Pigments and photosynthesis in a carotenoid-deficient mutant of Chlamydomonas

Phytoplankton in the Tara Ocean

Photosynthesis evolved in the ocean more than 2 billion years ago and is now performed by a wide range of evolutionarily distinct organisms, including both prokaryotes and eukaryotes. Our appreciation of their abundance, distributions, and contributions to primary production in the ocean has been increasing since they were first discovered in the seventeenth century and has now been enhanced by data emerging from the Tara Oceans project, which performed a comprehensive worldwide sampling of plankton in the upper layers of the ocean between 2009 and 2013. Largely using recent data from Tara Oceans, here we review the geographic distributions of phytoplankton in the global ocean and their diversity, abundance, and standing stock biomass. We also discuss how omics-based information can be incorporated into studies of photosynthesis in the ocean and show the likely importance of mixotrophs and photosymbionts.

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.

Carotenoid deficiency triggers autophagy in the model green alga Chlamydomonas reinhardtii

All aerobic organisms have developed sophisticated mechanisms to prevent, detect and respond to cell damage caused by the unavoidable production of reactive oxygen species (ROS). Plants and algae are able to synthesize specific pigments in the chloroplast called carotenoids to prevent photo-oxidative damage caused by highly reactive by-products of photosynthesis. In this study we used the unicellular green alga Chlamydomonas reinhardtii to demonstrate that defects in carotenoid biosynthesis lead to the activation of autophagy, a membrane-trafficking process that participates in the recycling and degradation of damaged or toxic cellular components. Carotenoid depletion caused by either the mutation of phytoene synthase or the inhibition of phytoene desaturase by the herbicide norflurazon, resulted in a strong induction of autophagy. We found that high light transiently activates autophagy in wild-type Chlamydomonas cells as part of an adaptation response to this stress. Our results showed that a Chlamydomonas mutant defective in the synthesis of specific carotenoids that accumulate during high light stress exhibits constitutive autophagy. Moreover, inhibition of the ROS-generating NADPH oxidase partially reduced the autophagy induction associated to carotenoid deficiency, which revealed a link between photo-oxidative damage, ROS accumulation and autophagy activation in Chlamydomonas cells with a reduced carotenoid content.

Coordinated regulation of gene expression for carotenoid metabolism in Chlamydomonas reinhardtii

Carotenoids are important plant pigments for both light harvesting and photooxidation protection. Using the model system of the unicellular green alga Chlamydomonas reinhardtii, we characterized the regulation of gene expression for carotenoid metabolism by quantifying changes in the transcript abundance of dxs, dxr and ipi in the plastidic methylerythritol phosphate pathway and of ggps, psy, pds, lcyb and bchy, directly involved in carotenoid metabolism, under different photoperiod, light and metabolite treatments. The expression of these genes fluctuated with light/dark shifting. Light treatment also promoted the accumulation of transcripts of all these genes. Of the genes studied, dxs, ggps and lcyb displayed the typical circadian pattern by retaining a rhythmic fluctuation of transcript abundance under both constant light and constant dark entrainments. The expression of these genes could also be regulated by metabolic intermediates. For example, ggps was significantly suppressed by a geranylgeranyl pyrophosphate supplement and ipi was upregulated by isopentenyl pyrophosphate. Furthermore, CrOr, a C. reinhardtii homolog of the recently characterized Or gene that accounts for carotenoid accumulation, also showed co-expression with carotenoid biosynthetic genes such as pds and lcyb. Our data suggest a coordinated regulation on carotenoid metabolism in C. reinhardtii at the transcriptional level.

The ultrastructure of a Chlamydomonas reinhardtii mutant strain lacking phytoene synthase resembles that of a colorless alga

Chlamydomonas reinhardtii strains lacking phytoene synthase, the first enzyme of carotenoid biosynthesis, are white. They lack carotenoid pigments, have very low levels of chlorophyll, and can grow only heterotrophically in the dark. Our electron and fluorescence microscopic studies showed that such a mutant strain (lts1-204) had a proliferated plastid envelope membrane but no stacks of thylakoid membranes within the plastid. It accumulated cytoplasmic compartments that appeared to be autophagous vacuoles filled with membranous material. The lts1 mutants apparently lacked pyrenoid bodies, which normally house ribulose bisphosphate carboxylase-oxygenase (Rubisco), and accumulated many starch granules. Although these mutant strains cannot synthesize the carotenoid and carotenoid-derived pigments present in the phototactic organelle (eyespot), the mutant we examined made a vestigial eyespot that was disorganized and often mislocalized to the posterior end of the cell. The absence of a pyrenoid body, the accumulation of starch, and the disorganization of the eyespot may all result from the absence of thylakoids. The ultrastructure of lts1 mutant strains is similar to but distinct from that of previously described white and yellow mutant strains of C. reinhardtii and is similar to that of naturally colorless algae of the Polytoma group.

