRNAs, miRNA-responsive 3'UTRs, miRNA decoys, and self-regulatory loops. These tools will facilitate the engineering of gene expression for new applications and improved traits in this alga.

Deletion of BSG1 in Chlamydomonas reinhardtii leads to abnormal starch granule size and morphology

Chlamydomonas reinhardtii represents an ideal model microbial system to decipher starch metabolism. In this green algae, in cells growing in photosynthetic conditions, starch mainly accumulates as a sheath surrounding the pyrenoid while in cells subjected to a nutrient starvation, numerous starch granules are filling up the plastid stroma. The mechanisms underlying and regulating this switch from photosynthetic to storage starch metabolisms are not known. In this work, we have isolated a Chlamydomonas mutant strain containing a deletion in chromosome 2 which displays abnormal starch granule distribution. Under nitrogen starvation, this strain contains an additional starch granules population. These granules are twice as big as the wild-type granules and display characteristics of photosynthetic starch. Genetic and functional complementation analyses allowed us to identify the gene responsible for this original phenotype which was called BSG1 for "Bimodal Starch Granule". Possible roles of BSG1 in starch metabolism modifications during the transition from photosynthetic to starved growth conditions are discussed.

Chlamydomonas as a tool to study tubulin polyglutamylation

The diversity of α- and β-tubulin is facilitated by various post-translational modifications (PTMs), such as acetylation, tyrosination, glycylation, glutamylation, phosphorylation and methylation. These PTMs affect the stability and structure of microtubules as well as the interaction between microtubules and microtubule-associated proteins, including molecular motors. Therefore, it is extremely important to investigate the roles of tubulin PTMs for understanding the cell cycle, cell motility and intracellular trafficking. Tubulin PTMs were first studied in the 1980s, and considerable progress has been made since then; it is likely that additional mechanisms remain yet to be elucidated. Here, we discuss one such modification, tubulin glutamylation, and introduce our research on the eukaryotic flagellum of the unicellular green alga Chlamydomonas reinhardtii.

The lipid biochemistry of eukaryotic algae

Algal lipid metabolism fascinates both scientists and entrepreneurs due to the large diversity of fatty acyl structures that algae produce. Algae have therefore long been studied as sources of genes for novel fatty acids; and, due to their superior biomass productivity, algae are also considered a potential feedstock for biofuels. However, a major issue in a commercially viable "algal oil-to-biofuel" industry is the high production cost, because most algal species only produce large amounts of oils after being exposed to stress conditions. Recent studies have therefore focused on the identification of factors involved in TAG metabolism, on the subcellular organization of lipid pathways, and on interactions between organelles. This has been accompanied by the development of genetic/genomic and synthetic biological tools not only for the reference green alga Chlamydomonas reinhardtii but also for Nannochloropsis spp. and Phaeodactylum tricornutum. Advances in our understanding of enzymes and regulatory proteins of acyl lipid biosynthesis and turnover are described herein with a focus on carbon and energetic aspects. We also summarize how changes in environmental factors can impact lipid metabolism and describe present and potential industrial uses of algal lipids.

Ten antenna proteins are associated with the core in the supramolecular organization of the photosystem I supercomplex in Chlamydomonas reinhardtii

Photosystem I (PSI) is a large pigment-protein complex mediating light-driven charge separation and generating a highly negative redox potential, which is eventually utilized to produce organic matter. In plants and algae, PSI possesses outer antennae, termed light-harvesting complex I (LHCI), which increase the energy flux to the reaction center. The number of outer antennae for PSI in the green alga Chlamydomonas reinhardtii is known to be larger than that of land plants. However, their exact number and location remain to be elucidated. Here, applying a newly established sample purification procedure, we isolated a highly pure PSI-LHCI supercomplex containing all nine LHCA gene products under state 1 conditions. Single-particle cryo-EM revealed the 3D structure of this supercomplex at 6.9 Å resolution, in which the densities near the PsaF and PsaJ subunits were assigned to two layers of LHCI belts containing eight LHCIs, whereas the densities between the PsaG and PsaH subunits on the opposite side of the LHCI belt were assigned to two extra LHCIs. Using single-particle cryo-EM, we also determined the 2D projection map of the lhca2 mutant, which confirmed the assignment of LHCA2 and LHCA9 to the densities between PsaG and PsaH. Spectroscopic measurements of the PSI-LHCI supercomplex suggested that the bound LHCA2 and LHCA9 proteins have the ability to increase the light-harvesting energy for PSI. We conclude that the PSI in C. reinhardtii has a larger and more distinct outer-antenna organization and higher light-harvesting capability than that in land plants.

Rapid and high efficiency transformation of Chlamydomonas reinhardtii by square-wave electroporation

Chlamydomonas reinhardtii, the unicellular green algae, is the model organism for studies in various physiological processes and for bioindustrial applications. To explore the molecular mechanisms underlying physiological processes or to establish engineered cell lines, the exogenous DNA needs to be integrated into the genome for the insertional mutagenesis or transgene expression. However, the amount of selected marker DNA is not seriously considered in the existing electroporation methods for mutants library construction. Here, we reported a rapid-and-high-efficiency transformation technique for cell-walled strains using square-wave electroporation system. The final yield with this electroporation method was 2-6 × 10³ transformants per μg exogenous DNA for cell-walled strains in a strain-dependent manner. In general, this electroporation technique was the easy and applicable way to build a mutant library for screening phenotypes of interest.

Marine and Freshwater Plants: Challenges and Expectations

The past decades have seen an increasing interest on the biology of photosynthetic species living in aquatic environments, including diverse organisms collectively called "algae." If we consider the relative size of scientific communities, marine and freshwater plants have been overall less studied than terrestrial ones. The efforts put on land plants were motivated by agriculture and forestry, applications for human industry, easy access to terrestrial ecosystems, and convenient cultivation methods in fields or growth chambers. By contrast, the fragmentary knowledge on the biology of algae, the hope to find in this biodiversity inspiration for biotechnologies, and the emergency created by the environmental crisis affecting oceans, lakes, rivers, or melting glaciers, have stressed the importance to make up for lost time. Needed efforts embrace a broad spectrum of disciplines, from environmental and evolutionary sciences, to molecular and cell biology. In this multiscale view, functional genomics and ecophysiology occupy a pivotal position linking molecular and cellular analyses and ecosystem-level studies. Without pretending to be exhaustive and with few selected references, six grand challenges, requiring multidisciplinary approaches, are introduced below.

Characterization of Fatty Acid Exporters involved in fatty acid transport for oil accumulation in the green alga Chlamydomonas reinhardtii

BACKGROUND

In the past few decades, microalgae biofuel has become one of the most interesting sources of renewable energy. However, the higher cost of microalgae biofuel compared to that of petroleum prevented microalgae biofuel production. Therefore, the research on increasing lipid productivity from microalgae becomes more important. The lipid production source, triacylglycerol biosynthesis in microalgae requires short chain fatty acids as substrates, which are synthesized in chloroplasts. However, the transport mechanism of fatty acids from microalgae chloroplasts to cytosol remains unknown.

RESULTS

cDNAs from two homologs of the Arabidopsis fatty acid exporter 1 (FAX1) were cloned from Chlamydomonas reinhardtii and were named crfax1 and crfax2. Both CrFAXs were involved in fatty acid transport, and their substrates were mainly C16 and C18 fatty acids. Overexpression of both CrFAXs increased the accumulation of the total lipid content in algae cells, and the fatty acid compositions were changed under normal TAP or nitrogen deprivation conditions. Overexpression of both CrFAXs also increased the chlorophyll content. The MGDG content was decreased but the TAG, DAG, DGDG and other lipid contents were increased in CrFAXs overexpression strains.