White mutants of Chlamydomonas reinhardtii are defective in phytoene synthase

Carotenoids play an integral and essential role in photosynthesis and photoprotection in plants and algae. A collection of Chlamydomonas reinhardtii mutants lacking carotenoids was characterized for pigment and tocopherol (vitamin E) composition, growth phenotypes under different light conditions, and the molecular basis of their mutant phenotype. The carotenoid-less mutants, or "white" mutants, were also deficient in chlorophylls but had approximately twice the tocopherol content of the wild type. White mutants grew in the dark but were unable to survive in the light, even under very low light conditions on acetate-containing medium. Genetic crosses and recombination tests revealed that all individual white mutants in the collection are alleles of a single gene, lts1, and the white phenotype was closely linked to a marker located in the phytoene synthase gene. DNA sequencing of the phytoene synthase gene from each of the mutants revealed nonsense, missense, frameshift, and splice site mutations. Transformation with a wild-type copy of the phytoene synthase gene was able to complement the lts1-210 mutation. Together, these results show that all the white mutants examined in this work are affected in the phytoene synthase gene.

Diversifying carotenoid biosynthetic pathways by directed evolution

Microorganisms and plants synthesize a diverse array of natural products, many of which have proven indispensable to human health and well-being. Although many thousands of these have been characterized, the space of possible natural products--those that could be made biosynthetically--remains largely unexplored. For decades, this space has largely been the domain of chemists, who have synthesized scores of natural product analogs and have found many with improved or novel functions. New natural products have also been made in recombinant organisms, via engineered biosynthetic pathways. Recently, methods inspired by natural evolution have begun to be applied to the search for new natural products. These methods force pathways to evolve in convenient laboratory organisms, where the products of new pathways can be identified and characterized in high-throughput screening programs. Carotenoid biosynthetic pathways have served as a convenient experimental system with which to demonstrate these ideas. Researchers have mixed, matched, and mutated carotenoid biosynthetic enzymes and screened libraries of these "evolved" pathways for the emergence of new carotenoid products. This has led to dozens of new pathway products not previously known to be made by the assembled enzymes. These new products include whole families of carotenoids built from backbones not found in nature. This review details the strategies and specific methods that have been employed to generate new carotenoid biosynthetic pathways in the laboratory. The potential application of laboratory evolution to other biosynthetic pathways is also discussed.

Molecular genetics of xanthophyll-dependent photoprotection in green algae and plants

The involvement of excited and highly reactive intermediates in oxygenic photosynthesis inevitably results in the generation of reactive oxygen species. To protect the photosynthetic apparatus from oxidative damage, xanthophyll pigments are involved in the quenching of excited chlorophyll and reactive oxygen species, namely 1Chl*, 3Chl*, and 1O2*. Quenching of 1Chl* results in harmless dissipation of excitation energy as heat and is measured as non-photochemical quenching (NPQ) of chlorophyll fluorescence. The multiple roles of xanthophylls in photoprotection are being addressed by characterizing mutants of Chlarnydomonas reinhardtii and Arabidopsis thaliana. Analysis of Arabidopsis mutants that are defective in 1Chl* quenching has shown that, in addition to specific xanthophylls, the psbS gene is necessary for NPQ. Double mutants of Chlamydomonas and Arabidopsis that are deficient in zeaxanthin, lutein and NPQ undergo photo-oxidative bleaching in high light. Extragenic suppressors of the Chlamydomonas npq1 lor1 double mutant identify new mutations that restore varying levels of zeaxanthin accumulation and allow survival in high light.

Eyespot-assembly mutants in Chlamydomonas reinhardtii

Chlamydomonas reinhardtii is a single-celled green alga that phototaxes toward light by means of a light-sensitive organelle, the eyespot. The eyespot is composed of photoreceptor and Ca(++)-channel signal transduction components in the plasma membrane of the cell and reflective carotenoid pigment layers in an underlying region of the large chloroplast. To identify components important for the positioning and assembly of a functional eyespot, a large collection of nonphototactic mutants was screened for those with aberrant pigment spots. Four loci were identified. eye2 and eye3 mutants have no pigmented eyespots. min1 mutants have smaller than wild-type eyespots. mlt1(ptx4) mutants have multiple eyespots. The MIN1, MLT1(PTX4), and EYE2 loci are closely linked to each other; EYE3 is unlinked to the other three loci. The eye2 and eye3 mutants are epistatic to min1 and mlt1 mutations; all double mutants are eyeless. min1 mlt1 double mutants have a synthetic phenotype; they are eyeless or have very small, misplaced eyespots. Ultrastructural studies revealed that the min1 mutants are defective in the physical connection between the plasma membrane and the chloroplast envelope membranes in the region of the pigment granules. Characterization of these four loci will provide a beginning for the understanding of eyespot assembly and localization in the cell.