CONCLUSION

These results reveal that CrFAX1 and CrFAX2 were involved in mediating fatty acid export for lipids biosynthesis in C. reinhardtii. In addition, overexpression of both CrFAXs obviously increased the intracellular lipid content, especially the triacylglycerol content in microalgae, which provides a potential technology for the production of more biofuels using microalgae.

Nitrogen-dependent coordination of cell cycle, quiescence and TAG accumulation in Chlamydomonas

Microalgae hold great promises as sustainable cellular factories for the production of alternative fuels, feeds, and biopharmaceuticals for human health. While the biorefinery approach for fuels along with the coproduction of high-value compounds with industrial, therapeutic, or nutraceutical applications have the potential to make algal biofuels more economically viable, a number of challenges continue to hamper algal production systems at all levels. One such hurdle includes the metabolic trade-off often observed between the increased yields of desired products, such as triacylglycerols (TAG), and the growth of an organism. Initial genetic engineering strategies to improve lipid productivity in microalgae, which focused on overproducing the enzymes involved in fatty acid and TAG biosynthesis or inactivating competing carbon (C) metabolism, have seen some successes albeit at the cost of often greatly reduced biomass. Emergent approaches that aim at modifying the dynamics of entire metabolic pathways by engineering of pertinent transcription factors or signaling networks appear to have successfully achieved a balance between growth and neutral lipid accumulation. However, the biological knowledge of key signaling networks and molecular components linking these two processes is still incomplete in photosynthetic eukaryotes, making it difficult to optimize metabolic engineering strategies for microalgae. Here, we focus on nitrogen (N) starvation of the model green microalga, Chlamydomonas reinhardtii, to present the current understanding of the nutrient-dependent switch between proliferation and quiescence, and the drastic reprogramming of metabolism that results in the storage of C compounds following N starvation. We discuss the potential components mediating the transcriptional repression of cell cycle genes and the establishment of quiescence in Chlamydomonas, and highlight the importance of signaling pathways such as those governed by the target of rapamycin (TOR) and sucrose nonfermenting-related (SnRK) kinases in the coordination of metabolic status with cellular growth. A better understanding of how the cell division cycle is regulated in response to nutrient scarcity and of the signaling pathways linking cellular growth to energy and lipid homeostasis, is essential to improve the prospects of biofuels and biomass production in microalgae.

The flagellar membrane glycoprotein FMG-1B Is necessary for expression of force at the flagellar surface

In addition to bend propagation for swimming, Chlamydomonas cells use their flagella to glide along a surface. When polystyrene microspheres are added to cells, they attach to and move along the flagellar surface, thus serving as a proxy for gliding that can be used to assay for the flagellar components required for gliding motility. Gliding and microsphere movement are dependent on intraflagellar transport (IFT). Circumstantial evidence suggests that mechanical coupling of the IFT force-transducing machinery to a substrate is mediated by the flagellar transmembrane glycoprotein FMG-1B. Cells carrying an insertion in the 5’-UTR of the FMG-1B gene lack FMG-1B protein, yet assemble normal length flagella despite the loss of the major protein component of the flagellar membrane. Transmission electron microscopy shows a complete loss of the glycocalyx normally observed on the flagellar surface, suggesting it is composed of the ectodomains of FMG-1B molecules. Microsphere movements and gliding motility are also greatly reduced in the 5’-UTR mutant. Together, these data provide the first rigorous demonstration that FMG-1B is necessary for the normal expression of force at the flagellar surface in Chlamydomonas.

The mitochondrial alternative oxidase from Chlamydomonas reinhardtii enables survival in high light

Photosynthetic organisms often experience extreme light conditions that can cause hyper-reduction of the chloroplast electron transport chain, resulting in oxidative damage. Accumulating evidence suggests that mitochondrial respiration and chloroplast photosynthesis are coupled when cells are absorbing high levels of excitation energy. This coupling helps protect the cells from hyper-reduction of photosynthetic electron carriers and diminishes the production of reactive oxygen species (ROS). To examine this cooperative protection, here we characterized Chlamydomonas reinhardtii mutants lacking the mitochondrial alternative terminal respiratory oxidases, CrAOX1 and CrAOX2. Using fluorescent fusion proteins, we experimentally demonstrated that both enzymes localize to mitochondria. We also observed that the mutant strains were more sensitive than WT cells to high light under mixotrophic and photoautotrophic conditions, with the aox1 strain being more sensitive than aox2 Additionally, the lack of CrAOX1 increased ROS accumulation, especially in very high light, and damaged the photosynthetic machinery, ultimately resulting in cell death. These findings indicate that the Chlamydomonas AOX proteins can participate in acclimation of C. reinhardtii cells to excess absorbed light energy. They suggest that when photosynthetic electron carriers are highly reduced, a chloroplast-mitochondria coupling allows safe dissipation of photosynthetically derived electrons via the reduction of O₂ through AOX (especially AOX1)-dependent mitochondrial respiration.

MAPINS, a Highly Efficient Detection Method That Identifies Insertional Mutations and Complex DNA Rearrangements

Insertional mutagenesis, in which a piece of exogenous DNA is integrated randomly into the genomic DNA of the recipient cell, is a useful method to generate new mutants with phenotypes of interest. The unicellular green alga Chlamydomonas reinhardtii is an outstanding model for studying many biological processes. We developed a new computational algorithm, MAPINS (mapping insertions), to efficiently identify insertion sites created by the integration of an APHVIII (aminoglycoside 3'-phosphotransferase VIII) cassette that confers paromomycin resistance. Using whole-genome sequencing data, this method eliminates the need for genomic DNA manipulation and retains all the sequencing information provided by paired-end sequencing. We experimentally verified 38 insertion sites out of 41 sites (93%) identified by MAPINS from 20 paromomycin-resistant strains. Using meiotic analysis of 18 of these strains, we identified insertion sites that completely cosegregate with paromomycin resistance. In six of the seven strains with a mutant phenotype, we demonstrated complete cosegregation of the mutant phenotype and the verified insertion site. In addition, we provide direct evidence of complex rearrangements of genomic DNA in five strains, three of which involve the APHVIII insertion site. We suggest that strains obtained by insertional mutagenesis are more complicated than expected from previous analyses in Chlamydomonas To map the locations of some complex insertions, we designed 49 molecular markers based on differences identified via whole-genome sequencing between wild-type strains CC-124 and CC-125. Overall, MAPINS provides a low-cost, efficient method to characterize insertional mutants in Chlamydomonas.

Ciliary proteins Fap43 and Fap44 interact with each other and are essential for proper cilia and flagella beating

Cilia beating is powered by the inner and outer dynein arms (IDAs and ODAs). These multi-subunit macrocomplexes are arranged in two rows on each outer doublet along the entire cilium length, except its distal end. To generate cilia beating, the activity of ODAs and IDAs must be strictly regulated locally by interactions with the dynein arm-associated structures within each ciliary unit and coordinated globally in time and space between doublets and along the axoneme. Here, we provide evidence of a novel ciliary complex composed of two conserved WD-repeat proteins, Fap43p and Fap44p. This complex is adjacent to another WD-repeat protein, Fap57p, and most likely the two-headed inner dynein arm, IDA I1. Loss of either protein results in altered waveform, beat stroke and reduced swimming speed. The ciliary localization of Fap43p and Fap44p is interdependent in the ciliate Tetrahymena thermophila.