PHOTOPROTECTION REVISITED:Genetic and Molecular Approaches

The involvement of excited and highly reactive intermediates in oxygenic photosynthesis poses unique problems for algae and plants in terms of potential oxidative damage to the photosynthetic apparatus. Photoprotective processes prevent or minimize generation of oxidizing molecules, scavenge reactive oxygen species efficiently, and repair damage that inevitably occurs. This review summarizes several photoprotective mechanisms operating within chloroplasts of plants and green algae. The recent use of genetic and molecular biological approaches is providing new insights into photoprotection, especially with respect to thermal dissipation of excess absorbed light energy, alternative electron transport pathways, chloroplast antioxidant systems, and repair of photosystem II.

The roles of specific xanthophylls in photoprotection

Xanthophyll pigments have critical structural and functional roles in the photosynthetic light-harvesting complexes of algae and vascular plants. Genetic dissection of xanthophyll metabolism in the green alga Chlamydomonas reinhardtii revealed functions for specific xanthophylls in the nonradiative dissipation of excess absorbed light energy, measured as nonphotochemical quenching of chlorophyll fluorescence. Mutants with a defect in either the alpha- or beta-branch of carotenoid biosynthesis exhibited less nonphotochemical quenching but were still able to tolerate high light. In contrast, a double mutant that was defective in the synthesis of lutein, loroxanthin (alpha-carotene branch), zeaxanthin, and antheraxanthin (beta-carotene branch) had almost no nonphotochemical quenching and was extremely sensitive to high light. These results strongly suggest that in addition to the xanthophyll cycle pigments (zeaxanthin and antheraxanthin), alpha-carotene-derived xanthophylls such as lutein, which are structural components of the subunits of the light-harvesting complexes, contribute to the dissipation of excess absorbed light energy and the protection of plants from photo-oxidative damage.

Photoinhibition of photosystem II from higher plants. Effect of copper inhibition

Strong illumination of Cu(II)-inhibited photosystem II membranes resulted in a faster loss of oxygen evolution activity compared with that of the intact samples. The phenomenon was oxygen- and temperature-dependent. However, D1 protein degradation rate was similar in both preparations and slower than that found in non-oxygen evolving PSII particles (i.e. Mn-depleted photosystem II). These results seem to indicate that during illumination Cu(II)-inhibited samples do not behave as a typical non-oxygen evolving photosystem II. Cytochrome b559 was functional in the presence of Cu(II). The effect of Cu(II) inhibition decreased the amount of photoreduced cytochrome b559 and slowed down the rate of its photoreduction. The presence of Cu(II) during illumination seems to protect P680 against photodamage as occurs in photosystem II reaction centers when the acceptor side is protected. The data were consistent with the finding that production of singlet oxygen was highly reduced in the preparations treated with Cu(II). EPR spin trapping experiments showed that inactivation of Cu(II)-treated samples was dominated by hydroxyl radical, and the loss of oxygen evolution activity was diminished by the presence of superoxide dismutase and catalase. These results indicate that the rapid loss of oxygen evolution activity in the presence of Cu(II) is mainly due to the formation of .OH radicals from superoxide ion via a Cu(II)-catalyzed Haber-Weiss mechanism. Considering that this inactivation process was oxygen-dependent, we propose that the formation of superoxide occurs in the acceptor side of photosystem II by interaction of molecular oxygen with reduced electron acceptor species, and thus, the primarily Cu(II)-inhibitory site in photosystem II is on the acceptor side.

Autoregulation of rhodopsin synthesis in Chlamydomonas reinhardtii

A sensitive assay for the induction of carotenoid and rhodopsin synthesis, based on the phototactic response, has been developed in a mutant of the unicellular alga Chlamydomonas reinhardtii. In the dark, the mutant fails to synthesize carotene and retinal, but it contains the apoprotein opsin. When retinal synthesis is induced by light treatment, the retinal combines with opsin to form rhodopsin, and the cells swim away from a source of light. Since the amount of light required to trigger a phototactic response is inversely proportional to the concentration of rhodopsin, the decrease in amount of light necessary to generate that response can serve as a measure of the amount of retinal synthesized in cells after induction. Using this assay, we found that (i) light induction of retinal depends linearly on light exposure and rhodopsin concentration during the exposure; (ii) the action spectrum of light induction is identical with that for phototaxis for which the receptor pigment is rhodopsin; and (iii) incubation with all-trans-7,8-dihydroretinal before light exposure shifts the action-spectrum peak for light induction 0.41 eV (-71 nm). We conclude that the photopigment for induction of retinal synthesis is a rhodopsin. The time lag required for induction of retinal synthesis and preliminary experiments with transcription or translation inhibitors suggest that alterations in gene expression could be involved in the induction process. Its control could be similar to other processes in which membrane receptors for hormones, neurotransmitters, or growth factors regulate gene expression.