A Musashi Splice Variant and Its Interaction Partners Influence Temperature Acclimation in Chlamydomonas

Microalgae contribute significantly to carbon fixation on Earth. Global warming influences their physiology and growth rates. To understand algal short-term acclimation and adaptation to changes in ambient temperature, it is essential to identify and characterize the molecular components that sense small temperature changes as well as the downstream signaling networks and physiological responses. Here, we used the green biflagellate alga Chlamydomonas reinhardtii as a model system in which to study responses to temperature. We report that an RNA recognition motif (RRM)-containing RNA-binding protein, Musashi, occurs in 25 putative splice variants. These variants bear one, two, and three RRM domains or even lack RRM domains. The most abundant Musashi variant, 12, with a molecular mass of 60 kD, interacts with two clock-relevant members of RNA metabolism, the subunit C3 of the RNA-binding protein CHLAMY1 and the 5'-3' exoribonuclease XRN1. These proteins are able to integrate temperature information by up- or down-regulation of their protein levels in cells grown at low (18°C) or high (28°C) temperature. We further show that the 60-kD Musashi variants with three RRM domains can bind to (UG)₇ repeat-containing RNAs and are up-regulated in cells grown at a higher temperature during early night. Intriguingly, the 60-kD Musashi variant 12, as well as C3 and XRN1, confer thermal acclimation to C. reinhardtii, as shown with mutant lines. Our data suggest that these three proteins of the RNA metabolism machinery are key members of the thermal signaling network in C. reinhardtii.

The labile interactions of cyclic electron flow effector proteins

The supramolecular organization of membrane proteins (MPs) is sensitive to environmental changes in photosynthetic organisms. Isolation of MP supercomplexes from the green algae Chlamydomonas reinhardtii, which are believed to contribute to cyclic electron flow (CEF) between the cytochrome b6f complex (Cyt-b6f) and photosystem I (PSI), proved difficult. We were unable to isolate a supercomplex containing both Cyt-b6f and PSI because in our hands, most of Cyt-b6f did not comigrate in sucrose density gradients, even upon using chemical cross-linkers or amphipol substitution of detergents. Assisted by independent affinity purification and MS approaches, we utilized disintegrating MP assemblies and demonstrated that the algae-specific CEF effector proteins PETO and ANR1 are bona fide Cyt-b6f interactors, with ANR1 requiring the presence of an additional, presently unknown, protein. We narrowed down the Cyt-b6f interface, where PETO is loosely attached to cytochrome f and to a stromal region of subunit IV, which also contains phosphorylation sites for the STT7 kinase.

From molecular manipulation of domesticated Chlamydomonas reinhardtii to survival in nature

In the mid-20th century, the unicellular and genetically tractable green alga Chlamydomonas reinhardtii was first developed as a model organism to elucidate fundamental cellular processes such as photosynthesis, light perception and the structure, function and biogenesis of cilia. Various studies of C. reinhardtii have profoundly advanced plant and cell biology, and have also impacted algal biotechnology and our understanding of human disease. However, the 'real' life of C. reinhardtii in the natural environment has largely been neglected. To extend our understanding of the biology of C. reinhardtii, it will be rewarding to explore its behavior in its natural habitats, learning more about its abundance and life cycle, its genetic and physiological diversity, and its biotic and abiotic interactions.

Thermotaxis in Chlamydomonas is brought about by membrane excitation and controlled by redox conditions

Temperature is physiologically critical for all living organisms, which cope with temperature stress using metabolic and behavioral responses. In unicellular and some multicellular organisms, thermotaxis is a behavioral response to avoid stressful thermal environments and promote accumulation in an optimal thermal environment. In this study, we examined whether Chlamydomonas reinhardtii, a unicellular green alga, demonstrated thermotaxis. We found that between 10 °C and 30 °C, Chlamydomonas cells migrated toward lower temperatures independent of cultivation temperature. Interestingly, when we applied reagents to change intracellular reduction-oxidation (redox) conditions, we saw that thermotaxis was enhanced, suppressed, or reversed, depending on the redox conditions and cultivation temperature. Thermotaxis was almost absent in ppr2 and ppr3 mutants, which cannot swim backward because of a defect in generating calcium current in flagella. The frequency of spontaneous backward swimming was lower at more favorable temperature, suggesting a pivotal role of spontaneous backward swimming generated by flagellar membrane excitation.