Thylakoid membrane biogenesis in Chlamydomonas reinhardtii 137+. II. Cell-cycle variations in the synthesis and assembly of pigment

Synthesis of the chlorophyll and the major carotenoid pigments and their assembly into thylakoid membrane have been studied throughout the 12-h light/12-h dark vegetative cell cycle of synchronous Chlamydomonas reinhardtii 137+ (wild-type). Pulse exposure of cells to radioactive acetate under conditions in which labeling accurately reflects lipogenesis, followed by cellular fractionation to purify thylakoid membrane, allowed direct analysis of the pigment synthesis and assembly attendant to thylakoid biogenesis. All pigments are synthesized and assembled into thylakoids continuously, but differentially, with respect to cell-cycle time. Highest synthesis and assembly rates are confined to the photoperiod (mid-to-late G1) and support chlorophyll and carotenoid accretion before M-phase. The lower levels at which these processes take place during the dark period (S, M, and early-to-mid G1) have been ascribed to pigment turnover. Within this general periodic pattern, pigment synthesis and assembly occur in a "multi-step" manner, i.e., by a temporally-ordered, stepwise integration of the various pigments into the thylakoid membrane matrix. The cell-cycle kinetics of pigment assembly at the subcellular level mirror the kinetics of pigment synthesis at the cellular level, indicating that pigment synthesis not only provides chlorophyll and carotenoid for thylakoid biogenesis but may also serve as a critical rate-determinant to pigment assembly.

A series of mutant strains of Scenedesmus obliquus with abnormal carotenoid compositions

Several mutant strains of Scenedesmus obliquus (Chlorophyta) have been isolated which, when cultured heterotrophically, are pale green or yellow, in contrast to the dark green of the wild type. On the basis of their carotenoid compositions, four groups of pale-green strains have been delineated. These accumulate, respectively, no carotenoid, phytoene, mainly zeta-carotene and mainly zeta-carotene together with some neurosporene and lycopene. All these strains synthesized no chlorophyll b and only small amounts of chlorophyll a. A further group of yellow strains produced the normal Scenedesmus obliquus range of cyclic carotenes and xanthophylls, but no chlorophyll. Most of the pale-green strains were killed by exposure to light, but two strains, PG1 and 1E, which accumulated predominantly zeta-carotene when grown in the dark, survived exposure to the light and developed photosynthetically active chloroplasts containing the normal pigments. The possible biosynthetic implications of the carotenoid composition of these mutant strains, and the relationshp between the carotenoid composition and protection of the cells from photooxidative destruction are discussed.

[Relations between chlorophyll content and chloroplast fine structure in a Chlorina mutant of Arabidopsis thaliana (L.) Heynh]

In a chlorina mutant (ch 3) of Arabidopsis thaliana the total chlorophyll content was reduced to about 1/10 the amount of the green wild-type. At the same time the ratio of chlorophyll a/b was markedly increased. The electron microscopic analysis of the chloroplasts showed a considerable reduction in the membrane formation. Especially an inhibition of the grana differentiation was apparent, leading in some stages to an entirely abnormal thylakoid stacking. Depending on developmental as well as environmental conditions, chlorophyll content and chloroplast structure varied in the mutant in a different manner. These changes induced by endogenous and exogenous factors were comparatively investigated in order to reveal the relations between pigment deficiency and structural disturbances in the chloroplasts.The characteristically deviating a/b-ratio (i.e. the relative chlorophyll b deficiency) in the mutant was "normalized" under particular experimental conditions in two different ways: 1. Under the influence of continous illumination the relative chlorophyll b content increased together with the total amount of chlorophyll, obviously because a threshold of concentration of chlorophyll a was exceeded and thus a normal synthesis of chlorophyll b (from chlorophyll a?) became possible. 2. In cultures of seedlings under an 8:16 hr light-dark-succession as well as in old bleaching rosette leaves the "normalization" of the a/b-ratio was due to a relatively more rapid destruction of chlorophyll a.In electron microscopic cross sections the number, differentiation, and stacking of the thylakoids increased with an increasing total amount of the chlorophylls, while with decreasing chlorophyll content the membranes evidently disintegrated. However, no relation between chloroplast differentiation and absolute or relative chlorophyll b content could be established. Indeed, the proof that chlorophyll b is actually not necessary for the formation of a normal chloroplast structure was furnished by the electron microscopic analysis of another, chlorophyll b-less mutant (ch (1)), in the chloroplasts of which a membrane differentiation with typical grana piles could be demonstrated.