The cryo-EM structure of intraflagellar transport trains reveals how dynein is inactivated to ensure unidirectional anterograde movement in cilia

Movement of cargos along microtubules plays key roles in diverse cellular processes, from signalling to mitosis. In cilia, rapid movement of ciliary components along the microtubules to and from the assembly site is essential for the assembly and disassembly of the structure itself¹. This bidirectional transport, known as intraflagellar transport (IFT)², is driven by the anterograde motor kinesin-2³ and the retrograde motor dynein-1b (dynein-2 in mammals)^4,5. However, to drive retrograde transport, dynein-1b must first be delivered to the ciliary tip by anterograde IFT⁶. Although, the presence of opposing motors in bidirectional transport processes often leads to periodic stalling and slowing of cargos⁷, IFT is highly processive^1,2,8. Using cryo-electron tomography, we show that a tug-of-war between kinesin-2 and dynein-1b is prevented by loading dynein-1b onto anterograde IFT trains in an autoinhibited form and by positioning it away from the microtubule track to prevent binding. Once at the ciliary tip, dynein-1b must transition into an active form and engage microtubules to power retrograde trains. These findings provide a striking example of how coordinated structural changes mediate the behaviour of complex cellular machinery.

Advanced genetic tools enable synthetic biology in the oleaginous microalgae Nannochloropsis sp

Nannochloropsis is a genus of fast-growing microalgae that are regularly used for biotechnology applications. Nannochloropsis species have a high triacylglycerol content and their polar lipids are rich in the omega-3 long-chain polyunsaturated fatty acid, eicosapentaenoic acid. Placed in the heterokont lineage, the Nannochloropsis genus has a complex evolutionary history. Genome sequences are available for several species, and a number of transcriptomic datasets have been produced, making this genus a facile model for comparative genomics. There is a growing interest in Nannochloropsis species as models for the study of microalga lipid metabolism and as a chassis for synthetic biology. Recently, techniques for gene stacking, and targeted gene disruption and repression in the Nannochloropsis genus have been developed. These tools enable gene-specific, mechanistic studies and have already allowed the engineering of improved Nannochloropsis strains with superior growth, or greater bioproduction.

Configuration of Ten Light-Harvesting Chlorophyll a/b Complex I Subunits in Chlamydomonas reinhardtii Photosystem I

In plants, the photosystem I (PSI) core complex stably associates with its light-harvesting chlorophyll a/b complex I (LHCI) to form the PSI-LHCI supercomplex. The vascular plant PSI core complex associates with four distinct LHCI subunits, whereas that of the green alga Chlamydomonas reinhardtii binds nine distinct LHCI subunits (LHCA1-LHCA9). The stoichiometry and configuration of these LHCI subunits in the PSI-LHCI supercomplex of C. reinhardtii remain controversial. Here, we determined the stoichiometry of the nine distinct LHCI subunits relative to PSI subunits through uniform labeling of total proteins using ¹⁴C. We separated the nine LHCI polypeptides by three different sodium dodecyl sulfate-polyacrylamide gel electrophoresis systems. Our data revealed that the PSI-LHCI supercomplex contains two LHCA1 proteins and one of each of the other eight LHCI subunits. Subsequently, we identified their cross-linked products by immunodetection and mass spectrometry to determine the configuration of the 10 LHCI subunits within the PSI-LHCI supercomplex. Furthermore, analyses of PSI-LHCI complexes isolated from ΔLHCA2 and ΔLHCA5 mutants and oligomeric LHCI from a PSI-deficient (ΔpsaA/B) mutant provided supporting evidence for the LHCI subunit configuration. In conclusion, eight LHCI subunits bind to the PSI core at the site of PSAF subunit in two layers: LHCA1-LHCA8-LHCA7-LHCA3 from PSAG to PSAK, in the inner layer, and LHCA1-LHCA4-LHCA6-LHCA5 in the outer layer. The other two LHCI subunits, LHCA2 and LHCA9, bind PSAB between PSAG and PSAH, PSAG-LHCA9-LHCA2-PSAH. Our study provides new insights into the LHCI configuration linked to the PSI core.